Search

Background: Previously, we discovered a strain of Kunming mice, referred to as the KM ush/ush strain, that exhibited notably abnormal electroretinogram (ERG) readings and elevated thresholds for auditory brainstem responses (ABRs), which resembled the characteristics of Usher Syndrome (USH). We successfully identified the pathogenic genes, Pde6b and Adgrv1, after KM ush/ush crossbred with CBA/CaJ mice, referred to as CBA-1 ush/ush , CBA-2 ush/ush or CBA-2 ush/ush . In this investigation, we crossbred KM ush/ush and CBA/J mice to establish novel recombinant inbred lines and analysed their phenotypic and genotypic characteristics., Methods: ERG readings, ABR testing, fundus morphology, histological examination of the retina and inner ear, reverse transcription-quantitative polymerase chain reaction (RT-qPCR) analysis, western blotting, DNA sequence analysis and behavioural experiments were performed to assess the phenotypes and genotypes of the progeny lines., Results: No obvious waveforms in the ERG were detected in F1 hybrid mice while normal ABR results were recorded. The F2 hybrids, which were called J1 ush/ush or J2 ush/ush , exhibited segregated hearing-loss phenotypes. J1 ush/ush mice had a retinitis pigmentosa (RP) phenotype with elevated ABR thresholds, whereas J2 ush/ush mice exhibited only the RP phenotype. Interestingly, J1 ush/ush mice showed significantly higher ABR thresholds than wild-type mice at 28 days post born (P28), and RT-qPCR and DNA-sequencing analysis showed that Adgrv1 gene expression was significantly altered in J1 ush/ush mice, but histological analysis showed no significant structural changes in the organ of Corti or spiral ganglia. Further elevation of ABR-related hearing thresholds by P56 manifested only as a reduced density of spiral ganglion cells, which differed significantly from the previous pattern of cochlear alterations in CBA-2 ush/ush mice., Conclusions: We successfully introduced the hearing-loss phenotype of inbred mice with USH into CBA/J mice, which provides a good animal model for future studies on the important physiological roles of the Adgrv1 gene in inner-ear structure and for therapeutic studies targeting Adgrv1-mutated USH., 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.)

Parental selection is perhaps the most critical decision a breeder makes, establishing the foundation of the entire program for years to come. Cross selection based on predicted mean and genetic variance can be further expanded to multiple-trait improvement by predicting the genetic correlation ( r G ) between pairs of traits. Our objective was to empirically assess the ability to predict the family mean, genetic variance, superior progeny mean and genetic correlation through genomic prediction in a soybean population. Data made available through the Soybean Nested Association Mapping project included phenotypic data on seven traits (days to maturity, lodging, oil, plant height, protein, seed size, and seed yield) for 39 families. Training population composition followed a leave-one-family-out cross-validation scheme, with the validation family genetic parameters predicted using the remaining families as the training set. The predictive abilities for family mean and superior progeny mean were significant for all traits while predictive ability of genetic variance was significant for four traits. We were able to validate significant predictive abilities of r G for 18 out of 21 (86%) pairwise trait combinations (P < 0.05). The findings from this study support the use of genome-wide marker effects for predicting r G in soybean biparental crosses. If successfully implemented in breeding programs, this methodology could help to increase the rate of genetic gain for multiple correlated traits., (© 2024. The Author(s).)

Genetic information of bean seed traits can be an immense help to the breeder in selection of suitable genotypes and the appropriate breeding strategies. Therefore, the investigation aims to assess the genetic variability and to elucidate the genetic analysis of seed dietary fibre, carbohydrate, seed calcium and phosphorus contents of Phaseolus vulgaris in the high Guinean Savannah zone conditions. 5 × 5 half-diallel crosses of these traits were conducted in randomized complete block design with three replications. Results revealed high differences between five lines beans (p < 0.05), suggesting the sufficient genetic diversity for these traits. High broad sense heritability values were recorded for seed dietary fibre, carbohydrate and seed calcium content, attesting a strong implication of the genetic factors in the control of these traits; thereby, these traits can be improved through regular selection. The ratio GCA/SCA was greater than unity only for seed phosphorus content. It indicates the prevalence of additive gene effect in the involvement of the genetic control for this trait. The combining ability analysis revealed highly significant differences between parental GCA effects and F 1 cross SCA effects. The PB, BI, CT and PR lines beans will prove useful in common bean breeding programmes as donor genotypes, in the development of bean genetic resources for betterment improvement of nutritional traits., (© 2024. The Author(s).)

Within biology, there have been long-standing goals to understand how traits impact fitness, determine the degree of adaptation, and predict responses to selection. One key step in answering these questions is to study the mode of gene action or genetic architecture of traits. The genetic architecture underlying a trait will ultimately determine whether selection can lead to a change in the phenotype. Theoretical and empirical research have shown that additive architectures are most responsive to selection. The genus Solanum offers a unique system to quantify the genetic architecture of traits. Crosses between Solanum pennellii and S. lycopersicum , which have evolved unique adaptive traits for very different environments, offer an opportunity to investigate the genetic architecture of a variety of morphological traits that often are not variable within species. We generated cohorts between strains of these two Solanum species and collected phenotypic data for eight morphological traits. The genetic architectures underlying these traits were estimated using an information-theoretic approach to line cross analysis. By estimating the genetic architectures of these traits, we were able to show a key role for maternal and epistatic effects and infer the accessibility of these traits to selection., Competing Interests: The authors declare that they have no competing interests., (© 2024 Burch et al.)

Cucurbita moschata varieties grown in Africa have very low yield. They have been neglected, and totally ignored in agricultural research programs. However, interest in their fruits, seeds, flowers and leaves is growing nowadays due to their nutritional and medicinal potentials. That growing interest has prompted plant breeders and agronomists to develop research programs for their improvement. A complete diallel cross analysis of four parental lines, Long, Zouan-H, Oval, and Soubre and their twelve F1 hybrids, was carried out in a farming environment at the University Nangui Abrogoua, Abidjan, Côte d'Ivoire. The four parental lines and the F1 hybrids were evaluated for their general performances, combining abilities, potency ratio and heterosis effects. The investigated traits included plant height, and eleven fruit- and seed-related characters. The analysis of variance showed significant differences for all traits studied. In addition, the diallel model yielded highly significant gca effects of the female parents. The gca effects of the male parents were significant for all traits except plant height, length of the fruit, width of the fruit and length of the seed. Highly significant sca effects were observed in the crosses for all the traits. Strong maternal effects were observed for the weight and diameter of the fruit, weight of the pulp, number of seeds per fruit, weight of the fresh seeds and 100-seed weight. The general predictive ratio approached the value 1 for all the traits except weight of the fresh seed and width of the dry seed. Most of the characters under this study are predominantly determined by the effects of additive genes. But, weight of the fresh seed and width of the dry seed may be controlled by non-additive genes. Mid-parent heterosis was significant for all measured traits in the crosses, except the length of the fruit. And better-parent heterosis was significant for all traits except plant height, number of fruits per plant and length of the fruit. Gene expression is described by a super-dominance for many traits, and partial dominance for some other traits in all twelve F1 hybrids. Classification of the parental lines based on the effects of their general combining ability grouped the Soubre lines as promising contributors to fruit yield. The parental lines Long and Oval formed another group likely on the basis of the small size of their fruits, the small pulps, the smaller number of fruits per plant and the large number of seeds per fruit. However, Long would be a candidate parent for the development of cultivars with longer vegetative growth. The parental line Zouan-H formed the third group and it was mostly characterized by its large number of seeds per fruit and relatively large fruits., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 KOUAGO 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.)

