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Exaggerated ornaments provide opportunities to understand how selection can operate at different levels to shape the evolution of a trait. While these features aid their bearer in attracting mates or fending off competitors, they can also be costly and influenced by the environment and genetic variation. The eyestalks of the stalk-eyed fly, Teleopsis dalmanni, are of interest because eyestalk length is the target of both intra- and intersexual selection and is also reduced by loci on a highly-divergent sex ratio X chromosome (XSR), a meiotic driver accounting for up to 30% of wild X chromosomes. Male stalk-eyed flies fight to control access to females and over food using a combination of low-intensity displays and highintensity physical fights. We staged, filmed, and scored contests between pairs of eyespan-matched males to evaluate whether X chromosome type impacts the behavior and outcome of aggressive interactions. While our results broadly match expectations from previous studies, we found that XSR males used more high-intensity behaviors than males carrying a non-driving, standard X chromosome (XST), particularly when their eyestalks were of similar size or smaller than their opponents. Additionally, we found that when XSR males use high-intensity behaviors, they win more bouts than when they use low-intensity behaviors. Taken together, these results suggest that XSR impacts male aggressive behavior to compensate for the shorter eyestalks of XSR males and may help to explain how this selfish chromosome is maintained. [ABSTRACT FROM AUTHOR]

Chromosomal regions with meiotic drivers exhibit biased transmission (> 50 %) over their competing homologous chromosomal region. These regions often have two prominent genetic features: suppressed meiotic crossing over and rapidly evolving multicopy gene families. Heteromorphic sex chromosomes (e.g., XY) often share these two genetic features with chromosomal regions exhibiting meiotic drive. Here, we discuss parallels between meiotic drive and sex chromosome evolution, how the divergence of heteromorphic sex chromosomes can be influenced by meiotic drive, experimental approaches to study meiotic drive on sex chromosomes, and meiotic drive in traditional and non-traditional model organisms with high-quality genome assemblies. The newly available diversity of high-quality sex chromosome sequences allows us to revisit conventional models of sex chromosome evolution through the lens of meiotic drive. [ABSTRACT FROM AUTHOR]

Errors during female meiosis lead to embryonic aneuploidy and miscarriage and occur with increasing frequency during aging. The underlying molecular changes that drive female meiotic instability remain a subject of debate. Developing oocytes undergo a tremendous increase in cytoplasmic volume over several months of follicle development and rely on long-lived mRNAs and ribosomes accumulated during this growth phase for subsequent meiotic maturation. In this point of view article, we discuss how the unique reliance on stores of long-lived mRNAs and ribosomes may represent an Achilles' heel for oocyte function and how alterations that reduce the translational capacity of oocytes could be a factor significantly contributing to female infertility. Understanding these mechanisms could lead to new therapeutic strategies to improve fertility outcomes. [ABSTRACT FROM AUTHOR]

The article considers the distribution and mechanisms of the meiotic drive as a phenomenon manifested in unequal transmission of gene alleles and/or homologous chromosomes into gametes during meiosis. The meiotic drive has been studied in the most detail in Drosophila, mice, corn, and ascomycete fungi of the genera Neurospora and Podospora. The consequence of the meiotic drive is a shift in the frequencies of alleles in the gene pool and the maintenance of nonadaptive traits in the population. [ABSTRACT FROM AUTHOR]

Hybrid male sterility is one of the fastest evolving intrinsic reproductive barriers between recently isolated populations. A leading explanation for the evolution of hybrid male sterility involves genomic conflicts with meiotic drivers in the male germline. There are, however, few examples directly linking meiotic drive to hybrid sterility. In this study, we report that the Sex-Ratio chromosome of Drosophila pseudoobscura , which causes X-chromosome drive within the USA subspecies, causes near-complete male sterility when it is moved into the genetic background of the Bogota subspecies. In addition, we show that this new form of sterility is genetically distinct from the sterility of F1 hybrid males in crosses between USA males and Bogota females. Our observations provide a tractable study system where noncryptic drive within species is transformed into strong hybrid sterility between very young subspecies. [ABSTRACT FROM AUTHOR]

Meiotic drivers are selfish genetic loci that can be transmitted to more than half of the viable gametes produced by a heterozygote. This biased transmission gives meiotic drivers an evolutionary advantage that can allow them to spread over generations until all members of a population carry the driver. This evolutionary power can also be exploited to modify natural populations using synthetic drivers known as "gene drives." Recently, it has become clear that natural drivers can spread within genomes to birth multicopy gene families. To understand intragenomic spread of drivers, we model the evolution of 2 or more distinct meiotic drivers in a population. We employ the wtf killer meiotic drivers from Schizosaccharomyces pombe , which are multicopy in all sequenced isolates, as models. We find that a duplicate wtf driver identical to the parent gene can spread in a population unless, or until, the original driver is fixed. When the duplicate driver diverges to be distinct from the parent gene, we find that both drivers spread to fixation under most conditions, but both drivers can be lost under some conditions. Finally, we show that stronger drivers make weaker drivers go extinct in most, but not all, polymorphic populations with absolutely linked drivers. These results reveal the strong potential for natural meiotic drive loci to duplicate and diverge within genomes. Our findings also highlight duplication potential as a factor to consider in the design of synthetic gene drives. [ABSTRACT FROM AUTHOR]

