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Sustainability in dairy cattle farms depends on the efficiency of milk yield and reproductive traits. Thus, this study aimed to investigate the effect of the FGF-2/Csp6I gene and major environmental factors on these traits in Holstein-Friesian cattle. A total of 212 whole blood samples were collected from the Vena coccygea of cattle and the data obtained from these samples were used in all statistical analyses. Then, the restriction fragment length polymorphism (RFLP) method (determination of genotypes) was conducted and programs including PopGene (allele and genotype frequencies), Minitab (association analyses) and MTDFREML (variance components and genetic parameters) were used. Alleles A (0.4269) and G (0.5731) as well as genotypes AA (0.174), AG (0.505) and GG (0.321) were found, indicating that the population is polymorphic and in Hardy-Weinberg equilibrium (P > 0.05). The effect of the Csp6I polymorphism of FGF-2 gene on peak milk yield (PMY) (P < 0.01); lactation milk yield (LMY), milking time (MT), 305-day and 200-day lactation milk yield (LMY 305 and LMY 200 ), average daily milk yield (ADMY) (P < 0.05); 100-day lactation milk yield (LMY 100 ), age of using in first breeding (AUFB) and number of inseminations per conception (NIPC) (P < 0.10) were significant. The heritability of milk yield traits and the correlation between direct and maternal heritability for reproductive traits were high. Furthermore, the breeding value of PMY was higher for the AA genotype (0.745 ± 0.292) than for the AG genotype (-0.268 ± 0.171) (P < 0.05). As a result, the A allele and AA genotype for the FGF-2/Csp6I gene had an increasing effect on milk yield without compromising reproductive performance in Holstein-Friesian dairy cattle., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Recently, infertility has emerged as a significant and prevalent public health concern warranting considerable attention. Apoptosis, recognized as programmed cell death, constitutes a crucial process essential for the maintenance of normal spermatogenesis. Multiple investigations have illustrated that the dysregulated apoptosis of reproductive cells, encompassing spermatogonial stem cells, Sertoli cells, and Leydig cells, serves as a causative factor in male infertility. MicroRNAs represent a class of small RNA molecules that exert negative regulatory control over gene expression using direct interaction with messenger RNA transcripts. Previous studies have established that aberrant expression of miRNAs induces apoptosis in reproductive tissues, correlating with reproductive dysfunctions and infertility. In this review, we offer a comprehensive overview of miRNAs and their respective target genes implicated in the apoptotic process. As well, miRNAs are involved in multiple apoptotic signaling pathways, namely the PI3K/AKT, NOTCH, Wnt/β-catenin, and mTOR signaling cascades, exerting both negative and positive effects. We additionally elucidate the significant functions played by lncRNAs and circular RNAs as competing endogenous RNAs in the process of apoptosis within reproductive cells. We further illustrate that external factors, including silica nanoparticles, Cyclosporine A, and smoking, induce dysregulation of miRNAs, resulting in apoptosis within reproductive cells and subsequent male reproductive toxicity. Further, we discuss the implication of heat stress, hypoxia, and diabetes in reproductive cell apoptosis induced by miRNA dysregulation in male infertility. Finally, we demonstrate that the modulation of miRNAs via traditional and novel medicine could protect reproductive cells from apoptosis and be implemented as a therapeutic approach in male infertility., Competing Interests: Declarations. Ethics approval and consent to participate: Not applicable. Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

Female mosquitoes are vectors of many devastating human diseases because they require blood feeding to initiate reproduction. Thus, elucidation of molecular mechanisms managing female mosquito reproduction is essential. Although the regulation of gene expression during the mosquito gonadotrophic cycle has been studied in detail, how this process is controlled at the chromatin level remains unclear. Chromatin must be accessible for transcription factors (TFs) governing gene expression. A specialized class of TFs, called pioneer factors (PFs), binds and remodels closed chromatin, permitting other TFs to bind DNA and activate the gene expression. Here, we identified a homolog of the vertebrate PF FoxA in the mosquito Aedes aegypti and used the CRISPR-Cas9 system to generate mosquitoes deficient in AaFoxA . We found that ovary development was severely retarded in mutant females. Multiomics and molecular biology analyses have shown that AaFoxA increased histone acetylation and decreased methylation of H3K27 by controlling the chromatin accessibility of histone modification enzymes and chromatin remodelers. AaFoxA is bound to the loci of chromatin remodelers, changing their chromatin accessibility and modulating their temporal expression patterns. AaFoxA increased the accessibility of the ecdysone receptor (EcR) and E74 loci, indicating the important role of AaFoxA in the hormonal regulation of mosquito reproductive events. Further, the CUT&RUN and ATAC-seq analyses revealed that AaFoxA temporarily bound closed chromatin, making it differentially accessible during the mosquito gonadotrophic cycle. Hence, this study demonstrates that AaFoxA modulates chromatin dynamics throughout female mosquito reproduction., Competing Interests: Competing interests statement:The authors declare no competing interest.

Diversified reproductive systems can be observed in the plant kingdom and applied in crop breeding; however, their impacts on crop genomic variation and breeding remain unclear. Grapevine (Vitis vinifera L.), a widely planted fruit tree, underwent a shift from dioecism to monoecism during domestication and involves crossing, self-pollination, and clonal propagation for its cultivation. In this study, we discover that the reproductive types, namely, crossing, selfing, and cloning, dramatically impact genomic landscapes and grapevine breeding based on comparative genomic and population genetics of wild grapevine and a complex pedigree of Pinot Noir. The impacts are widely divergent, which show interesting patterns of genomic purging and the Hill-Robertson interference. Selfing reduces genomic heterozygosity, while cloning increases it, resulting in a "double U-shaped" site frequency spectrum (SFS). Crossing and cloning conceal while selfing purges most deleterious and structural burdens. Moreover, the close leakage of large-effect deleterious and structural variations in repulsion phases maintains heterozygous genomic regions in 4.3% of the grapevine genome after successive selfing for nine generations. Our study provides new insights into the genetic basis of clonal propagation and genomic breeding of clonal crops by purging deleterious variants while integrating beneficial variants through various reproductive systems., Competing Interests: Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

Obligate brood parasites delegate the workload of costly parental care to their hosts. Theory predicts that release from demanding parental care increases the importance of other factors to shape mating patterns. However, behavioural observations and parentage estimates are notoriously difficult to obtain in species with covert reproductive strategies, such as brood parasites, and evidence for their mating strategies are scarce. Molecular genetic methods provide a powerful tool to identify concealed mating patterns. Here, we reconstruct the parentage of cuckoo catfish (Synodontis multipunctatus) clutches collected in the wild using a combination of newly developed microsatellite markers, mitochondrial markers, and maximum likelihood estimates of pairwise relatedness. Cuckoo catfish parasitise mouthbrooding cichlids in Lake Tanganyika, but a natural spawning of the brood parasite has never been observed. We examined 429 females of confirmed host cichlid species (parasitism prevalence 6%; 24 parasitised clutches with 1-14 embryos) and found that 46% of clutches with three or more offspring (i.e., 6 out of 13) were parented by more than two catfish individuals. We demonstrated variable mating patterns including polyandrous and polygynous mating, and host sharing by separate, genetically monogamous, catfish pairs. This indicates that cuckoo catfish parasitism involves groups of catfish with reduced capability to monopolise mating opportunities. In general, our results demonstrate how reproductive strategy and mating patterns in a species with concealed breeding behaviour can be investigated and provide valuable insights into the mating system of a brood parasitic species other than hitherto studied avian brood parasites., (© 2025 The Author(s). Molecular Ecology published by John Wiley & Sons Ltd.)

Background: Intentionally impairing the fecundity of mass-reared insects has important utility in controlling pest species. Typically, sterilized individuals are competed against wild counterparts, reducing pest population size. A novel consideration is creating biocontrol agents with lower reproductive capacity that are less likely to establish permanently or admix with wild populations, which are both emerging as legal barriers. Hymenopterans have diploid females, but archetypically infertile polyploid triploid females occur for various parasitoid species. As a first test of polyploid utility for these biocontrol concerns, we assessed the species with the best characterized polyploid biology, the gregarious idiobiont Nasonia vitripennis, for triploid female host-killing ability on pupal blowfly hosts (Calliphora vomitoria)., Results: We examined four polyploid lines: the old Whiting polyploid line (WPL) derived from a spontaneous mutation, and new polyploid lines made through RNAi knockdown of sex determination genes transformer, transformer-2 and wasp-overruler-of-masculinization. For diploid and triploid females of each polyploid line, and control diploids of the STDR and oyster lines used to maintain them, we measured lifetime number of hosts killed; lifetime number of hosts that produced at least one offspring; the percentage of the hosts killed and the percentage of hosts that produced offspring out of those offered; and lifespan. For all lines, triploids produced viable offspring in far fewer hosts than their diploid counterparts (≤70% less). Surprisingly though, they killed as many or more hosts than diploids over similar lifespans. The offspring production ability of the WPL triploid was half that of the other lines, but lines varied only slightly in the number of hosts killed (±10) among the polyploids., Conclusion: The ability of reproductively impaired triploids to kill as many hosts as fertile diploids demonstrate high biocontrol utility for polyploidized females, and downstream potential for reducing ecological risk. © 2024 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry., (© 2024 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.)