In this study, we address the mate selection problem in the hybridization stage of a breeding pipeline, which constitutes the multi-objective breeding goal key to the performance of a variety development program. The solution framework we formulate seeks to ensure that individuals with the most desirable genomic characteristics are selected to cross in order to maximize the likelihood of the inheritance of desirable genetic materials to the progeny. Unlike approaches that use phenotypic values for parental selection and evaluate individuals separately, we use a criterion that relies on the genetic architecture of traits and evaluates combinations of genomic information of the pairs of individuals. We introduce the expected cross value (ECV) criterion that measures the expected number of desirable alleles for gametes produced by pairs of individuals sampled from a population of potential parents. We use the ECV criterion to develop an integer linear programming formulation for the parental selection problem. The formulation is capable of controlling the inbreeding level between selected mates. We evaluate the approach or two applications: (i) improving multiple target traits simultaneously, and (ii) finding a multi-parental solution to design crossing blocks. We evaluate the performance of the ECV criterion using a simulation study. Finally, we discuss how the ECV criterion and the proposed integer linear programming techniques can be applied to improve breeding efficiency while maintaining genetic diversity in a breeding program., (© 2024. The Author(s).)

Inbreeding depression refers to the reduced performance arising from increased homozygosity, a phenomenon that is the reverse of heterosis and exists among plants and animals. As a natural self-pollinated crop with strong heterosis, the mechanism of inbreeding depression in rice is largely unknown. To understand the genetic basis of inbreeding depression, we constructed a successive inbreeding population from the F 2 to F 4 generation and observed inbreeding depression of all heterotic traits in the progeny along with the decay of heterozygosity in each generation. The expected depression effect was largely explained by 13 QTLs showing dominant effects for spikelets per panicle, 11 for primary branches, and 12 for secondary branches, and these loci constitute the main correlation between heterosis and inbreeding depression. However, the genetic basis of inbreeding depression is also distinct from that of heterosis, such that a biased transmission ratio of alleles for QTLs with either dominant or additive effects in four segregation distortion regions would result in minor effects in expected depression. Noticeably, two-locus interactions may change the extent and direction of the depression effects of the target loci, and overall interactions would promote inbreeding depression among generations. Using an F 2:3 variation population, the actual performance of the loci showing expected depression was evaluated considering the heterozygosity decay in the background after inbreeding. We found inconsistent or various degrees of background depression from the F 2 to F 3 generation assuming different genotypes of the target locus, which may affect the actual depression effect of the locus due to epistasis. The results suggest that the genetic architecture of inbreeding depression and heterosis is closely linked but also differs in their intrinsic mechanisms, which expand our understanding of the whole-genome architecture of inbreeding depression., (© 2024. Science China Press.)

Key Message: Rhizome formation of Oryza longistaminata was dependent on the bud shape. The loci qBS3.1, qBS3.2 and qBS3.3 for controlling rhizome formation were functional redundant under Oryza longistaminata background. The rhizome, a root-like underground stem, is the key organ for grasses to achieve perennial growth. Oryza longistaminata, the only rhizomatous wild Oryza species with the same AA genome as cultivated rice, is an important germplasm for developing perennial rice. Our study found that the rhizome formation of O. longistaminata was dependent on the bud shape: the dome-like axillary bud (dome bud) usually penetrated through the leaf sheaths, developing into rhizome (extravaginal branching), but the flat axillary bud (flat bud) wrapped by the leaf sheaths only developed into tiller (intravaginal branching). The genetic loci (QTL) controlling the bud shape (BS) were mapped by entire population genotyping method (F 2 population from crossing O. longistaminata with Balilla (Oryza sativa) and selective genotyping mapping method (BC 1 F 2 population from backcrossing F 1 with Balilla). A total of twelve loci were identified, including four major-effect QTL: qBS2, qBS3.1, qBS3.2 and qBS3.3, and the genetic network of these twelve loci was established. The dome bud lost the potential to develop into rhizome with the increase in backcross generations under Balilla background. Considering the rapid loss of rhizome under Balilla background, the near-isogenic lines under O. longistaminata background were used to identify the effect of major-effect loci. According to the BC 3 F 2 , BC 4 F 2 and BC 5 F 2 under O. longistaminata background, there was some functional redundancy among qBS3.1, qBS3.2 and qBS3.3. Our results provided a new perspective for analyzing the genetic basis of perenniality and laid the foundation for fine mapping and verification of related genes., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Key Message: Phenotypical, physiological and genetic characterization was carried out on the hybrid necrosis gene from Haynaldia villosa, and the related gene Ne-V was mapped to chromosome arm 2VL. Introducing genetic variation from wild relatives into common wheat through wide crosses is a vital strategy for enriching genetic diversity and promoting wheat breeding. However, hybrid necrosis, a genetic autoimmunity syndrome, often occurs in the offspring of interspecific or intraspecific crosses, restricting both the selection of hybrid parents and the pyramiding of beneficial genes. To utilize the germplasms of Haynaldia villosa (2n = 2x = 14, VV), we conducted wide hybridization between durum wheat (2n = 4x = 28, AABB) and multiple H. villosa accessions to synthesize the amphiploids (2n = 6x = 42, AABBVV). This study revealed that 61.5% of amphiploids derived from the above crosses exhibited hybrid necrosis, with some amphiploids even dying before reaching maturity. However, the initiation time and severity of necrosis varied dramatically among the progenies, suggesting that there were multiple genetic loci or multiple alleles in the same genetic locus conferring to hybrid necrosis in H. villosa accessions. Genetic analysis was performed on the F 2 and derived F 2:3 populations, which were constructed between amphiploid STH59-1 with normal leaves and amphiploid STH59-2 with necrotic leaves. A semidominant hybrid necrosis-related gene, Ne-V, was mapped to an 11.8-cM genetic interval on the long arm of chromosome 2V, representing a novel genetic locus identified in Triticum-related species. In addition, the hybrid necrosis was correlated with enhanced H 2 O 2 accumulation and cell death, and it was influenced by the temperature and light. Our findings provide a foundation for cloning the Ne-V gene and exploring its molecular mechanism., (© 2024. The Author(s).)

Direct observation is central to our understanding of adaptation, but evolution is rarely documented in a large, multicellular organism for more than a few generations. In this study, we observed evolution across a century-scale competition experiment, barley composite cross II (CCII). CCII was founded in 1929 in Davis, California, with thousands of genotypes, but we found that natural selection has massively reduced genetic diversity, leading to a single lineage constituting most of the population by generation 50. Selection favored alleles originating from climates similar to that of Davis and targeted loci contributing to reproductive development, including the barley diversification loci Vrs1 , HvCEN , Ppd-H1 , and Vrn-H2 . Our findings point to selection as the predominant force shaping genomic variation in one of the world's oldest biological experiments.

The contribution of non-additive genetic effects to the genetic architecture of fitness and to the evolutionary potential of populations has been a topic of theoretical and empirical interest for a long time. Yet, the empirical study of these effects in natural populations remains scarce, perhaps because measuring dominance and epistasis relies heavily on experimental line crosses. In this study, we explored the contribution of dominance and epistasis in natural alpine populations of Arabidopsis thaliana for 2 fitness traits, the dry biomass and the estimated number of siliques, measured in a greenhouse. We found that, on average, crosses between inbred lines of A. thaliana led to mid-parent heterosis for dry biomass but outbreeding depression for an estimated number of siliques. While heterosis for dry biomass was due to dominance, we found that outbreeding depression for an estimated number of siliques could be attributed to the breakdown of beneficial epistatic interactions. We simulated and discussed the implication of these results for the adaptive potential of the studied populations, as well as the use of line-cross analyses to detect non-additive genetic effects., (© 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.)

Breeding high yielding groundnut cultivars with 2-3 weeks of fresh seed dormancy, particularly in Spanish-type cultivars, enhances the sustainability of agriculture in groundnuts. In this context, we conducted a comprehensive phenotypic and genotypic evaluation of advanced breeding lines developed in the genetic background of Spanish types. By employing multi-phenotyping and marker data, we identified PBS 15044, 16004, 16013, 16015, 16016, 16017, 16020, 16021, 16026, 16031, 16035, 16037, 16038, 16039, 16041, and 16042 with 2-3 weeks dormancy (> 90%).The various parametric and non-parametric estimates identified the stable fresh dormant genotypes with one or more superior economic trait. PBS 16021, 15044, 16038, and 16039 identified with high hundred pod weight (HPW) were also reported having high intensity of dormancy (> 90% for up to 3 weeks); PBS 15044, 16016, PBS 16038 and PBS 16039 with high hundred kernel weight (HKW) also reported with up to 3 weeks fresh seed dormancy; and PBS 16013, 16031, and 16038 with up to 3 weeks fresh seed dormancy had high shelling percentage (SP). They can be used to develop lines with the desired level of dormancy, and high yields, by designing appropriate breeding strategies., (© 2024. The Author(s).)