In social animals, reproductive activity and ageing are influenced by group composition. In monogynous (single-queen) insect societies, queen presence affects worker fecundity and longevity, but less is known about worker responses to queen number variation in polygynous (multi-queen) species or how queens age in these systems. We created queenless, one-queen and two-queen colonies of the invasive, polygynous ant Tapinoma magnum to examine the effect of queen number on worker survival, ovary and oocyte development, oxidative stress resistance and fat body gene expression. We also compared the fecundity and brain and fat body transcriptomes between young and old queens. Queenless workers experienced the highest mortality, contrasting with monogynous species, where queen removal typically extends lifespan. Workers lived longer and had more developing oocytes in their ovaries in single-queen than in two-queen colonies. Queen number did not directly affect oxidative stress resistance or fat body gene expression, though its effect on the latter differed between inside and outside workers. Furthermore, inside-likely younger-workers produced more oocytes, showed higher oxidative stress resistance and upregulated antioxidant genes compared to outside-likely older-workers. Minimal shifts in fecundity and gene expression of differently aged queens indicated their physiological stability. Our research highlights distinct caste- and tissue-specific responses to varying queen numbers in workers of a highly polygynous species., (© 2025 The Author(s). Molecular Ecology published by John Wiley & Sons Ltd.)

The concept of severity in healthcare is multidimensional and subjective. It is a primary consideration in reproductive genetic carrier screening design where the focus is providing reproductive couples with information about the chance of severe genetic conditions in their offspring. When offering this screening, it is important to understand how condition severity is perceived and incorporated into reproductive decision-making. We analysed data from 41 semi-structured interviews with people who received a screening result indicating an increased chance for having children with a genetic condition. Thematic analysis revealed a desire for comprehensive information about the condition including clinical features, prognosis, impact on quality of life and treatment/management options. Participants integrated this information with their personal circumstances, beliefs/values and lived experience to form a perception of the severity of the condition. For rare and reduced-penetrance conditions where clinical information was limited or ambiguous, decision-making was more complex and greater anxiety was experienced. For conditions with a severity spectrum, reproductive decisions were based on the 'worst-case' clinical presentation. Where the impact of the condition was perceived as significant, the imperative to avoid that condition in future children appeared to be the greatest. Participants reported feeling that knowing their increased reproductive chance of the condition conferred a responsibility to avoid the condition, to prevent suffering and/or reduced quality of life for their children and future generations. These findings offer critical insight into how severity is perceived and the role it plays in reproductive decision-making and justifies a carefully considered approach to screening panel design., Competing Interests: Competing interests: The authors declare no competing interests. Ethics approval and consent to participate: Ethics approval was granted by the Royal Children’s Hospital Human Research Ethics Committee (2019.097) and ratified by the University of Technology Sydney Human Research Ethics Committee (ETH22-7554) for this sub-study. Interview participants provided informed verbal consent after reviewing the participant information content., (© 2024. The Author(s), under exclusive licence to European Society of Human Genetics.)

Populus tomentosa, a deciduous tree species distinguished by its significant economic and ecological value, enjoys a wide-ranging natural distribution. However, its long juvenile period severely restricts the advancement of breeding work. The SPL gene family, a distinctive class of transcription factors exclusive to the plant kingdom, is critical in various processes of plant growth and development. The miR156-SPL molecular module stands as an indispensable regulatory mechanism in the transition from the vegetative juvenile phase to the adult phase in plants. Consequently, this research endeavored a methodical and exhaustive exploration of the SPL gene family within the P.tomentosa species, synergistically integrating the miR156 family into the analysis. A total of 56 PtSPL genes were identified and subjected to a comprehensive analysis of their gene structure, conserved motifs, collinearity relationships, chromosomal localization, and promoter cis-acting elements. Further analysis of gene expression profiles confirmed the pivotal role of PtSPLs in the reproductive phase and tissue development of P. tomentosa. In addition, 11 members of miR156 in P. tomentosa were identified and their sequences analyzed, elucidating the miR156-SPL regulatory network. The target relationship between miR156k and PtSPLs was further validated by detecting the expression levels of PtSPLs in transgenic poplars overexpressing 35S::MIR156k. This comprehensive study lays a robust theoretical foundation for the continued exploration and application of the SPL genes in P. tomentosa, opening avenues for future research and potential advancements in plant biology and breeding strategies., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2025. Published by Elsevier B.V.)

Karyotype changes are a formidable evolutionary force by directly impacting cross-incompatibility, gene dosage, genetic linkage, chromosome segregation, and meiotic recombination landscape. These changes often arise spontaneously and are commonly detected within plant lineages, even between closely related accessions. One element that can influence drastic karyotype changes after only one (or few) plant generations is the alteration of the centromere position, number, distribution, or even its strength. Here, we briefly explore how these different centromere configurations can directly result in karyotype rearrangements, impacting plant reproduction and meiotic recombination., (© 2025 The Author(s). New Phytologist © 2025 New Phytologist Foundation.)

Monochamus saltuarius is an important vector of pinewood nematode in Eurasia with a high reproductive capacity. Endocrine hormones play a key role in insect reproduction. Understanding the mechanism of internal regulation can provide targets for pest control. However, this type of research on M. saltuarius remain limited. Our study constructed transcriptome of the internal reproductive systems in male and female M. saltuarius across three development stages. Interference experiments targeting the MSALMet1 and exploring its critical role in reproduction. Transcriptome results revealed that 42 genes related to the juvenile hormone and ecdysteroid pathways were identified. Among them, 12 genes were significantly enriched in reproduction-related pathways, and the expression patterns of 14 genes aligned with the developmental trend of the internal reproductive system, suggesting that they may play a regulatory role in reproductive processes. Furthermore, protein-protein interaction networks elucidated the complex interactions among these genes, shedding light on their diverse functions. Notably, bioinformatics analysis and interference experiments revealed that MSALMet1 having the profound effect on reproductive system development in both sexes. These findings highlight the critical role of endocrine-related genes in regulating reproductive development and provide a theoretical foundation for regulating reproduction at molecular level, potentially contributing to M. saltuarius population control., Competing Interests: Declaration of competing interest The authors declare no conflicts of interest., (Copyright © 2025 Elsevier B.V. All rights reserved.)

Background: Reproduction is vital to welfare, health, and economics in animal husbandry and breeding. Health and reproduction are increasingly being considered because of the observed genetic correlations between reproduction, health, conformation, and performance traits in dairy cattle. Understanding the detailed genetic architecture underlying these traits would represent a major step in comprehending their interplay. Identifying known, putative or novel associations in genomics could improve animal health, welfare, and performance while allowing further adjustments in animal breeding., Results: We conducted genome-wide association studies for 25 different traits belonging to four different complexes, namely reproduction (n = 13), conformation (n = 6), production (n = 3), and metabolism (n = 3), using a cohort of over 235,000 dairy cows. As a result, we identified genome-wide significant signals for all the studied traits. The obtained summary statistics collected served as the input for a Mendelian randomisation approach (GSMR) to infer causal associations between putative exposure and reproduction traits. The study considered conformation, production, and metabolism as exposure and reproduction as outcome. A range of 139 to 252 genome-wide significant SNPs per combination were identified as instrumental variables (IVs). Out of 156 trait combinations, 135 demonstrated statistically significant effects, thereby enabling the identification of the responsible IVs. Combinations of traits related to metabolism (38 out of 39), conformation (68 out of 78), or production (29 out of 39) were found to have significant effects on reproduction. These relationships were partially non-linear. Moreover, a separate variance component estimation supported these findings, strongly correlating with the GSMR results and offering suggestions for improvement. Downstream analyses of selected representative traits per complex resulted in identifying and investigating potential physiological mechanisms. Notably, we identified both trait-specific SNPs and genes that appeared to influence specific traits per complex, as well as more general SNPs that were common between exposure and outcome traits., Conclusions: Our study confirms the known genetic associations between reproduction traits and the three complexes tested. It provides new insights into causality, indicating a non-linear relationship between conformation and reproduction. In addition, the downstream analyses have identified several clustered genes that may mediate this association., Competing Interests: Declarations. Ethics approval and consent to participate: Not applicable. No animals or animal materials have been used in this study, and ethical approval for the use of animals was not necessary. Consent for publication: Not applicable. Competing interests: The authors declare that they have no competing interests., (© 2025. The Author(s).)