Wild species are an invaluable source of new traits for crop improvement. Over the years, the tomato community bred cultivated lines that carry introgressions from different species of the tomato tribe to facilitate trait discovery and mapping. The next phase in such projects is to find the genes that drive the identified phenotypes. This can be achieved by genotyping a few thousand individuals resulting in fine mapping that can potentially identify the causative gene. To couple trait discovery and fine mapping, we are presenting large, recombination-rich, Backcross Inbred Line (BIL) populations involving an unexplored accession of the wild, green-fruited species Solanum pennellii (LA5240; the 'Lost' Accession) with two modern tomato inbreds: LEA, determinate, and TOP, indeterminate. The LEA and TOP BILs are in BC2F6-8 generation and include 1400 and 500 lines, respectively. The BILs were genotyped with 5000 SPET markers, showing that in the euchromatic regions there was one recombinant every 17-18 Kb while in the heterochromatin a recombinant every 600-700 Kb (TOP and LEA respectively). To gain perspective on the topography of recombination we compared five independent members of the Self-pruning gene family with their respective neighboring genes; based on PCR markers, in all cases we found recombinants. Further mapping analysis of two known morphological mutations that segregated in the BILs (self-pruning and hairless) showed that the maximal delimited intervals were 73 Kb and 210 Kb, respectively, and included the known causative genes. The 'Lost'&#95;BILs provide a solid framework to study traits derived from a drought-tolerant wild tomato., (© 2024 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.)

BRRI31R is one of the Bangladesh's most promising restorer lines due to its abundant pollen producing capacity, strong restoring ability, good combining ability, high outcrossing rate and genetically diverse from cytoplasmic male sterile (CMS) line. But the drawback of this line is that it is highly susceptible to bacterial blight (BB) disease of rice caused by Xanthomonas oryzae pv. oryzae. The present study highlighted the pyramiding of effective BB resistance genes (xa5, xa13 and Xa21) into the background of BRRI31R, through marker-assisted backcrossing (MABC). Backcross progenies were confirmed and advanced based on the foreground selection of target genes. Pyramided lines were used for pathogenicity test against five Bangladeshi Xanthomonas oryzae (BXo) races (BXo93, BXo220, BXo822, BXo826, BXo887) and confirmed the dominant fertility restore genes, Rf3 and Rf4 and further validated against SNP markers for more confirmation of target resistance genes. All pyramided restorer lines consisted of Xa4 (in built), xa5, xa13, Xa21, and Chalk5 with two fertility restorer genes, Rf3, Rf4. and these restorer lines showed intermediate amylose content (<25%). Restorer lines BRRI31R-MASP3 and BRRI31R-MASP4 showed high levels of resistance against five virulent BXo races and SNP genotyping revealed that these lines also contained a blast resistance gene Pita races. Gene pyramided restorer lines, BRRI31R-MASP3 and BRRI31R-MASP4 can directly be used as a male parent for the development of new BB resistant hybrid rice variety or could be used as a replacement of restorer line of BRRI hybrid dhan5 and 7 to enhance the quality of hybrid seeds as well as rice production in Bangladesh., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Akter 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: Carcass traits are essential economic traits in the commercial pig industry. However, the genetic mechanism of carcass traits is still unclear. In this study, we performed a genome-wide association study (GWAS) based on the specific-locus amplified fragment sequencing (SLAF-seq) to study seven carcass traits on 223 four-way intercross pigs, including dressing percentage (DP), number of ribs (RIB), skin thinkness (ST), carcass straight length (CSL), carcass diagonal length (CDL), loin eye width (LEW), and loin eye thickness (LET)., Results: A total of 227,921 high-quality single nucleotide polymorphisms (SNPs) were detected to perform GWAS. A total of 30 SNPs were identified for seven carcass traits using the mixed linear model (MLM) (p < 1.0 × 10 - 5 ), of which 9 SNPs were located in previously reported quantitative trait loci (QTL) regions. The phenotypic variation explained (PVE) by the significant SNPs was from 2.43 to 16.32%. Furthermore, 11 candidate genes (LYPLAL1, EPC1, MATN2, ZFAT, ZBTB10, ZNF704, INHBA, SMYD3, PAK1, SPTBN2, and ACTN3) were found for carcass traits in pigs., Conclusions: The GWAS results will improve our understanding of the genetic basis of carcass traits. We hypothesized that the candidate genes associated with these discovered SNPs would offer a biological basis for enhancing the carcass quality of pigs in swine breeding., (© 2024. The Author(s).)

In this study the pattern of color of inheritance based on Mendel's laws on the Clarias gariepinus strain was evaluated, to ascertain the different traits of albino, normally pigmented, and a combination of both traits that could be passed across from the parent stocks to the progenies. Since albinism is caused by a series of genetic abnormalities resulting in the reduction of melanin production, partial diallel cross between normally pigmented and albino fish was carried out using two females (albino and normal pigmented brood fish) weighing 2.5 kg and 3 kg, respectively; they were used in crossing two males (albino and normal pigmented brood fish) that weighed 1.5 kg and 1 kg, respectively. They were paired with normal pigmented (♂Np × ♀Np) and albino C. gariepinus (♂Ae × ♀Ae) fish to produce a pure strain of normally pigmented and albino strain, respectively. To produce the hybrids, they were paired (♂Np × ♀Ae) and (♂Ae × ♀Np), respectively. The outcomes of this study showed that crossbreeding between normally pigmented females and albino males produced all normally pigmented F1 generation, while some quantity of albino (36.67%) at crossing male albino to normally pigmented females were produced. However, the pure strains breed true (100%). Each hybrid exhibits heterosis after 56 days of rearing compared to the normal strain that was crossed, although the normally pigmented fish gives a better SGR. Hence, there is a need to investigate if sex is linked with albinism., (© 2023. The Author(s), under exclusive licence to Springer Nature B.V.)

Background: Salinity is a significant abiotic stress that affects plants from germination through all growth stages. This study was aimed to determine the morpho-physiological and genetic variations in BC 1 F 2 , BC 2 F 1 and F 3 generations resulting from the cross combination WH1105 × Kharchia 65., Results: A significant reduction in germination percentage was observed under salt stress in BC 1 F 2 and F 3 seeds. Correlation, heritability in the broad sense, phenotypic coefficient of variability (PCV) and genotypic coefficient of variability (GCV) were measured for all traits. The presence of both Nax1 and Nax2 loci was confirmed in twenty-nine plants using the marker-assisted selection technique. Genetic relationships among the populations were assessed using twenty-four polymorphic SSR markers., Conclusion: Cluster analysis along with two and three-dimensional PCA scaling (Principal Component Analysis) revealed the distinct nature of WH 1105 and Kharchia 65. Six plants closer to the recurrent parent (WH1105) selected through this study can serve as valuable genetic material for salt-tolerant wheat improvement programs., (© 2024. The Author(s).)

In this study, BC3F2 convergent population [(K343*3/RML22 × K343*3/DHMAS) × K343] was constructed by marker-assisted backcross breeding using K343 as the recurrent parent. DHMAS and RML22 were used as donor parents for the rice blast resistance genes Pi54 and Pi9, respectively. The population was first characterized using GGT 2.0 software, which showed 96.7% of the recurrent genome recovery covering 13953.6 cM, while DHMAS and RML22 showed 1.6% (235.5 cM) and 1.2% (177.1 cM) introgression respectively. The chromosomal segment substitution lines (CSSLs) were then identified using CSSL Finder software. A total of 36 CSSLs were identified, including 22 for DHMAS/K343 and 14 for RML22/K343. Introgression rates for donor substituted segments in DHMAS/K343 CSSLs ranged from 0.54% to 5.99%, with donor coverage of 44.5%, while in RML22/K343 CSSLs, introgression rates ranged from 0.54% to 4.75%, with donor coverage of 24.5%. The identified CSSLs would be a valuable genetic pool and could be used as genomic resources for the discovery and mapping of important genes and QTLs in rice genetic improvement.

Species of the genus Drosophila have served as favorite models in speciation studies; however, genetic factors of interspecific reproductive incompatibility are under-investigated. Here, we performed an analysis of hybrid female sterility by crossing Drosophila melanogaster females and Drosophila simulans males. Using transcriptomic data analysis and molecular, cellular, and genetic approaches, we analyzed differential gene expression, transposable element (TE) activity, piRNA biogenesis, and functional defects of oogenesis in hybrids. Premature germline stem cell loss was the most prominent defect of oogenesis in hybrid ovaries. Because of the differential expression of genes encoding piRNA pathway components, rhino and deadlock , the functional RDC mel complex in hybrid ovaries was not assembled. However, the activity of the RDC sim complex was maintained in hybrids independent of the genomic origin of piRNA clusters. Despite the identification of a cohort of overexpressed TEs in hybrid ovaries, we found no evidence that their activity can be considered the main cause of hybrid sterility. We revealed a complicated pattern of Vasa protein expression in the hybrid germline, including partial AT-chX piRNA targeting of the vasa sim allele and a significant zygotic delay in vasa mel expression. We arrived at the conclusion that the hybrid sterility phenotype was caused by intricate multi-locus differences between the species.

The presence of incompatibility alleles in primary amphidiploids constitutes a reproductive barrier in newly synthesized wheat-rye hybrids. To overcome this barrier, the genome stabilization process includes large-scale chromosome rearrangements. In incompatible crosses resulting in fertile amphidiploids, the elimination of one of the incompatible alleles Eml-A1 or Eml-R1b can occur already in the somatic tissue of the wheat × rye hybrid embryo. We observed that the interaction of incompatible loci Eml-A1 of wheat and Eml-R1b of rye after overcoming embryo lethality leads to hybrid sterility in primary triticale. During subsequent seed reproductions (R 1 , R 2 or R 3 ) most of the chromosomes of A, B, D and R subgenomes undergo rearrangement or eliminations to increase the fertility of the amphidiploid by natural selection. Genotyping-by-sequencing (GBS) coverage analysis showed that improved fertility is associated with the elimination of entire and partial chromosomes carrying factors that either cause the disruption of plant development in hybrid plants or lead to the restoration of the euploid number of chromosomes (2n = 56) in the absence of one of the incompatible alleles. Highly fertile offspring obtained in compatible and incompatible crosses can be successfully adapted for the production of triticale pre-breeding stocks., (© 2024. The Author(s).)

Crossbred cattle are commonly used for milk production in the tropics, combining the potential benefits of pure breeds with the heterosis effects of the offspring. However, no comprehensive assessment of lifetime productivity for crossbred versus purebred cattle in low-altitude tropical environments has been carried out. The present study compares the lifetime productivity of purebred Holstein (HO, n = 17,269), Gyr (GY4, n = 435), and Brahman (BR4, n = 622) with crossbreds Gyr × Holstein (GY × HO, n = 5521) and Brahman×Holstein (BR × HO, n = 5429) cows from dairy farms located in low and medium altitude tropical regions in Costa Rica. The production traits of interest were age at first calving (AFC), days open (DO), milk production per lactation (TMP), lactation length (LLEN), age at culling (ACUL), and number of lactations (NLAC). Estimates of heterosis were also calculated. The AFC for GY × HO crosses (33-34 months) was not significantly different (p > .05) from HO (33.8 months). For BR × HO crosses, a significant (p < .05) decrease in AFC (BR3HO1 35.6 months, BR2HO2 34.5 months, and BR1H03 33.3 months) was observed as the fraction of HO breed increased. Estimates of heterosis for AFC were favourable for both crosses, of a magnitude close to 3%. The DO for F1 crosses (GY2HO2 94 days; BR2HO2 96 days) was significantly (p < .05) lower than HO (123 days). Estimates of heterosis for DO were also favourable and above 15% for both crosses. The TMP and LLEN were higher for HO (TMP = 5003 kg; LLEN = 324 days) compared with GY × HO (TMP = 4428 to 4773 kg; LLEN = 298 to 312 days) and BR × HO (TMP = 3950 to 4761 kg; LLEN = 273 to 313 days) crosses. Heterosis for TMP was favourable but low for both crosses, with a magnitude below 3.0%. The NLAC for HO (4.6 lactations) was significantly (p < .05) lower than F1 (GY2HO2, 5.8 lactations; BR2HO2, 5.4 lactations). Heterosis for NLAC was above 6.0% for both crosses. Overall, estimates of lifetime income over feed costs per cow on average were USD 2637 (30.3%) and USD 734 (8.4%) higher in F1 GY × HO and BR × HO, respectively, compared to HO. In conclusion, crossbred animals, specifically those with Gyr and Brahman genetics, extend the productive lifespan, increasing economic returns., (© 2024 The Authors. Reproduction in Domestic Animals published by Wiley‐VCH GmbH.)

Limited commercial quality protein maize (QPM) varieties with low grain yield potential are currently grown in Eastern and Southern Africa (ESA). This study was conducted to (i) assess the performance of single-cross QPM hybrids that were developed from elite inbred lines using line-by-tester mating design and (ii) estimate the general (GCA) and specific (SCA) combining ability of the QPM inbred lines for grain yield, agronomic and protein quality traits. One hundred and six testcrosses and four checks were evaluated across six environments in ESA during 2015 and 2016. Significant variations (P ≤ 0.01) were observed among environments, genotypes and genotype by environment interaction (GEI) for most traits evaluated. Hybrids H80 and H104 were the highest-yielding, most desirable, and stable QPM hybrids. Combining ability analysis showed both additive and non-additive gene effects to be important in the inheritance of grain yield. Additive effects were more important for agronomic and protein quality traits. Inbred lines L19 and L20 depicted desirable GCA effects for grain yield. Various other inbred lines with favorable GCA effects for agronomic traits, endosperm modification, and protein quality traits were identified. These inbred lines could be utilized for breeding desirable QPM cultivars. The QPM hybrids identified in this study could be commercialized after on-farm verification to replace the low-yielding QPM hybrids grown in ESA., (© 2024. The Author(s).)

The Brown planthopper (Nilaparvata lugens Stål; BPH) is known to cause significant damage to rice crops in Asia, and the use of host-resistant varieties is an effective and environmentally friendly approach for controlling BPH. However, genes limited resistance genes that are used in insect-resistant rice breeding programs, and landrace rice varieties are materials resources that carry rich and versatile genes for BPH resistance. Two landrace indica rice accessions, CL45 and CL48, are highly resistant to BPH and show obvious antibiosis against BPH. A novel resistance locus linked to markers 12M16.983 and 12M19.042 was identified, mapped to chromosome 12 in CL45, and designated Bph46. It was finely mapped to an interval of 480 kb and Gene 3 may be the resistance gene. Another resistance locus linked to markers RM26567 and 11MA104 was identified and mapped to chromosome 11 in CL48 and designated qBph11.3 according to the nominating rule. It was finely mapped to an interval of 145 kb, and LOC&#95;Os11g29090 and LOC&#95;Os11g29110 may be the resistance genes. Moreover, two markers, 12M16.983 and 11MA104, were developed for CL45 and CL48, respectively, using marker-assisted selection (MAS) and were confirmed by backcrossing individuals and phenotypic detection. Interestingly, we found that the black glume color is closely linked to the BPH resistance gene in CL48 and can effectively assist in the identification of positive individuals for breeding. Finally, several near-isogenic lines with a 9311 or KW genetic background, as well as pyramid lines with two resistance parents, were developed using MAS and exhibited significantly high resistance against BPHs., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Li 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.)