Manipulating spawning seasons of Atlantic salmon (Salmo salar) is a common practice to facilitate year-round harvesting in salmon aquaculture. This process involves adjusting water temperature and light regime to control female broodstock maturation. However, recent studies have indicated that altered spawning seasons can significantly affect the nutritional status and growth performance of the offspring. Therefore, gaining a deeper understanding of the biological regulations influenced by these alterations is crucial to enhance the growth performance of fish over multiple generations. In this study, we investigated omics data from four different spawning seasons achieved through recirculating aquaculture systems (RAS) and sea-pen-based approaches. In addition to the normal spawning season in November (sea-pen), three altered seasons were designated: off-season (five-month advance, RAS), early season (two-month advance, sea-pen), and late season (two-month delay, sea-pen). We conducted comprehensive gene expression and DNA methylation analysis on liver samples collected from the start-feeding larvae of the next generation. Our results revealed distinct gene expression and DNA methylation patterns associated with the altered spawning seasons. Specifically, offspring from RAS-based off-season exhibited altered lipid-mediated regulation, while those from sea-pen-based early and late seasons showed changes in cellular processes, particularly in cell cycle regulation when compared to the normal season. The consequences of our findings are significant for growth and health, potentially providing information for developing valuable tools for assessing growth potential and optimizing production strategies in aquaculture., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2025 Saito et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

The community-based breeding program was introduced to enhance the productivity of Bonga sheep. Data evaluating animals' potential regarding key traits was gathered from 2009-2021. This study estimated covariance components and genetic parameters for growth (birth, weaning, and six-months weight), reproductive (lambing interval, annual reproductive rate, litter size at birth and weaning, litter weight at birth and weaning), and survival (0-3, 3-6, and 0-6 months) traits using a multivariate animal model. The Average Information Restricted Maximum Likelihood method in WOMBAT was used for growth and reproductive traits, while Derivative-free MUltivariate analysis was employed for survival traits. The results revealed that the additive heritability for growth, reproductive, and survival traits ranged from 0.15-0.26, 0.06-0.08, and 0.10-0.17, respectively. The variance ratio of maternal permanent environment for growth traits ranged from 0.07-0.25, while that of animal environment for reproductive traits ranged from 0.33-0.45. Maternal genetic heritability for birth, weaning, and six-months weights were 0.14, 0.19, and 0.19, respectively, while it ranged from 0.01-0.14 for reproductive traits. Additive genetic correlations among growth traits ranged from 0.04-0.79, and from 0.36-0.62 between growth and reproductive traits. Low to high additive genetic correlations (0.002-0.537) were recorded between growth and survival traits. Significant (P<0.001) and positive genetic trends were observed for most reproductive traits, though annual genetic trends were low. Moderate additive heritability for growth traits indicates potential for genetic improvement via selection, while the pronounced environmental impact on reproductive and survival traits suggests the need for improved management practices in addition to selection. The presence of positive genetic correlations of growth traits with reproductive and with survival traits suggests that selecting for improved weaning/six-month weight has the potential to enhance ewe productivity and lamb survival. This highlights the importance of considering both growth and reproductive/survival traits in breeding programs to achieve optimal outcomes in sheep production., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2025 Mamiru et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

The cattle industry is critical for agriculture's development, and reproductive technology has revolutionized its development over the past century. The core task of developing the beef cattle industry is to increase quantity and improve quality, which cannot be separated from the key link of reproduction. It involves artificial insemination (AI), semen collection and freezing, multiple ovulation embryo transfer (MOET), and genome editing. Each technology greatly contributed to the industry's development at the time. In this review, we systematically summarize the development process of beef cattle breeding technology and provide reasonable suggestions for the needs of enterprises and individual breeders of different scales. Additionally, we summarize the contributions of these technologies to industry development and their impact on cattle farming today. Scientific feeding methods combined with current reproductive technology can fully realize the production potential of beef cattle and improve economic benefits, which has positive significance for expanding the beef cattle industry scale and promoting sustainable cattle industry development., Competing Interests: Declarations. Ethics approval: Review and approval by an ethics committee was not needed for this study, because all the data in this article comes from research in the database and has been integrated and reviewed. Competing interests: The authors declare no competing interests., (© 2025. The Author(s), under exclusive licence to Springer Nature B.V.)

In animals, a trade-off exists between reproduction and growth, which are the most fundamental traits. Males and females exhibit profound differences in reproduction and growth in fish species. However, the precise molecular mechanism governing this phenomenon is still not clear. Here, we uncovered that chr23-miR-200s and dmrt1 knockout specifically caused an impairment in reproduction and an increase in body growth in female and male zebrafish, respectively. Chr23-miR-200s and Dmrt1 directly regulate the stat5b gene by targeting its 3'UTR and promoter. The loss of stat5b completely abolished the elevated growth performance in chr23-miR-200s-KO or dmrt1 -/- zebrafish. Moreover, the dmrt1 transgenic zebrafish had significantly lower body length and body weight than the control males, accompanied by a significant reduction in stat5b expression in the liver of transgenic fish. In summary, our study proposes a regulatory model elucidating the roles of chr23-miR-200s and Dmrt1 in controlling the sexually dimorphic trade-off between reproduction and growth.

Follicle development in dairy goats is lower after induced estrus during the non-breeding season, reducing conception rates and challenging year-round milk supply. This study investigated follicle development during the breeding and non-breeding seasons and explored molecular mechanisms for variations in the proportions of follicles of different sizes using ovarian RNA-seq and in vitro experiments. Induced estrus during the non-breeding season used a simulated breeding season short photoperiod and male effect methods, while the male effect method was used during the breeding season. This study identified an increase in follicle size during the breeding season and performed RNA-seq on ovaries to explore the underlying causes. The RNA-seq analysis elucidated pathways associated with cellular and hormonal metabolism and identified adenylyl cyclase 5 ( ADCY5 ) as a key differentially expressed gene. In vitro experiments demonstrated that interfering with ADCY5 in ovarian granulosa cells (GCs) reduced steroid synthesis. Conversely, the overexpression of ADCY5 increased steroid synthesis. ADCY5 affects the biological function of GCs and consequently influences follicle development through the cAMP-response element binding protein (CREB) and p38 mitogen-activated protein kinase phosphorylation (MAPK) pathways. Overall, our findings demonstrate that follicle development in dairy goats differs between the breeding and non-breeding seasons and that the differential expression levels of the ADCY5 gene contribute to this discrepancy.

VEGETATIVE TO REPRODUCTIVE TRANSITION 2 (VRT-A2) is a subspecies-forming gene that confers the long-glume and large-grain traits of tetraploid Polish wheat (Triticum polonicum; AABB) and hexaploid Xinjiang rice wheat (T. petropavlovskyi; AABBDD). Transcriptional activation of VRT-A2 due to a natural sequence variation in its Intron-1 region significantly enhances grain weight but also causes some basal spikelets to fail to completely develop, thus decreasing grain number per spike and yield. This yield penalty has presented a challenge for the use of VRT-A2 in breeding high-yield wheat. Here, we report the characterization of 2 regulatory modules that fine-tune VRT-A2 expression in bread wheat (T. aestivum): (i) the APETALA2/Ethylene Responsive Factor (AP2/ERF)-type transcription factor MULTI-FLORET SPIKELET1 (TaMFS1) represses VRT-A2 expression by recruiting a transcriptional corepressor and a histone deacetylase and (ii) the STRUCTURE-SPECIFIC RECOGNITION PROTEIN 1 (TaSSRP1) facilitates VRT-A2 activation by assembling Mediator and further RNA polymerase II. Deleting TaMFS1 triggered moderate upregulation of VRT-A2 results in significantly increased grain weight without the yield penalty. Our study thus provides a feasible strategy for overcoming the tradeoffs of pleotropic genes by editing their upstream transcriptional regulators., Competing Interests: Conflict of interest statement. None declared., (© The Author(s) 2025. Published by Oxford University Press on behalf of American Society of Plant Biologists.)

Hemizygous genes, which are present on only one of the two homologous chromosomes of diploid organisms, have been mainly studied in the context of sex chromosomes and sex-linked genes. However, these genes can also occur on the autosomes of diploid plants due to structural variants (SVs), such as a deletion/insertion of one allele, and this phenomenon largely unexplored in plants. Here, we investigated the genomic and epigenomic landscapes of hemizygous genes across 22 genomes with varying propagation histories: eleven clonal lineages, seven outcrossed samples, and four inbred and putatively homozygous genomes. We identified SVs leading to genic hemizygosity. As expected, very few genes (0.01 to 1.2%) were hemizygous in the homozygous genomes, representing negative controls. Hemizygosity was appreciable among outcrossed lineages, averaging 8.7% of genes, but consistently elevated for the clonal samples at 13.8% genes, likely reflecting heterozygous SV accumulation during clonal propagation. Compared to diploid genes, hemizygous genes were more often situated in centromeric than telomeric regions and experienced weaker purifying selection. They also had reduced levels of expression, averaging ~20% of the expression levels of diploid genes, violating the evolutionary model of dosage compensation. We also detected higher DNA methylation levels in hemizygous genes and transposable elements, which may contribute to their reduced expression. Finally, expression profiles showed that hemizygous genes were more specifically expressed in contexts related to fruit development, organ differentiation, and stress responses. Overall, hemizygous genes accumulate in clonally propagated lineages and display distinct genetic and epigenetic features compared to diploid genes, shedding unique insights into genetic studies and breeding programs of clonal crops., Competing Interests: Competing interests statement:The authors declare no competing interest.

Centuries of clonal propagation in cassava (Manihot esculenta) have reduced sexual recombination, leading to the accumulation of deleterious mutations. This has resulted in both inbreeding depression affecting yield and a significant decrease in reproductive performance, creating hurdles for contemporary breeding programs. Cassava is a member of the Euphorbiaceae family, including notable species such as rubber tree (Hevea brasiliensis) and poinsettia (Euphorbia pulcherrima). Expanding upon preliminary draft genomes, we annotated 7 long-read genome assemblies and aligned a total of 52 genomes, to analyze selection across the genome and the phylogeny. Through this comparative genomic approach, we identified 48 genes under relaxed selection in cassava. Notably, we discovered an overrepresentation of floral expressed genes, especially focused at 6 pollen-related genes. Our results indicate that domestication and a transition to clonal propagation have reduced selection pressures on sexually reproductive functions in cassava leading to an accumulation of mutations in pollen-related genes. This relaxed selection and the genome-wide deleterious mutations responsible for inbreeding depression are potential targets for improving cassava breeding, where the generation of new varieties relies on recombining favorable alleles through sexual reproduction., Competing Interests: Conflicts of interest: The author(s) declare no conflicts of interest., (© The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America.)