Between 2016 and 2018, the Agriculture Research Center's Sakha Agriculture Research Station conducted two rounds of pedigree selection on a segregating population of cotton (Gossypium barbadense L.) using the F 2 , F 3 , and F 4 generations resulting from crossing Giza 94 and Suvin. In 2016, the top 5% of plants from the F 2 population were selected based on specific criteria. The superior families from the F 3 generation were then selected to produce the F 4 families in 2017, which were grown in the 2018 summer season in single plant progeny rows and bulk experiments with a randomized complete block design of three replications. Over time, most traits showed increased mean values in the population, with the F 2 generation having higher Genotypic Coefficient of Variance (GCV) and Phenotypic Coefficient of Variance (PCV) values compared to the succeeding generations for the studied traits. The magnitude of GCV and PCV in the F 3 and F 4 generations was similar, indicating that genotype had played a greater role than the environment. Moreover, the mean values of heritability in the broad sense increased from generation to generation. Selection criteria I2, I4, and I5 were effective in improving most of the yield and its component traits, while selection criterion I1 was efficient in improving earliness traits. Most of the yield and its component traits showed a positive and significant correlation with each other, highlighting their importance in cotton yield. This suggests that selecting to improveone or more of these traits would improve the others. Families number 9, 13, 19, 20, and 21 were the best genotypes for relevant yield characters, surpassing the better parent, check variety, and giving the best values for most characters. Therefore, the breeder could continue to use these families in further generations as breeding genotypes to develop varieties with high yields and its components., (© 2024. The Author(s).)

Random samples from generation S 41 of the Virginia high and low 8-week body weight lines formed the base population for producing a multigenerational reciprocal intercross population. Although genetic mapping from this intercross has been reported, lacking are phenotypic trends across multiple generations. Here, we provide phenotypic information for the parental base population, the F 1 reciprocal cross, and subsequent segregating recombinant generations F 2 to F 17 . Heterosis for the selected trait in the F 1 was negative for both reciprocal crosses. Phenotypic correlations for the selected trait in the recombinant generations were essentially nil for both males and females as was percent sexual dimorphism and coefficients of variation., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Genomic imprinting-the non-equivalence of maternal and paternal genomes-is a critical process that has evolved independently in many plant and mammalian species 1,2 . According to kinship theory, imprinting is the inevitable consequence of conflictive selective forces acting on differentially expressed parental alleles 3,4 . Yet, how these epigenetic differences evolve in the first place is poorly understood 3,5,6 . Here we report the identification and molecular dissection of a parent-of-origin effect on gene expression that might help to clarify this fundamental question. Toxin-antidote elements (TAs) are selfish elements that spread in populations by poisoning non-carrier individuals 7-9 . In reciprocal crosses between two Caenorhabditis tropicalis wild isolates, we found that the slow-1/grow-1 TA is specifically inactive when paternally inherited. This parent-of-origin effect stems from transcriptional repression of the slow-1 toxin by the PIWI-interacting RNA (piRNA) host defence pathway. The repression requires PIWI Argonaute and SET-32 histone methyltransferase activities and is transgenerationally inherited via small RNAs. Remarkably, when slow-1/grow-1 is maternally inherited, slow-1 repression is halted by a translation-independent role of its maternal mRNA. That is, slow-1 transcripts loaded into eggs-but not SLOW-1 protein-are necessary and sufficient to counteract piRNA-mediated repression. Our findings show that parent-of-origin effects can evolve by co-option of the piRNA pathway and hinder the spread of selfish genes that require sex for their propagation., (© 2024. The Author(s).)

Despite the fundamental importance of hybrid incompatibilities to the process of speciation, there are few cases where the evolution and genetic architecture of hybrid incompatibilities are understood. One of the longest studied hybrid incompatibilities causes F1 hybrid male inviability in crosses between Drosophila melanogaster females and males from the Drosophila simulans clade of species-Drosophila simulans, Drosophila mauritiana, and Drosophila sechellia. Here, we discover dramatic differences in the manifestation of this lethal hybrid incompatibility among the D. simulans clade of species. In particular, F1 hybrid males between D. melanogaster and D. sechellia are resistant to hybrid rescue through RNAi knockdown of an essential hybrid incompatibility gene. To understand the genetic basis of this inter-species difference in hybrid rescue, we developed a triple-hybrid mapping method. Our results show that 2 discrete large effect loci and many dispersed small effect changes across the genome underlie D. sechellia aversion to hybrid rescue. The large effect loci encompass a known incompatibility gene Lethal hybrid rescue (Lhr) and previously unknown factor, Sechellia aversion to hybrid rescue (Satyr). These results show that the genetic architecture of F1 hybrid male inviability is overlapping but not identical in the 3 inter-species crosses. Our results raise questions about whether new hybrid incompatibility genes can integrate into an existing hybrid incompatibility thus increasing in complexity over time, or if the continued evolution of genes can gradually strengthen an existing hybrid incompatibility., 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. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Crossbreeding plays a pivotal role within pig breeding programmes, aiming to maximize heterosis and improve reproductive traits in crossbred maternal lines. Nevertheless, there is evidence indicating that the performance of reciprocal crosses between two genetic lines might exhibit variability. These variations in performance can be attributed to differences in the correlations between gametic effects, acting as either sire or dam, within purebred and crossbred populations. To address this issue, we propose a multivariate gametic model that incorporates up to four correlated gametic effects for each parental population. The model is employed on a data set comprising litter size data (total number of piglets born-TNB- and number of piglets born alive-NBA-) derived from a reciprocal cross involving two Iberian pig populations: Entrepelado and Retinto. The data set comprises 6933 records from 1564 purebred Entrepelado (EE) sows, 4995 records from 1015 Entrepelado × Retinto (ER) crosses, 2977 records from 756 Retinto × Entrepelado (RE) crosses and 7497 records from 1577 purebred Retinto (RR) sows. The data set is further supplemented by a pedigree encompassing 6007 individual-sire-dam entries. The statistical model also included the order of parity (with six levels), the breed of the service sire (five levels) and the herd-year-season effects (141 levels). Additionally, the model integrates random dominant and permanent environmental sow effects. The analysis employed a Bayesian approach, and the results revealed all the posterior estimates of the gametic correlations to be positive. The range of the posterior mean estimates of the correlations varied across different gametic effects and traits, with a range between 0.04 (gametic correlation between the paternal effects for purebred and the maternal for crossbred in Retinto) and 0.53 (gametic correlation between the paternal effects for purebred and the paternal for crossbred in Entrepelado). Furthermore, the posterior mean variance estimates of the maternal gametic effects were consistently surpassed those for paternal effects within all four populations. The results suggest the possible influence of imprinting effects on the genetic control of litter size, and underscore the importance of incorporating crossbred data into the breeding value predictions for purebred individuals., (© 2023 The Authors. Journal of Animal Breeding and Genetics published by John Wiley & Sons Ltd.)

Sand fly transmitted Leishmania species are responsible for severe, wide ranging, visceral and cutaneous leishmaniases. Genetic exchange can occur among natural Leishmania populations and hybrids can now be produced experimentally, with limitations. Feeding Phlebotomus orientalis or Phlebotomus argentipes on two strains of Leishmania donovani yielded hybrid progeny, selected using double drug resistance and fluorescence markers. Fluorescence activated cell sorting of cultured clones derived from these hybrids indicated diploid progeny. Multilocus sequence typing of the clones showed hybridisation and nuclear heterozygosity, although with inheritance of single haplotypes in a kinetoplastid target. Comparative genomics showed diversity of clonal progeny between single chromosomes, and extraordinary heterozygosity across all 36 chromosomes. Diversity between progeny was seen for the HASPB antigen, which has been noted previously as having implications for design of a therapeutic vaccine. Genomic diversity seen among Leishmania strains and hybrid progeny is of great importance in understanding the epidemiology and control of leishmaniasis. As an outcome of this study we strongly recommend that wider biological archives of different Leishmania species from endemic regions should be established and made available for comparative genomics. However, in parallel, performance of genetic crosses and genomic comparisons should give fundamental insight into the specificity, diversity and limitations of candidate diagnostics, vaccines and drugs, for targeted control of leishmaniasis., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Sádlová 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.)