Trioecy, a rare reproductive system where hermaphrodites, females, and males coexist, is found in certain algae, plants, and animals. Though it has evolved independently multiple times, its rarity suggests it may be an unstable or transitory evolutionary strategy. In the well-studied Caenorhabditis elegans, attempts to engineer a trioecious strain have reverted to the hermaphrodite/male system, reinforcing this view. However, these studies did not consider the sex-determination systems of naturally stable trioecious species. The discovery of free-living nematodes of the Auanema genus, which have naturally stable trioecy, provides an opportunity to study these systems. In Auanema, females produce only oocytes, while hermaphrodites produce both oocytes and sperm for self-fertilization. Crosses between males and females primarily produce daughters (XX hermaphrodites and females), while male-hermaphrodite crosses result in sons only. These skewed sex ratios are due to X-chromosome drive during spermatogenesis, where males produce only X-bearing sperm through asymmetric cell division. The stability of trioecy in Auanema is influenced by maternal control over sex determination and environmental cues. These factors offer insights into the genetic and environmental dynamics that maintain trioecy, potentially explaining its evolutionary stability in certain species., Competing Interests: Conflicts of interest: The author(s) declare no conflict of interest., (© The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America.)

Intraspecific variation is necessary for evolutionary change and population resilience, but the extent to which it contributes to either depends on the causes of this variation. Understanding the causes of individual variation in traits involved with reproductive timing is important in the face of environmental change, especially in systems where reproduction must coincide with seasonal resource availability. However, separating the genetic and environmental causes of variation is not straightforward, and there has been limited consideration of how small-scale environmental effects might lead to similarity between individuals that occupy similar environments, potentially biasing estimates of genetic heritability. In ecological systems, environments are often complex in spatial structure, and it may therefore be important to account for similarities in the environments experienced by individuals within a population beyond considering spatial distances alone. Here, we construct multi-matrix quantitative genetic animal models using over 11,000 breeding records (spanning 35 generations) of individually-marked great tits (Parus major) and information about breeding proximity and habitat characteristics to quantify the drivers of variability in two key seasonal reproductive timing traits. We show that the environment experienced by related individuals explains around a fifth of the variation seen in reproductive timing, and accounting for this leads to decreased estimates of heritability. Our results thus demonstrate that environmental sharing between relatives can strongly affect estimates of heritability and therefore alter our expectations of the evolutionary response to selection., (© The Author(s) 2024. Published by Oxford University Press on behalf of The Society for the Study of Evolution (SSE).)

Lethal alleles are mutations in the genome that cause embryonic losses in affected homozygous embryos and, therefore, can negatively influence reproduction rates in commercial populations. Thus, this study aimed to identify genomic regions containing potential lethal haplotypes in Nellore breed; identify candidate genes located within these regions; and investigate the reproductive performance of heterozygous carriers of lethal haplotypes in Nellore cattle. Forty-five genomic regions harboring putative lethal haplotypes were identified, which overlap with 360 genes. Gene ontology analyses of these genes revealed biological processes associated with the development of sexual traits in males and females, key functions of the immune system, energy homeostasis, and embryonic development. The gene networks were involved in metabolic pathways including ovarian steroidogenesis, oocyte meiosis, and insulin secretion. Matings between carrier dam and carrier sire led to a reduction of up to -203.46% in pregnancy success probability, an increase of 275.15% in probability of pregnancy loss, 295.03% for stillbirth occurrence, and 301.40% for pre-weaning mortality when compared to non-carrier dam and sire matings. The results highlight the importance of identifying animals that are carriers of lethal haplotypes to avoid the propagation of these haplotypes in the population., Competing Interests: Declarations. Competing interests: The authors declare no competing interests. Ethics approval and consent to participate: Animal Care and Use Committee approval was not obtained for this study because all the analyses were performed using pre-existing datasets., (© 2025. The Author(s).)

Developmental toxicity testing is essential to identify substances that may harm embryonic development. This study aimed to establish a protocol for evaluating developmental toxicity using human induced pluripotent stem cells (iPSCs) by analyzing cellular activity and gene expression changes. Two ICH S5(R3) positive substances, valproic acid (VPA), which is a substance previously detected as positive by other test methods, and thalidomide (Thalido), were examined during early trichoderm differentiation without fetal bovine serum. RNA-seq analysis identified seven candidate genes, including TP63 , associated with altered expression following exposure to VPA or Thalido. These genes were implicated in pathways related to tissue development, cell growth, and molecular interactions. While the assay effectively detected VPA and Thalido, its limitations include testing only soluble substances and focusing on early differentiation stages. Nevertheless, the protocol demonstrates potential for the classification and evaluation of emerging modality drugs based on physical properties such as solubility, polarity, and pH. Integration with AI analysis may enhance its capacity to uncover genetic variations and evaluate previously uncharacterized substances. This study provides a foundation for alternative developmental toxicity testing methods, with further refinements in the culture method expected to improve accuracy and applicability in regulatory toxicology.

Twin births in dairy cattle is generally unfavorably associated with reproductive performance and calf survival in dairy cows. Genetic selection to reduce twinning rate in dairy cattle may be desirable, provided no undesirable correlated responses in other traits exist. The current study was undertaken to characterize the genomic architecture of twinning rate in the Irish Holstein-Friesian population, and to quantify the genetic relationship of twinning with other reproductive traits and milk yield. Calving records from the years 1996 to 2022 were used together with pedigree information to generate breeding value estimates for twinning rate. Genome-wide association analyses of twinning rate, calving interval, cow survival and age at first calving were conducted using de-regressed breeding values estimates for 2,656 Holstein-Friesian sires. Full genome sequence data imputed from ∼50,000 single nucleotide polymorphisms were available for all sires. The h 2 of twinning rate was 0.0118 ± 0.0010. Twinning rate was very weakly genetically correlated with both milk yield (0.13) and the reproductive traits (-0.26 to 0.14). Genomic analyses detected an association with twinning rate at 31.1 Mb on BTA11 in close proximity to genes for FSH receptor and luteinizing hormone-chorionic gonadotropin receptor, supporting previous studies. The most significant SNP in this region was not associated with milk yield, indicating the potential for selection to reduce twinning rate without detrimentally affecting milk yield. Novel SNP associations with age at first calving on BTA27 and from a meta-analysis of calving interval and age at first calving on BTA29 were also identified and are candidates for future validation and study., (The Authors. Published by Elsevier Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).)

Genomic prediction of daughter pregnancy rate (GDPR) and cow conception rate (GCCR) are fertility traits developed to help improve selection for reproductive performance. Although these traits overlap, their denominator can vary, and programs with different strategies combining estrus detection (ED) and timed AI might experience different associations with these traits (e.g., shorter interval for first service for high GDPR quartiles, but not for GCCR). The objectives were to assess days from calving to first service (TP1), AI at ED (AIE), pregnancy at the first service (P1), pregnancy loss for the first service (PL), and number of services to conception (NSFC) in 2 reproductive programs (RepP) combining variable ED length and timed AI (TAI) and their relationship with GDPR and GCCR. Holstein cows from a single farm were randomly allocated to 2 different programs, the short RepP (n = 982) or long RepP (n = 942). In the short RepP, cows were enrolled in a Presynch-Ovsynch (PGF 2α : 36 ± 3 and 50 ± 3 DIM) followed by ED and AI from 50 ± 3 to 62 ± 3 DIM. Cows not detected in estrus underwent in the Ovsynch (GnRH: 62 ± 3, PGF 2α : 69 ± 3, GnRH: 71 ± 3 and TAI :72 ± 3 DIM). In the long RepP, cows received a PGF 2α at 50 ± 3 DIM followed by AI at ED up to 81 ± 3 DIM. Cows with no ED were enrolled in an Ovsynch (GnRH:82 ± 3, PGF 2α :89 ± 3, GnRH:91 ± 3 and TAI:92 ± 3 DIM). Cows were categorized into quartiles (Q1 to Q4) considering their GDPR (qGDPR) and GCCR (qGCCR). Statistical analyses included logistic regression used for AIE, P1, and PL; Poisson regression for the NSFC; and linear regression for TP1. Models included AIE, P1, PL, NSFC, and TP1 as dependent variables, with RepP and qGDPR for GDPR and RepP and qGCCR for GCCR as independent variables. Time to pregnancy was analyzed using Cox's proportional hazard model. The short RepP had a shorter TP1 (short = 64.3 vs. long = 72.1) and fewer NSFC than the long RepP (short = 2.9 vs. long = 3.1). The long RepP had a higher AIE (short = 45.2% vs. long = 73.2%). The P1 tended to be greater in the short than the long RepP (short = 33.7% vs. long = 30.0%). Cows in Q4 (GDPR and GCCR) had lower TP1 and NSFC, greater AIE and P1 compared with the lowest quartiles (Q1). Interactions between RepP and GDPR were present for TP1, AIE, and P1, but no interactions were observed between RepP and GCCR. The short program had a shorter interval from calving to pregnancy than the long program. Cows in the highest quartiles for GDPR and GCCR had shorter intervals from calving to pregnancy and higher pregnancy hazards than the lowest quartiles. The current study revealed that cows enrolled in long RepP that relied on longer ED intervals had lower reproductive outcomes than short RepP cows, and cows ranked in the highest GDPR and GCCR quartile for most responses had better outcomes independent of the RepP used., (The Authors. Published by Elsevier Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).)