Four parental genotypes of okra were crossed in complete diallel design to study the direction and extent of relative heterosis and heterobeltiosis for yield and its associated traits for utilization of existing genetic diversity to develop heterotic F 1 hybrids in okra. The additive genetic component ( D ) was significant in all studied traits except average pod weight. Nonadditive ( H 1 and H 2 ) components were found to be significant in all studied traits. However, the values of the dominant effect ( H 1 ) were smaller than the D components for no. of nodes/plant, no. of pods/plant, weight of medium pods, weight of large pods, and total fresh pod yield. The maximum significant MP heterosis in the desirable direction (149.9%) was recorded for the weight of large pods/plot. The maximum significant heterobeltiosis in the desirable direction (120.1%) was recorded for the weight of small pods/plot followed by total fresh pod yield (107.4%), the weight of large pods/plot (104.9%), weight of medium pods/plot (92.1%), average pod weight (51.8%), number of pods/plant (38.4%), and plant height (34.3%). It could be concluded that plant height, average pod weight, and the number of branches could be considered for the development of elite hybrids (heterosis breeding) or inbred lines (pure line selection) in succeeding generations. Therefore, these parameters can be considered for selecting genotypes to improve the pod yield of okra. The superior crosses identified through heterosis analysis were Egyptian Balady × Line 4.1.18 (30.8 ton/ha), Line 4.1.18 × Egyptian Balady (29.8 ton/ha), Dwarf Green Long Pod × Line 4.1.18 (28.3 ton/ha), and Egyptian Balady × Dwarf Green Long Pod (27.6 ton/ha) as these crosses had high performance as well as significant and higher estimates of heterobeltiosis for fruit yield per plant and yield attributing other characters., Competing Interests: The authors declare that they have no conflicts of interest., (Copyright © 2024 Mohamed F. M. Abdelkader et al.)

Hybrid lethality, a type of postzygotic reproductive isolation, is an obstacle to wide hybridization breeding. Here, we report the hybrid lethality that was observed in crosses between the cultivated tobacco, Nicotiana tabacum (section Nicotiana ), and the wild tobacco species, Nicotiana simulans (section Suaveolentes ). Reciprocal hybrid seedlings were inviable at 28 °C, and the lethality was characterized by browning of the hypocotyl and roots, suggesting that hybrid lethality is due to the interaction of nuclear genomes derived from each parental species, and not to a cytoplasmic effect. Hybrid lethality was temperature-sensitive and suppressed at 36 °C. However, when hybrid seedlings cultured at 36 °C were transferred to 28 °C, all of them showed hybrid lethality. After crossing between an N. tabacum monosomic line missing one copy of the Q chromosome and N. simulans , hybrid seedlings with or without the Q chromosome were inviable and viable, respectively. These results indicated that gene(s) on the Q chromosome are responsible for hybrid lethality and also suggested that N. simulans has the same allele at the Hybrid Lethality A1 ( HLA1 ) locus responsible for hybrid lethality as other species in the section Suaveolentes . Haplotype analysis around the HLA1 locus suggested that there are at least six and two haplotypes containing Hla1-1 and hla1-2 alleles, respectively, in the section Suaveolentes .

Background: In tropical Africa animal trypanosomiasis is a disease that has severe impacts on the health and productivity of livestock in tsetse fly-infested regions. Trypanosoma congolense savannah (TCS) is one of the main causative agents and is widely distributed across the sub-Saharan tsetse belt. Population genetics analysis has shown that TCS is genetically heterogeneous and there is evidence for genetic exchange, but to date Trypanosoma brucei is the only tsetse-transmitted trypanosome with experimentally proven capability to undergo sexual reproduction, with meiosis and production of haploid gametes. In T. brucei sex occurs in the fly salivary glands, so by analogy, sex in TCS should occur in the proboscis, where the corresponding portion of the developmental cycle takes place. Here we test this prediction using genetically modified red and green fluorescent clones of TCS., Methods: Three fly-transmissible strains of TCS were transfected with genes for red or green fluorescent protein, linked to a gene for resistance to the antibiotic hygromycin, and experimental crosses were set up by co-transmitting red and green fluorescent lines in different combinations via tsetse flies, Glossina pallidipes. To test whether sex occurred in vitro, co-cultures of attached epimastigotes of one red and one green fluorescent TCS strain were set up and sampled at intervals for 28 days., Results: All interclonal crosses of genetically modified trypanosomes produced hybrids containing both red and green fluorescent proteins, but yellow fluorescent hybrids were only present among trypanosomes from the fly proboscis, not from the midgut or proventriculus. It was not possible to identify the precise life cycle stage that undergoes mating, but it is probably attached epimastigotes in the food canal of the proboscis. Yellow hybrids were seen as early as 14 days post-infection. One intraclonal cross in tsetse and in vitro co-cultures of epimastigotes also produced yellow hybrids in small numbers. The hybrid nature of the yellow fluorescent trypanosomes observed was not confirmed by genetic analysis., Conclusions: Despite absence of genetic characterisation of hybrid trypanosomes, the fact that these were produced only in the proboscis and in several independent crosses suggests that they are products of mating rather than cell fusion. The three-way strain compatibility observed is similar to that demonstrated previously for T. brucei, indicating that a simple two mating type system does not apply for either trypanosome species., (© 2024. The Author(s).)

Despite the benefits of crossbreeding on animal performance, genetic evaluation of sheep in the U.S. does not directly incorporate records from crossbred lambs. Crossbred animals may be raised in different environments as compared to purebreds. Systemic factors such as age of dam and birth and rearing type may, therefore, affect purebred and crossbred performance differently. Furthermore, crossbred performance may benefit from heterozygosity, and genetic and environmental variances may be heterogeneous in different breeds and their crosses. Such issues must be accounted for in a combined (purebred and crossbred) genetic evaluation. The objectives of this study were to i) determine the effect of dam age and birth type on birth weight, and dam age and birth-rearing type on weaning weight, in purebred and crossbred lambs, ii) test for heterogeneous genetic and environmental variances in those weights, and iii) assess the impact of including weights on crossbred progeny on sire estimated breeding values (EBV). Performance records were available on purebred Columbia and Suffolk lambs. Crossbred information was available on lambs sired by Suffolk, Columbia or Texel rams mated to Columbia, Suffolk, or crossbred ewes. A multiple-trait animal model was fitted in which weights from Columbia, Suffolk, or crossbred lambs were considered different traits. At birth, there were 4,160, 2,356, and 5,273 Columbia, Suffolk, and crossbred records, respectively, with means (SD) of 5.14 (1.04), 5.32 (1.14), and 5.43 (1.23) kg, respectively. At weaning, on average at 122 (12) d, there were 2,557, 980, and 3,876 Columbia, Suffolk, and crossbred records, respectively, with corresponding means of 39.8 (7.2), 40.3 (7.9), and 39.6 (8.0) kg. Dam age had a large positive effect on birth and weaning weight in pure and crossbred lambs. At birth, however, the predicted effect was larger in crossbred and Suffolk lambs. While an increase in a number of lambs born and reared had a strong and negative influence on birth and weaning weight, the size of the effect did not differ across-breed types. Environmental variances were similar at birth and weaning, but additive variances differed among breed types for both weights. Combining purebred and crossbred information in the evaluation not only improved predictions of genetic merit in purebred sires but also allowed for direct comparisons of sires of different breeds. Breeders thus can benefit from an additional tool for making selection decisions., (© The Author(s) 2023. Published by Oxford University Press on behalf of the American Society of Animal Science.)