Whole genome duplication (WGD) likely plays an important role in plant macroevolution, and has been implicated in diversification rate shifts, structural innovations, and increased disparity. But the general effects of WGD are challenging to evaluate, in part due to the difficulty of directly comparing morphological patterns across disparate clades. We explored relationships between WGD and the evolution of reproductive complexity across vascular plants using a metric based on the number of reproductive part types. We used multiple regression models to evaluate the relative importance of inferred WGD events, genome size, and a suite of additional variables relating to growth habit and reproductive biology in explaining part type complexity. WGD was a consistent predictor of reproductive complexity only among angiosperms. Across vascular plants generally, reproductive biology, clade identity, and the presence of bisexual strobili (those that produce microsporangiate and megasporangiate organs) were better predictors of complexity. Angiosperms are unique among vascular plants in combining frequent polyploidy with high-reproductive complexity. Whether WGD is mechanistically linked to floral complexity is unclear, but we suggest widespread polyploidy and increased complexity were ultimately facilitated by the evolution of herbaceous growth habits in early angiosperms., (© 2024 The Author(s). New Phytologist © 2024 New Phytologist Foundation.)

Alternative reproductive tactics are discrete, intrasexual differences in reproductive behaviour within a population. In some cases, these complex phenotypes are determined by autosomal supergenes or sex chromosomes-both of which exhibit reduced recombination and thus enable the linked inheritance of co-adapted alleles from multiple loci. Most alternative reproductive tactics in amphibians are plastic (and reversible), environmentally determined and lacking morphological differentiation, but a striking exception is found in the two-lined salamander (Eurycea bislineata) species complex. In some populations, two distinct male phenotypes coexist: 'searching' males have mental glands, protruding premaxillary teeth and elongate cirri used in terrestrial courtship, while 'guarding' males lack these traits and instead have hypertrophied jaw musculature used in mate guarding at aquatic nesting sites. These tactics differ in many morphological and behavioural phenotypes, but their proximate cause has not yet been described. Here, we generated genome-wide SNP data from > 130 Eurycea cf. wilderae collected from Highlands Biological Station. We provide evidence for an XY sex determination and for a Y-linked polymorphism underlying alternative reproductive tactics in this population. We then develop and validate a PCR-based genotyping assay and apply it to characterise the sex ratio and relative frequency of male tactics from a sample of larvae. Our results add to the growing body of literature exploring the importance of supergenes and sex chromosomes in complex intraspecific polymorphisms, and we highlight opportunities for future work to continue exploring the genomic architecture of these traits., (© 2024 John Wiley & Sons Ltd.)

After a long-distance migration, Avars with Eastern Asian ancestry arrived in Eastern Central Europe in 567 to 568 CE and encountered groups with very different European ancestry 1,2 . We used ancient genome-wide data of 722 individuals and fine-grained interdisciplinary analysis of large seventh- to eighth-century CE neighbouring cemeteries south of Vienna (Austria) to address the centuries-long impact of this encounter 1,2 . We found that even 200 years after immigration, the ancestry at one site (Leobersdorf) remained dominantly East Asian-like, whereas the other site (Mödling) shows local, European-like ancestry. These two nearby sites show little biological relatedness, despite sharing a distinctive late-Avar culture 3,4 . We reconstructed six-generation pedigrees at both sites including up to 450 closely related individuals, allowing per-generation demographic profiling of the communities. Despite different ancestry, these pedigrees together with large networks of distant relatedness show absence of consanguinity, patrilineal pattern with female exogamy, multiple reproductive partnerships (for example, levirate) and direct correlation of biological connectivity with archaeological markers of social status. The generation-long genetic barrier was maintained by systematically choosing partners with similar ancestry from other sites in the Avar realm. Leobersdorf had more biological connections with the Avar heartlands than with Mödling, which is instead linked to another site from the Vienna Basin with European-like ancestry. Mobility between sites was mostly due to female exogamy pointing to different marriage networks as the main driver of the maintenance of the genetic barrier., Competing Interests: Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

The reproductive characteristics of Hanwoo play a significant role in farm profitability by decreasing the generation interval. This study analyzed 1015 primiparous and 916 multiparous cows using a genome-wide association study with both single-locus (GEMMA, GCTA) and multi-locus models (FarmCPU, BLINK). A significant marker for age at first service was identified across all methods. For age at first conception, GEMMA identified two markers, while FarmCPU and BLINK identified 14 and two markers, respectively. Regarding age at first calving, GEMMA identified two markers, and FarmCPU and BLINK found 15 and two markers, respectively. In multiparous cows, except for days open, one marker for gestation length and two markers for calving interval were identified in the multi-locus models (FarmCPU and BLINK). Additionally, one marker for the number of services per conception was identified using GEMMA. Key candidate genes included PLCB1 (maintaining pregnancy), MUC1 (fetal development), and ADCY5 (associated with fetal birth), while TXNL1 regulates embryo implantation timing. Gene ontology functions associated with embryo implantation and placental regulation were also confirmed (GO:0046875). Although the multi-locus models identified a greater number of markers and candidate genes, there was no overlap with the results from the single-locus models. The multi-locus models showed enhanced detection power, but slight inflation in test statistics (λ values) necessitates cautious interpretation to avoid false positives. Thus, a combination of both models is recommended to improve reproductive efficiency in cows, providing valuable insights into the genetic aspects of reproductive traits., (© 2024 Stichting International Foundation for Animal Genetics.)

Maternal hormones can profoundly impact offspring physiology and behaviour in sex-dependent ways. Yet little is known about the molecular mechanisms linking these maternal effects to offspring phenotypes. DNA methylation, an epigenetic mechanism, is suggested to facilitate maternal androgens' effects. To assess whether phenotypic changes induced by maternal androgens associate with DNA methylation changes, we experimentally manipulated yolk testosterone levels in wild great tit eggs (Parus major) and quantified phenotypic and DNA methylation changes in the hatched offspring. While we found no effect on the handing stress response, increased yolk testosterone levels decreased the begging probability, emphasised sex differences in fledging mass, and affected methylation at 763 CpG sites, but always in a sex-specific way. These sites are associated with genes involved in growth, oxidative stress, and reproduction, suggesting sex-specific trade-offs to balance the costs and benefits of exposure to high yolk testosterone levels. Future studies should assess if these effects extend beyond the nestling stage and impact fitness., (© 2025 The Author(s). Molecular Ecology published by John Wiley & Sons Ltd.)

A unique cell size-sensing mechanism is at the heart of the life cycle of diatoms. During population growth, cell size decreases until a sexual size threshold (SST) is reached, below which cells become sexually competent. In most pennate diatoms, the two mating types undergo biochemical and behavioral differentiation below the SST, although the molecular pathways underlying their size-dependent maturation remain unknown. Here, we developed a method to shorten the generation time of Cylindrotheca closterium through single-cell microsurgery, enabling the transcriptomic comparison of genetically identical large and undifferentiated cells with small, sexually competent cells for six different genotypes. We identified 21 genes upregulated in small cells regardless of their mating type, revealing how cells undergo specific transcriptional reprogramming when passing the SST. Furthermore, we revealed a size-regulated gene cluster with three mating type-specific genes susceptible to sex-inducing pheromones. In addition, comparative transcriptomics confirmed the shared mating type specificity of Mating-type Related Minus 2 homologs in three pennate diatoms, suggesting them to be part of a conserved partner recognition mechanism. This study sheds light on how diatoms acquire sexual competence in a strictly size-dependent manner, revealing a complex machinery underlying size-dependent maturation, mating behavior, and heterothally in pennate diatoms., (© 2024 The Author(s). New Phytologist © 2024 New Phytologist Foundation.)

This study aimed to explore the impact of genomic imprinting on the genetic variance of composite reproductive traits across three parities in Baluchi sheep. The traits analyzed included litter mean weight per lamb born (LMWLB), litter mean weight per lamb weaned (LMWLW), total litter weight at birth (TLWB), and total litter weight at weaning (TLWW). We employed a univariate linear animal model for each trait, treating performance across parities as separate traits. Twenty-four animal models were assessed, incorporating direct additive genetic effects, maternal genetic effects, maternal permanent environmental effects, direct and maternal genetic covariances, as well as maternal and paternal imprinting. Model selection was based on Akaike's Information Criterion (AIC). Direct heritability estimates for the traits were generally low, ranging from 0.039 ± 0.017 for LMWLW to 0.085 ± 0.028 for TLWW. TLWB and TLWW exhibited higher heritability than LMWLB and LMWLW in their respective parities. In the best model (model 24), maternal imprinting heritability estimates from the first to third parity were 0.059 ± 0.016, 0.060 ± 0.013, and 0.085 ± 0.021 for TLWB, 0.075 ± 0.021, 0.068 ± 0.025, and 0.048 ± 0.016 for LMWLB, 0.051 ± 0.013, 0.065 ± 0.019, and 0.068 ± 0.020 for TLWW, and, 0.072 ± 0.012, 0.057 ± 0.018 and 0.054 ± 0.011 for LMWLW, respectively. Paternal imprinting heritability estimates were consistently lower than maternal imprinting estimates, with values across parities ranging from 0.001 ± 0.024 to 0.019 ± 0.032 for TLWB, 0.005 ± 0.022-0.010 ± 0.019 for LMWLB, 0.012 ± 0.05-0.017 ± 0.05 for TLWW and, 0.013 ± 0.01-0.016 ± 0.01 for LMWLW. In conclusion, imprinting effects should be included in breeding programs to increase the accuracy of genetic evaluation., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this article., (Copyright © 2024 Elsevier B.V. All rights reserved.)