Parasites and their hosts are engaged in reciprocal coevolution that balances competing mechanisms of virulence, resistance, and evasion. This often leads to host specificity, but genomic reassortment between different strains can enable parasites to jump host barriers and conquer new niches. In the apicomplexan parasite Cryptosporidium , genetic exchange has been hypothesized to play a prominent role in adaptation to humans. The sexual lifecycle of the parasite provides a potential mechanism for such exchange; however, the boundaries of Cryptosporidium sex are currently undefined. To explore this experimentally, we established a model for genetic crosses. Drug resistance was engineered using a mutated phenylalanyl tRNA synthetase gene and marking strains with this and the previously used Neo transgene enabled selection of recombinant progeny. This is highly efficient, and genomic recombination is evident and can be continuously monitored in real time by drug resistance, flow cytometry, and PCR mapping. Using this approach, multiple loci can now be modified with ease. We demonstrate that essential genes can be ablated by crossing a Cre recombinase driver strain with floxed strains. We further find that genetic crosses are also feasible between species. Crossing Cryptosporidium parvum, a parasite of cattle and humans, and Cryptosporidium tyzzeri a mouse parasite resulted in progeny with a recombinant genome derived from both species that continues to vigorously replicate sexually. These experiments have important fundamental and translational implications for the evolution of Cryptosporidium and open the door to reverse- and forward-genetic analysis of parasite biology and host specificity., Competing Interests: Competing interests statement:The authors declare no competing interest.

Genetic mapping is the determination of the position and relative genetic distance between genes or molecular markers in the chromosomes of a particular species. The construction of genetic maps uses data from the genotyping of the mapping population. Among the different mapping populations used, two are relatively common: the F 2 and recombinant inbred lines (RILs) obtained as a result of the controlled crossing of genetically diverse parental forms (e.g., inbred lines). Also, the dihaploid (DH) population is often used in plants, but obtaining DHs in different crops, including rye, is very difficult or even impossible. Any molecular marker system can be used for genotyping. Polymorphic markers are used for linkage analysis, differentiating parental forms with segregation in the mapping population, consistent with the appropriate single-gene model. A genetic map is a great source of information on a species and can be an exquisite tool for analyzing important quantitative traits (QT).This chapter presents the procedure of genetic map construction with two different algorithms using the JoinMap5.0 program. First, the Materials section briefly informs about the mapping program, showing how to obtain a mapping population and prepare data for mapping. Finally, the Methods section describes the protocol for the mapping procedure itself., (© 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

Here, we present a protocol for generating gene-specific split-GAL4 drivers from coding intronic Minos-mediated integration cassette/CRISPR-mediated integration cassette (MiMIC/CRIMIC) lines in Drosophila. We describe steps for four rounds of in vivo genetic crosses, PCR genotyping, and fluorescence imaging to ensure correct orientation of split-GAL4 integration before establishing stable fly stocks. This protocol offers a cost-effective alternative to traditional microinjection techniques for converting coding intronic MiMIC/CRIMIC lines into gene-specific split-GAL4 lines that are adaptable for fly researchers working on different tissues. For complete details on the use and execution of this protocol, please refer to Chen et al. 1 ., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2023 The Author(s). Published by Elsevier Inc. All rights reserved.)

This study aimed to compare growth performance between Moghani sheep and crossbred lambs resulting from crossbreeding between Moghani pure breed ewes and the lines of rams e.g., Texel Tamlet, Texel Dalzell, Booroola Merino, and Booroola Romney. The first visible phenotypic characteristic was the presence of lean tail in all F1 crossbred lambs, whereas Moghani pure sheep is a well-known large fat-tailed breed. Moreover, the first generation of backcross (BC1) lambs from mating four types of F1 crossbred rams with Moghani pure ewes revealed lean-tailed to short fat-tailed. Comparative results showed that the F1 crossbred lambs had significantly ( p  < 0.0001) greater birth weight (BW) than the Moghani pure breed lambs. Despite no significant differences observed between Moghani pure breed sheep and its F1 crossbred lambs for body weight at pre-weaning, but F1 crossbred lambs achieved significantly ( p  < 0.0001) greater body weight after weaning compared to Moghani sheep. The growth performance of BC1 lambs was outperformed than F1 crossbred and Moghani sheep. These results encourage the continuation of the Moghani sheep crossbreeding programs to improve overall lamb growth, particularly post-weaning and to benefit from a better reproductive efficiency by elimination or reduction of the fat tail.

Interploidy hybridization between hexaploid and tetraploid genotypes occurred repeatedly during genomic introgression events throughout wheat evolution, and is commonly employed in wheat breeding programs. Hexaploid wheat usually serves as maternal parent because the reciprocal cross generates progeny with severe defects and poor seed germination, but the underlying mechanism is poorly understood. Here, we performed detailed analysis of phenotypic variation in endosperm between two interploidy reciprocal crosses arising from tetraploid (Triticum durum, AABB) and hexaploid wheat (Triticum aestivum, AABBDD). In the paternal- versus the maternal-excess cross, the timing of endosperm cellularization was delayed and starch granule accumulation in the endosperm was repressed, causing reduced germination percentage. The expression profiles of genes involved in nutrient metabolism differed strongly between these endosperm types. Furthermore, expression patterns of parental alleles were dramatically disturbed in interploidy versus intraploidy crosses, leading to increased number of imprinted genes. The endosperm-specific TaLFL2 showed a paternally imprinted expression pattern in interploidy crosses partially due to allele-specific DNA methylation. Paternal TaLFL2 binds to and represses a nutrient accumulation regulator TaNAC019, leading to reduced storage protein and starch accumulation during endosperm development in paternal-excess cross, as confirmed by interploidy crosses between tetraploid wild-type and clustered regularly interspaced palindromic repeats (CRISPR) - CRISPR-associated protein 9 generated hexaploid mutants. These findings reveal a contribution of genomic imprinting to paternal-excess interploidy hybridization barriers during wheat evolution history and explains why experienced breeders preferentially exploit maternal-excess interploidy crosses in wheat breeding programs., (© 2023 The Authors. Journal of Integrative Plant Biology published by John Wiley & Sons Australia, Ltd on behalf of Institute of Botany, Chinese Academy of Sciences.)

Cardinal features of lupus include elevated B cell activation and autoantibody production with a female sex preponderance. We quantified interactions of sex and genetic variation on the development of autoimmune B-cell phenotypes and autoantibodies in the BXD2 murine model of lupus using a cohort of backcrossed progeny (BXD2 x C57BL/6J) x BXD2. Sex was the key factor leading to increased total IgG, IgG2b, and autoantibodies. The percentage of T-bet + CD11c + IgD + activated naive B cells (aNAV) was higher in females and was associated with increased T-bet + CD11c + IgD - age-related B cells, Fas + GL7 + germinal center B cells, Cxcr5 - Icos + peripheral T-helper cells, and Cxcr5 + Icos + follicular T-helper cells. IFN-β was elevated in females. Variation in aNAV cells was mapped to Chr 7 in a locus that shows significant interactions between the female sex and heterozygous B/D variant. Our results suggest that activation of naive B cells forms the basis for the female-predominant development of autoantibodies in lupus-susceptible BXD2 mice., Competing Interests: Declaration of Competing Interest The Authors declare that there is no conflict of interest., (Published by Elsevier Inc.)

Purpose: Down syndrome (DS) is linked to a higher prevalence of obstructive sleep apnea (OSA) than in the general population, which in turn contributes to worse cognitive impairment in DS. However, the shared pathogenic mechanisms for DS and OSA remain incompletely illustrated. This study was designed to decipher the genetic cross-talk between DS and OSA by bioinformatics approach., Methods: Transcriptomic datasets of DS (GSE59630) and OSA (GSE135917) were accessed from the Gene Expression Omnibus (GEO) repository. After screening out the common differentially expressed genes (DEGs) for DS and OSA, gene ontology (GO) functional enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were carried out. A protein-protein interaction (PPI) network was then constructed to determine essential modules and hub genes. Finally, based on hub genes, transcriptional factor (TF)-gene interaction and TF-miRNA regulatory networks were constructed., Results: DS and OSA showed 229 DEGs. Functional analyses revealed how oxidative stress and inflammatory response were critical in the progression of DS and OSA. Ten significant hub genes were identified, including TLR4, SOD1, IGF1, FGF2, NFE2L2, PECAM1, S100A8, S100A9, FCGR3A, and KCNA1, which were candidate targets for DS and OSA., Conclusions: We found that DS and OSA display similarities in their pathogenesis. Key genes and signaling pathways revealed to be in common between the two conditions could lead us to new therapeutic targets for DS and OSA., (© 2023. The Author(s), under exclusive licence to Springer Nature Switzerland AG.)