The domestic cat ( Felis catus ) has been a popular companion animal for about 12,000 years, initially valued for rodent control before evolving into pets that provide affection and companionship. Unlike dogs, cats were not selectively bred for specific roles until the late 1800s, resulting in breeds defined primarily by appearance, which sometimes leads to genetic disorders. Modern animal welfare concerns emphasize longevity and health, prompting research into factors affecting cat lifespans, including sex, reproductive status, and breed. This study aims to expand on previous UK research by analyzing these interactions and highlighting the potential negative impacts of pure breeding on cat health. Data from 7,708 cats receiving veterinary care in the UK during 2019 were analyzed, focusing on reproductive status, breeding status, age at death, and sex. Data were analyzed using ANOVA and Cox proportional hazards models to assess survival differences. The overall mean lifespan of cats in the UK is 11.83 years. Analysis indicates that male cats live shorter lives than females, attributed to higher trauma rates and health issues among males. Neutered/spayed cats generally exhibit longer lifespans compared to entire cats. Tom cats have the shortest lifespan, while spayed females (mollies) live the longest. Moggies tend to outlive both pure and cross-bred cats, suggesting that genetic diversity may contribute to greater longevity. The results of this study emphasize the influence of sex, reproductive status, and cat type on feline lifespan, highlighting the need for targeted health interventions, particularly for male cats. The findings underscore the complex interplay of genetic and environmental factors in determining the health and longevity of domestic cats. This research not only contributes to existing knowledge but also advocates for the consideration of these variables in future studies and veterinary practices., Competing Interests: Fernando Mata is an Academic Editor for PeerJ., (© 2025 Mata.)

The Tapetum Determinant 1 (TPD1) family proteins are known to play a crucial role in the regulation of reproduction in plants, including Cenchrus americanus (pearl millet). However, members of TPD1 family proteins have not been fully identified. The current study aims to identify and characterize the TPD1 family proteins in Cenchrus americanus (L.) Morrone. Seven transmembrane proteins (from 127 to 172 aa) comprising TPD1 domain were identified via genome-wide mining. Analysis of gene expression during developmental stages revealed high expression of four CaTPD1s in reproductive organs. Treatment with phytohormones showed that the expression of CaTPD1s was repressed by hormone treatments except CaTPD1&#95;Ch4.1 and CaTPD1&#95;Ch4.3 which are highly expressed in response to brassinolide and auxin, respectively. Screening of cis-elements in the promoter of CaTPD1s revealed various cis-elements related to phytohormone regulation, wound response, abiotic stress defense, and light response. The phylogenetic tree revealed distinct clustering of CaTPD1&#95;Ch6 and CaTPD1&#95;Ch5 among the other CaTPD1s, which revealed close relationships with the orthologs from Arabidopsis and rice that are known to have a critical role in tapetum development and pollen and ovule production. Hence, this study affirms the role of the CaTPD1s genes in the growth and reproduction during pearl millet developmental stages., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2025 Zainab M. Almutairi. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Thrips tabaci is the main thrips species affecting onion and related species. It is a cryptic species complex comprising three phylogenetic groups characterized by different reproductive modes (thelytoky or arrhenotoky) and host plant specialization. Thrips tabaci populations vary widely in genetic diversity, raising questions about the factor(s) that drive this diversity. We investigated the genetic diversity, reproductive mode, and heteroplasmy frequency in T. tabaci populations from different Allium spp fields in six locations in the Netherlands in 2021 and at two locations from the North and South of Uruguay over three years to unravel how the diversity is structured in the populations and if changes can be associated with weather variables. The thrips populations from each location studied were characterized by sequencing 33 individuals per sampling using the cytochrome oxidase subunit I (COI) gene. The reproductive mode was determined using specific primers and a phylogenetic analysis. Daily data for the weather variables was obtained from agrometeorological experimental stations located in the Uruguayan sampled crop fields. The diversity, reproductive mode, and heteroplasmy of T. tabaci populations in onion crops exhibited significant year-to-year variation depending on the location. Changes in the relative frequency of each reproductive mode in populations are associated with weather variables: precipitation, temperature, number of frosts, and relative humidity. Heteroplasmy frequency was associated with the same weather variables except temperature. In Uruguay and the Netherlands, T. tabaci thelytokous haplotype H1 was the most common, showing different heteroplasmy levels within and between the populations. In the field populations, a high frequency of heteroplasmic H1 individuals was associated with low precipitation, while all H1 individuals were also associated with high temperature and high relative humidity. In Uruguay, heteroplasmy was associated with arrhenotokous T. tabaci haplotypes, which were highly common in the North, pointing at specific adaptations leading to a faster population build-up. All this information may be instrumental for designing more precise integrated pest management techniques in both conventional and organic production., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2025 Porta et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Background: Tris (2-chloroethyl) phosphate (TCEP), a widely used flame retardant, is widespread in the environment and potentially harmful to organisms. However, the specific mechanisms of TCEP-induced neurological and reproductive toxicity in fish are largely unknown. Turbot (Scophthalmus maximus) is cultivated on a large scale, and the emergence of pollutants with endocrine disrupting effects seriously affects its economic benefits. This study aimed to investigate the toxic effects of TCEP on turbot by integrating physio-biochemical and transcriptomic analyses., Results: TCEP exposure induced severe neuroendocrine disrupting effects in turbot. Firstly, the hormone levels of luteinizing hormone (LH), follicle-stimulating hormone (FSH), estradiol (E2), and 11-ketotestosterone (11-KT) were significantly decreased under prolonged TCEP stress, which may have a negative impact on normal reproductive function. We identified and summarized representative differentially expressed genes (DEGs) and their functions, such as endocrine system and oxidative stress. Pathway enrichment showed that the toxicological characteristics of TCEP on turbot were neuroendocrine regulation disorders, including oxidative phosphorylation, apoptosis, steroid biosynthesis, GnRH signaling pathway and so on. Weighted gene co-expression network analysis (WGCNA) also revealed key genes involved in these pathways. Among these genes, those encoding the components of the electron transport chain presented an initial increase in expression followed by a decrease, indicating that TCEP stress might affect mitochondrial function and lead to cell damage. This finding was also supported by the upregulation of apoptosis-related gene expression. Moreover, acute exposure to TCEP regulated MAPK-mediated transduction and regulation of GnRH signaling, thereby altering the expression of hypothalamic-pituitary-gonadal (HPG) axis-related genes., Conclusions: These findings revealed the endocrine disrupting effects of TCEP on turbot and identified biomarkers related to reproductive toxicity, providing early warning for the monitoring of healthy aquaculture., Competing Interests: Declarations. Ethics approval and consent to participate: All of the turbot collections and the anatomy experiments were conducted in accordance with the National Research Council’s Guide for the Care and Use of Laboratory Animals, which was approved and supervised by the Ethic Committee in First Institute of Oceanography, MNR. All efforts were made to minimize the suffering of the animals. The supporting document was shown in the supplementary material. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

Low fertility in cows leads to early removal from herds. Since reproductive traits are complex and have low heritability, genetic analysis can aid in improving reproduction. This study identified key genes linked to fertility by conducting genome- and transcriptome-wide association studies, RNA-seq analysis, meta-analysis, weighted gene co-expression network analysis, and functional enrichment analysis. Through these methods, we identified candidate genes related to Cow conception rate (CCR), Daughter pregnancy rate (DPR), Heifer conception rate (HCR), and overall fertility traits, helping to improve genetic selection for reproductive success in cows. The identified genes include RPL12, FKBP1B, FZD10, COX10, COX7A2, GAA, ETFBKMT, ACSM5, NUDT9, TIGAR, PAIP2, and PSMB5. Notably, GAA, ETFBKMT, COX10, and COX7A2 are involved in the "generation of precursor metabolites and energy" process. COX10, GAA, ETFBKMT, ACSM5, NUDT9, and TIGAR exhibit significant impacts on CCR, DPR, and HCR. COX7A2, PAIP2, and PSMB5 have been identified as hub genes related to fertility traits. RPL12 plays a role in protein synthesis, essential for gametogenesis and embryo development, while FKBP1B regulates calcium signaling, particularly in oocyte aging and fertility decline, and FZD10 is crucial in Wnt signaling. The identified genes serve as markers for genomic selection aimed at enhancing reproductive traits in cow., Competing Interests: Declarations. Ethics approval and consent to participate: All animal-related experimental protocols conducted in this research study received authorization from the Animal Ethics Committee at the Department of Animal Science, University of Tabriz, Iran. Our adherence to ARRIVE guidelines has been ensured during the submission process. Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

In Brief: Modes of reproduction across limbed vertebrates are diverse, but the molecular mechanisms required for the development and maintenance of reproductive tract tissue architecture are poorly understood. This paper describes gene expression changes across the regions of the reproductive tract of the adult female brown anole, Anolis sagrei., Abstract: The morphological diversity and functional role of the organs of the female reproductive system across tetrapods (limbed vertebrates) are relatively poorly understood. Although some features are morphologically similar, species-specific modification makes comparisons between species and inference about evolutionary origins challenging. In combination with the study of morphological changes, studying differences in gene expression in the adult reproductive system in diverse species can clarify the function of each organ. Here, we use the brown anole, Anolis sagrei, to study gene expression differences within the reproductive tract of the adult female. We generated gene expression profiles of four biological replicates of the three regions of the female reproductive tract, the infundibulum, glandular uterus, and nonglandular uterus, by RNA-sequencing. We aligned reads to the recently published A. sagrei genome and identified significantly differentially expressed genes between the regions using DESeq2. Each organ expressed approximately 14,600 genes, and comparison of gene expression profiles between organs revealed between 367 and 883 differentially expressed genes. We identify shared and region-specific transcriptional signatures for the three regions and compare gene expression in the brown anole reproductive tract to known gene expression patterns in other tetrapods. We find that genes in the Hox cluster have an anterior-posterior, collinear expression pattern as has been described in mammals. We also define a secretome for the glandular uterus. These data provide fundamental information for functional studies of the reproductive tract organs in the brown anole and an important phylogenetic anchor for comparative studies of the evolution of the female reproductive tract.