Genomic resources are becoming available for Pisum but to link these to phenotypic diversity requires well marked populations segregating for relevant traits. Here we describe two such resources. Two recombinant inbred populations, derived from wide crosses in Pisum are described. One high resolution mapping population involves cv Caméor, for which the first pea whole genome assembly was obtained, crossed to JI0281, a basally divergent P. sativum sativum landrace from Ethiopia. The other is an inter sub-specific cross between P. s. sativum and the independently domesticated P. s. abyssinicum. The corresponding genetic maps provide information on chromosome level sequence assemblies and identify structural differences between the genomes of these two Pisum subspecies. In order to visualise chromosomal translocations that distinguish the mapping parents, we created a simplified version of Threadmapper to optimise it for interactive 3-dimensional display of multiple linkage groups. The genetic mapping of traits affecting seed coat roughness and colour, plant height, axil ring pigmentation, leaflet number and leaflet indentation enabled the definition of their corresponding genomic regions. The consequence of structural rearrangement for trait analysis is illustrated by leaf serration. These analyses pave the way for identification of the underlying genes and illustrate the utility of these publicly available resources. Segregating inbred populations derived from wide crosses in Pisum, together with the associated marker data, are made publicly available for trait dissection. Genetic analysis of these populations is informative about chromosome scale assemblies, structural diversity in the pea genome and has been useful for the fine mapping of several discrete and quantitative traits., (© 2023. The Author(s).)

Breakdown of reproductive isolation facilitates flow of useful trait genes into crop plants from their wild relatives. Hybrid sterility, a major form of reproductive isolation exists between cultivated rice (Oryza sativa) and wild rice (O. meridionalis, Mer). Here, we report the cloning of qHMS1, a quantitative trait locus controlling hybrid male sterility between these two species. Like qHMS7, another locus we cloned previously, qHMS1 encodes a toxin-antidote system, but differs in the encoded proteins, their evolutionary origin, and action time point during pollen development. In plants heterozygous at qHMS1, ~ 50% of pollens carrying qHMS1-D (an allele from cultivated rice) are selectively killed. In plants heterozygous at both qHMS1 and qHMS7, ~ 75% pollens without co-presence of qHMS1-Mer and qHMS7-D are selectively killed, indicating that the antidotes function in a toxin-dependent manner. Our results indicate that different toxin-antidote systems provide stacked reproductive isolation for maintaining species identity and shed light on breakdown of hybrid male sterility., (© 2023. The Author(s).)

Background: The research focused on evaluating the biological and reproductive parameters of the species Spodoptera sunia with the introduction of field genetic material, in the Noctuid Insect Breeding Laboratory., Methods: The experiment consisted of three treatments and three repetitions involving 30 individuals each. Field-collected S. sunia population was reared in the laboratory under semi-controlled conditions of temperature and humidity for three generations. The progeny of the third generation was crossed with the laboratory population and the resulting progeny was observed for growth and reproductive fitness., Results: The results revealed that the hybrid progeny (T3) has a sex ratio (F: M) of 0.82, as against 1.22 and 0.76 observed in the field (T1) and lab populations (T2) respectively. The T1 females oviposited 196 egg masses as against 160 and 59 egg masses by T3 and T2 females respectively. The larval growth was more in hybrid progeny with shorter larval duration. However, no variation was observed in the incubation and pupal periods., Conclusions: Since the most optimal results were obtained in T2 and T3, it is recommended to introduce genetic material every six months to maintain a good laboratory population of the insect host under study and better breeding of its natural enemies., Competing Interests: No competing interests were disclosed., (Copyright: © 2023 Real-Baca CI and Zuniga-Gonzalez CA.)

The purebred-crossbred genetic correlation (r pc ) is a key parameter to determine whether the optimal selection of purebred animals to improve crossbred performance should rely on crossbred phenotypes, purebred phenotypes, or both. We reviewed published estimates of the r pc in poultry. In total, 19 studies were included, of which four were on broilers and 15 on laying hens, with 150 r pc estimates for nine different trait categories. Average reported r pc estimates were highest for egg weight, egg quality and egg colour (0.74-0.82), intermediate for BW, maturity and mortality (0.61-0.70) and egg number (0.58), and low for resilience (0.40) and body conformation (0.14). Most studies were based on measuring purebred and crossbred phenotypes in the same environment and thus did not capture the contribution of genotype by environment interactions to the r pc , suggesting that the presented average estimates may be higher than values that apply in practice. Nearly all studies were based on two-way crossbred animals. We hypothesised that r pc values for a two-way cross are good proxies for r pc of a four-way cross. Only eight out of 19 studies were published in the last 25 years, and only two of those used genomic data. We expect that more studies using genomic data may be published in the coming years, as the required data may be generated when implementing genomic selection for crossbred performance, which will lead to more accurate r pc estimates. Future studies that aim to estimate r pc are encouraged to capture the genotype by environment interaction component by housing purebred and crossbred animals differently as is done in practice. Moreover, there is a need for further studies that enable to explicitly estimate the magnitude of genotype by environment versus genotype by genotype interactions for multiple trait categories. Further, studies are advised to report: the specific housing conditions of the animals, any differences between measurements of purebred versus crossbred performance, and the heritabilities of purebred and crossbred performance., (Copyright © 2023 The Author(s). Published by Elsevier B.V. All rights reserved.)

Introduction: The simultaneous improvement of fiber quality and yield for cotton is strongly limited by the narrow genetic backgrounds of Gossypium hirsutum (Gh) and the negative genetic correlations among traits. An effective way to overcome the bottlenecks is to introgress the favorable alleles of Gossypium barbadense (Gb) for fiber quality into Gh with high yield., Objectives: This study was to identify superior loci for the improvement of fiber quality and yield., Methods: Two sets of chromosome segment substitution lines (CSSLs) were generated by crossing Hai1 (Gb, donor-parent) with cultivar CCRI36 (Gh) and CCRI45 (Gh) as genetic backgrounds, and cultivated in 6 and 8 environments, respectively. The kmer genotyping strategy was improved and applied to the population genetic analysis of 743 genomic sequencing data. A progeny segregating population was constructed to validate genetic effects of the candidate loci., Results: A total of 68,912 and 83,352 genome-wide introgressed kmers were identified in the CCRI36 and CCRI45 populations, respectively. Over 90 % introgressions were homologous exchanges and about 21 % were reverse insertions. In total, 291 major introgressed segments were identified with stable genetic effects, of which 66(22.98 %), 64(21.99 %), 35(12.03 %), 31(10.65 %) and 18(6.19 %) were beneficial for the improvement of fiber length (FL), strength (FS), micronaire, lint-percentage (LP) and boll-weight, respectively. Thirty-nine introgression segments were detected with stable favorable additive effects for simultaneous improvement of 2 or more traits in Gh genetic background, including 6 could increase FL/FS and LP. The pyramiding effects of 3 pleiotropic segments (A07:C45Clu-081, D06:C45Clu-218, D02:C45Clu-193) were further validated in the segregating population., Conclusion: The combining of genome-wide introgressions and kmer genotyping strategy showed significant advantages in exploring genetic resources. Through the genome-wide comprehensive mining, a total of 11 clusters (segments) were discovered for the stable simultaneous improvement of FL/FS and LP, which should be paid more attention in the future., 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 © 2023. Production and hosting by Elsevier B.V.)