Background: The profitability of the beef industry is directly influenced by the fertility rate and reproductive performance of both males and females, which can be improved through selective breeding. When performing genomic analyses, genetic markers located on the X chromosome have been commonly ignored despite the X chromosome being one of the largest chromosomes in the cattle genome. Therefore, the primary objectives of this study were to: (1) estimate variance components and genetic parameters for eighteen male and five female fertility and reproductive traits in Nellore cattle including X chromosome markers in the analyses; and (2) perform genome-wide association studies and functional genomic analyses to better understand the genetic background of male and female fertility and reproductive performance traits in Nellore cattle., Results: The percentage of the total direct heritability (h 2 total ) explained by the X chromosome markers (h 2 x ) ranged from 3 to 32% (average: 16.4%) and from 9 to 67% (average: 25.61%) for female reproductive performance and male fertility traits, respectively. Among the traits related to breeding soundness evaluation, the overall bull and semen evaluation and semen quality traits accounted for the highest proportion of h 2 x relative to h 2 total with an average of 39.5% and 38.75%, respectively. The total number of significant genomic markers per trait ranged from 7 (seminal vesicle width) to 43 (total major defects). The number of significant markers located on the X chromosome ranged from zero to five. A total of 683, 252, 694, 382, 61, and 77 genes overlapped with the genomic regions identified for traits related to female reproductive performance, semen quality, semen morphology, semen defects, overall bulls' fertility evaluation, and overall semen evaluation traits, respectively. The key candidate genes located on the X chromosome are PRR32, STK26, TMSB4X, TLR7, PRPS2, SMS, SMARCA1, UTP14A, and BCORL1. The main gene ontology terms identified are "Oocyte Meiosis", "Progesterone Mediated Oocyte Maturation", "Thermogenesis", "Sperm Flagellum", and "Innate Immune Response"., Conclusions: Our findings indicate the key role of genes located on the X chromosome on the phenotypic variability of male and female reproduction and fertility traits in Nellore cattle. Breeding programs aiming to improve these traits should consider adding the information from X chromosome markers in their genomic analyses., Competing Interests: Declarations. Ethics approval and consent to participate: Animal Care and Use Committee approval was not obtained for this study because all the analyses were performed using pre-existing datasets provided by commercial Nellore cattle breeding organizations. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

Transcription factors (TFs) involved in sexual reproduction in filamentous fungi have been characterized. However, we have little understanding of how these TFs synergize within regulatory networks resulting in sexual development. We investigated 13 TFs in Fusarium graminearum , whose knockouts exhibited abortive or arrested phenotypes during sexual development to elucidate the transcriptional regulatory cascade underlying the development of the sexual fruiting bodies. A Bayesian network of the TFs was inferred based on transcriptomic data from key stages of sexual development. We evaluated in silico knockout impacts to the networks of the developmental phenotypes among the TFs and guided knockout transcriptomics experiments to properly assess regulatory roles of genes with same developmental phenotypes. Additional transcriptome data were collected for the TF knockouts guided by the stage at which their phenotypes appeared and by the cognate in silico prediction. Global TF networks revealed that TFs within the mating-type locus ( MAT genes) trigger a transcriptional cascade involving TFs that affected early stages of sexual development. Notably, PNA1 , whose knockout mutants produced exceptionally small protoperithecia, was shown to be an upstream activator for MAT genes and several TFs essential for ascospore production. In addition, knockout mutants of SUB1 produced excessive numbers of protoperithecia, wherein MAT genes and pheromone-related genes exhibited dysregulated expression. We conclude that PNA1 and SUB1 play central and suppressive roles in initiating sexual reproduction, respectively. This comprehensive investigation contributes to our understanding of the transcriptional framework governing the multicellular body plan during sexual reproduction in F. graminearum .IMPORTANCEUnderstanding transcriptional regulation of sexual development is crucial to the elucidation of the complex reproductive biology in Fusarium graminearum . We performed gene knockouts on 13 transcription factors (TFs), demonstrating knockout phenotypes affecting distinct stages of sexual development. Using transcriptomic data across stages of sexual development, we inferred a Bayesian network of these TFs that guided experiments to assess the robustness of gene interactions using a systems biology approach. We discovered that the mating-type locus ( MAT genes) initiates a transcriptional cascade, with PNA1 identified as an upstream activator essential for early sexual development and ascospore production. Conversely, SUB1 was found to play a suppressive role, with knockout mutants exhibiting excessive protoperithecia due to abnormally high expression of MAT and pheromone-related genes. These findings highlight the central roles of PNA1 and SUB1 in regulating other gene activity related to sexual reproduction, contributing to a deeper understanding of the mechanisms of the multiple TFs that regulate sexual development., Competing Interests: The authors declare no conflict of interest.

Sea turtles are highly migratory and predominantly inhabit oceanic environments, which poses significant challenges to the study of their life cycles. Research has traditionally focused on nesting females, utilizing nest counts and mark-recapture methods, while male behavior remains understudied. To address this gap, previous studies have analyzed the genotypes of females and hatchlings to indirectly infer male genotypes and evaluate the extent of multiple paternity within populations. Our research aimed to investigate the presence of multiple paternity in loggerhead turtle ( Caretta caretta ) nests for the first time in Brazil. We analyzed 534 hatchlings from 43 nests associated with 42 females during the 2017/18 to 2019/20 nesting seasons, using four highly polymorphic, species-specific microsatellite markers (nDNA). Parentage tests were conducted to reconstruct paternal genotypes and determine the rates of multiple paternity within clutches. Our results revealed that 72.09% of clutches were sired by multiple males, with contributions ranging from one to six males per clutch. Additionally, seven out of 88 males (7.95%) were found to have sired clutches from multiple females, with some males contributing to more than one clutch within and across breeding seasons. The breeding sex ratio (BSR) was calculated to be 2.09 males per female. While multiple paternity is a common phenomenon among sea turtles, this study is the first to document polyandry in loggerheads in Brazil and the first to provide evidence of polygyny in this species globally. This research establishes a crucial database for future studies in Brazil, with a focus on the BSR of the Southwest Atlantic subpopulation, offering essential insights for developing effective management strategies for this vulnerable population., Competing Interests: The authors declare that they have no competing interests., (© 2025 Amorim et al.)

A wave of studies has recently emphasized the influence of sex chromosomes on both lifespan and actuarial senescence patterns across vertebrates and invertebrates. Basically, the heterogametic sex (XY males in XX/XY systems or ZW females in ZW/ZZ systems) typically displays a lower lifespan and a steeper rate of actuarial senescence than the homogametic sex. However, whether these effects extend to the senescence patterns of other phenotypic traits or physiological functions is yet to be determined. Here, we investigated whether sex chromosomes modulate reproductive senescence using females from the African pygmy mouse ( Mus minutoides ). This biological model exhibits an odd sex determining system with a third, feminizing sex chromosome, X*, resulting in three distinct female genotypes (XX, X*X, or X*Y) that coexist in natural populations. We found that the rate of senescence in litter size at birth is much more pronounced in heterogametic X*Y females than in homogametic XX or X*X females that may support the unguarded X or toxic Y hypotheses and can be directly linked to the complex and unique X*Y phenotype. A decrease in neonatal survival with mother's age has also been found, but this decline is not different between the three female genotypes., Competing Interests: Competing interests statement:The authors declare no competing interest.

Dispersal can evolve as an adaptation to escape competition with conspecifics or kin. Locations with a low density of conspecifics, however, may also lead to reduced opportunities for mating, especially in sessile marine invertebrates with proximity-dependent mating success. Since there are few experimental investigations, we performed a series of field experiments using an experimentally tractable species (the bryozoan Bugula neritina) to test the hypothesis that the density, spatial arrangement, and genetic relatedness of neighbours differentially affect survival, growth, reproduction, paternity, and sperm dispersal. We manipulated the density and relatedness of neighbours and found that increased density reduced survival but not growth rate, and that there was no effect of relatedness on survival, growth, or fecundity, in contrast to previous studies. We also manipulated the distances to the nearest neighbour and used genetic markers to assign paternity within known mother-offspring groups to estimate how proximity affects mating success. Distance to the nearest neighbour did not affect the number of settlers produced, the paternity share, or the degree of multiple paternity. Overall, larger than expected sperm dispersal led to high multiple paternity, regardless of the distance to the nearest neighbour. Our results have important implications for understanding selection on dispersal distance: in this system, there are few disadvantages to the limited larval dispersal that does occur and limited advantages for larvae to disperse further than a few 10s of metres., (© The Author(s) 2024. Published by Oxford University Press on behalf of the European Society of Evolutionary Biology. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

Balanced mating type polymorphisms offer a distinct window into the forces shaping sexual reproduction strategies. Multiple hermaphroditic genera in Juglandaceae, including walnuts ( Juglans ) and hickories ( Carya ), show a 1:1 genetic dimorphism for male versus female flowering order (heterodichogamy). We map two distinct Mendelian inheritance mechanisms to ancient (>37 million years old) genus-wide structural DNA polymorphisms. The dominant haplotype for female-first flowering in Juglans contains tandem repeats of the 3' untranslated region of a gene putatively involved in trehalose-6-phosphate metabolism and is associated with increased cis gene expression in developing male flowers, possibly mediated by small RNAs. The Carya locus contains ~20 syntenic genes and shows molecular signatures of sex chromosome-like evolution. Inheritance mechanisms for heterodichogamy are deeply conserved, yet may occasionally turn over, as in sex determination.

Fish exhibit diverse mechanisms of sex differentiation and determination, shaped by both external and internal influences, often regulated by distinct DNA methylation patterns responding to environmental changes. In S. senegalensis aquaculture, reproductive issues in captivity pose significant challenges, particularly the lack of fertilization capabilities in captive-bred males, hindering genetic improvement measures. This study analyzed the methylation patterns and transcriptomic profiles in gonadal tissue DNA from groups differing in rearing conditions and sexual maturity stages. RRBS (Reduced Representation Bisulfite Sequencing) was employed to detect notable methylation variations across groups, while RNA was extracted and sequenced for differential expression analysis. Our findings suggest that DNA methylation significantly regulates gene expression, acting as a mechanism that can both repress and enhance gene expression depending on the genomic context. The complexity of this epigenetic mechanism is evident from the varying levels of methylation and correlation rates observed in different CpGs neighboring specific genes linked to reproduction. Differential methylation comparisons revealed the highest number of differently methylated CpGs between maturation stages, followed by rearing conditions, and lastly between sexes. These findings underscore the crucial role of methylation in regulating gene expression and its potential role in sex differentiation, highlighting the complex interplay between epigenetic modifications and gene expression.

Age at first calving (AFC) is a measure of sexual maturity associated with the start of productive life of dairy animals. Additionally, a lower AFC reduces the generation interval and early culling of females. However, AFC has low heritability, making it a trait highly influenced by environmental factors. In this scenario, one way to improve the reproductive performance of buffalo cows is to select robust animals according to estimated breeding value (EBV) using models that include genotype-environment interaction (GEI) with the application of reaction norm models (RNMs). This can be achieved by understanding the genomic basis related to GEI of AFC. Thus, in this study, we aimed to predict EBV considering GEI via the RNM and identify candidate genes related to this component in dairy buffaloes through genome-wide association studies (GWAS). We used 1795 AFC records from three Murrah buffalo herds and formed environmental gradients (EGs) from contemporary group solutions obtained from genetic analysis of 270-day cumulative milk yield. Heritability estimates ranged from 0.15 to 0.39 along the EG. GWAS of the RNM slope parameter identified important genomic regions. The genomic window that explained the highest percentage of genetic variance of the slope (0.67%) was located on BBU1. After functional analysis, five candidate genes were detected, involved in two biological processes. The results suggested the existence of a GEI for AFC in Murrah buffaloes, with reclassification of animals when different environmental conditions were considered. The inclusion of genomic information increased the accuracy of breeding values for the intercept and slope of the reaction norm. GWAS analysis suggested that important genes associated with the AFC reaction norm slope were possibly also involved in biological processes related to lipid metabolism and immunity., (© 2024 Wiley‐VCH GmbH. Published by John Wiley & Sons Ltd.)

In tropical beef cattle production systems, animals are commonly raised on pastures, exposing them to potential stressors. The end of gestation typically overlaps with a dry period characterized by limited food availability. Late gestation is pivotal for fetal development, making it an ideal scenario for inter- and transgenerational effects of the maternal gestational environment. Intergenerational effects occur due to exposure during gestation, impacting the development of the embryo and its future germline. Transgenerational effects, however, extend beyond direct exposure to the subsequent generations. The objective of the present study was to verify these effects on the post-natal performance of zebu beef cattle. We extended the use of a reaction norm model to identify genetic variation in the animals' responses to transgenerational effects. The inter- and transgenerational effects were predominantly positive (-0.09% to 19.74%) for growth and reproductive traits, indicating improved animal performance on the phenotypic scale in more favourable maternal gestational environments. Additionally, these effects were more pronounced in the reproductive performance of females. On average, the ratio of direct additive genetic variances of the slope and intercept of the reaction norm ranged from 1.23% to 3.60% for direct and from 10.17% to 11.42% for maternal effects. Despite its relatively modest magnitude, this variation proved sufficient to prompt modifications in parameter estimates. The average percentage variation of direct heritability estimates ranged from 19.3% for scrotal circumference to 33.2% for yearling weight across the environmental descriptors evaluated. Genetic correlations between distant environments for the studied traits were generally high for direct effects and far from unity for maternal effects. Changes in EBV rankings of sires across different gestational environments were also observed. Due to the multifaceted nature of inter- and transgenerational effects of the maternal gestational environment on various traits of beef cattle raised under tropical pasture conditions, they should not be overlooked by producers and breeders. There were differences in the specific response of beef cattle to variations in the quality of the maternal gestational environment, which can be partially explained by transgenerational epigenetic inheritance. Adopting a reaction norm model to capture a portion of the additive variance induced by inter- or transgenerational effects could be an alternative for future research and animal genetic evaluations., (© 2024 Wiley‐VCH GmbH. Published by John Wiley & Sons Ltd.)

Accurate genomic predictions of breeding values for traits included in the selection indexes are paramount for optimizing genetic progress in populations under selection. The size of the reference populations is a major factor influencing the accuracy of genomic predictions, which is even more important for lowly heritable traits, such as fertility and reproduction indicators. Combining data from different geographical regions or countries can be beneficial for genomic prediction of these lowly heritable traits. Therefore, the objectives of this study were to (1) evaluate the benefits of performing across-regional genomic evaluations for reproduction traits in Chinese Holstein cattle and (2) assess the feasibility of validating genomic predictions across environments based on reaction norm models (RNM) and the linear regression (LR) method after accounting for genotype-by-environment interactions. Phenotypic records from 194,574 cows collected across 47 farms located in 2 regions of China were used for this study. The reference and validation populations were defined based on birth year for applying the LR validation method. The traits evaluated included: interval from first to last insemination (IFL), conception rate at the first insemination (CR&#95;f), and number of inseminations (NS) recorded in heifers and first-parity cows. The results indicated that combining data from different regions resulted in greater genomic prediction accuracies compared with using data from single regions, with increases ranging from 2.74% to 93.81%. This improvement was particularly notable for the region with the least amount of available data, where the increases ranged from 26.49% to 93.81%. Furthermore, the predictive abilities could be validated for all studied traits based on the LR method across different environments when fitting RNM. The prediction accuracies and bias of genomic breeding values based on RNM were better than regular single-trait animal models in extreme climatic conditions for IFL and NS, whereas limited increases in predictive abilities were observed for CR&#95;f. Across-regional genomic prediction by RNM can account for genotype-by-environment interactions, potentially increase the accuracy of genomic prediction, and predict the performances of individuals in the environments with limited phenotypic data available., (The Authors. Published by Elsevier Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).)

Although mammalian carnivores are ecologically important, they also drive human-wildlife conflicts. Managing carnivores using lethal control is controversial, in part because the impact of control effort is often uncertain due to limited abundance monitoring. We used an Australian metapopulation of wild dogs as a model system to investigate the feasibility of monitoring effective population size ( N e ) to detect reductions in census population size ( N c ) following control. Based on microsatellite data collected over an 11-year period, we parameterised an individual-based spatial population model for wild dogs that integrated demography, genetics, random or hierarchical mating, dispersal between subpopulations and compensatory immigration. N c and N ̂ e trajectories were simulated under different proportional culling rates and genetic sampling regimes. We also used simulations without culling as null models to define 95% critical values for assessing the significance of empirical changes in N ̂ e over time. We concluded there were significant reductions (39%-62%) in N ̂ e in each subpopulation of the wild dog metapopulation, mostly likely due to control. In simulations assuming a hierarchical rather than random mating system, the impact of control on N c was weakened because reproduction by subordinate individuals increased as dominant individuals were removed, yet N ̂ e reduced following culling. Sensitivity analyses demonstrated that N ̂ e becomes an unreliable proxy of N c when compensatory immigration is strong and compensatory reproduction is weak, in which case N ̂ e can increase following culling due to the immigration of new genotypes. Nonetheless, our results suggest N ̂ e can provide information about wild dog N c over sufficiently short timescales to inform management., (© 2024 John Wiley & Sons Ltd.)