X chromosome centromeric drive may explain the prevalence of polycystic ovary syndrome and contribute to oocyte aneuploidy, menopause, and other conditions. The mammalian X chromosome may be vulnerable to meiotic drive because of X inactivation in the female germline. The human X pericentromeric region contains genes potentially involved in meiotic mechanisms, including multiple SPIN1 and ZXDC paralogs. This is consistent with a multigenic drive system comprising differential modification of the active and inactive X chromosome centromeres in female primordial germ cells and preferential segregation of the previously inactivated X chromosome centromere to the polar body at meiosis I. The drive mechanism may explain differences in X chromosome regulation in the female germlines of the human and mouse and, based on the functions encoded by the genes in the region, the transmission of X pericentromeric genetic or epigenetic variants to progeny could contribute to preeclampsia, autism, and differences in sexual differentiation. [ABSTRACT FROM AUTHOR]

Chromosome number is a fundamental genomic trait that is often the first recorded characteristic of a genome. Across large clades, a common pattern emerges: many or even most lineages exhibit relative stasis, while a handful of lineages or species exhibit striking variation. Despite recent developments in comparative methods, most of this heterogeneity is still poorly understood. It is essential to understand why some lineages have rapid rates of chromosome number evolution, as it can impact a variety of other traits. Previous research suggests that biased female meiotic drive may shape rates of karyotype evolution in some mammals. However, Carnivora exhibits variation that this female meiotic drive model cannot explain. We hypothesize that variation in effective population size may underlie rate variation in Carnivora. To test this hypothesis, we estimated rates of fusions and fissions while accounting for range size, which we use as a proxy for effective population size. We reason fusions and fissions are deleterious or underdominant and that only in lineages with small range sizes will these changes be able to fix due to genetic drift. In this study, we find that the rates of fusions and fissions are elevated in taxa with small range sizes relative to those with large range sizes. Based on these findings, we conclude that 1) naturally occurring structural mutations that change chromosome number are underdominant or mildly deleterious, and 2) when population sizes are small, structural rearrangements may play an important role in speciation and reduction in gene flow among populations. [ABSTRACT FROM AUTHOR]

Sex-ratio meiotic drivers are selfish genes or gene complexes that bias the transmission of sex chromosomes resulting in skewed sex ratios. Existing theoretical models have suggested the maintenance of a four-chromosome equilibrium (with driving and standard X and suppressing and susceptible Y) in a cyclic dynamic, but studies of natural populations have failed to capture this pattern. Although there are several plausible explanations for this lack of cycling, interference from autosomal suppressors has not been studied using a theoretical population genetic framework even though autosomal suppressors and Y-linked suppressors coexist in natural populations of some species. In this study, we use a simulation-based approach to investigate the influence of autosomal suppressors on the cycling of sex chromosomes. Our findings demonstrate that the presence of an autosomal suppressor can hinder the invasion of a Y-linked suppressor under some parameter space, thereby impeding the cyclic dynamics, or even the invasion of Y-linked suppression. Even when a Y-linked suppressor invades, the presence of an autosomal suppressor can prevent cycling. Our study demonstrates the potential role of autosomal suppressors in preventing sex chromosome cycling and provides insights into the conditions and consequences of maintaining both Y-linked and autosomal suppressors. [ABSTRACT FROM AUTHOR]

The XX/XY sex chromosome system is deeply conserved in therian mammals, as is the role of Sry in testis determination, giving the impression of stasis relative to other taxa. However, the long tradition of cytogenetic studies in mammals documents sex chromosome karyotypes that break this norm in myriad ways, ranging from fusions between sex chromosomes and autosomes to Y chromosome loss. Evolutionary conflict, in the form of sexual antagonism or meiotic drive, is the primary predicted driver of sex chromosome transformation and turnover. Yet conflict-based hypotheses are less considered in mammals, perhaps because of the perceived stability of the sex chromosome system. To address this gap, we catalog and characterize all described sex chromosome variants in mammals, test for family-specific rates of accumulation, and consider the role of conflict between the sexes or within the genome in the evolution of these systems. We identify 152 species with sex chromosomes that differ from the ancestral state and find evidence for different rates of ancestral to derived transitions among families. Sex chromosome-autosome fusions account for 79% of all variants whereas documented sex chromosome fissions are limited to three species. We propose that meiotic drive and drive suppression provide viable explanations for the evolution of many of these variant systems, particularly those involving autosomal fusions. We highlight taxa particularly worthy of further study and provide experimental predictions for testing the role of conflict and its alternatives in generating observed sex chromosome diversity. [ABSTRACT FROM AUTHOR]

CRISPR-Cas9 homing gene drives are designed to induce a targeted double-stranded DNA break at a wild type allele ('recipient'), which, when repaired by the host cell, is converted to the drive allele from the homologous ('donor') chromosome. Germline localisation of this process leads to super-Mendelian inheritance of the drive and the rapid spread of linked traits, offering a novel strategy for population control through the deliberate release of drive individuals. During the homology-based DNA repair, additional segments of the recipient chromosome may convert to match the donor, potentially impacting carrier fitness and strategy success. Using Anopheles gambiae strains with variations around the drive target site, here we assess the extent and nature of chromosomal conversion. We show both homing and meiotic drive contribute as mechanisms of inheritance bias. Additionally, over 80% of homing events resolve within 50 bp of the chromosomal break, enabling rapid gene drive transfer into locally-adapted genetic backgrounds. Homing-based gene drives show promise for malaria control through reducing or modifying mosquito populations, but understanding gene drive mechanisms is vital for policy. Here, authors show minimal carryover of extra sequences with gene drives, and potential for mixed methods of gene drive inheritance. [ABSTRACT FROM AUTHOR]

The multiparent advanced generation intercross (MAGIC) population is characterized with great potentials in power and resolution of quantitative trait locus (QTL) mapping, but single nucleotide polymorphism (SNP)-based GWAS does not fully reach its potential. In this study, a MAGIC population of 1021 lines was developed from four Xian and four Geng varieties from five subgroups of rice. A total of 44 000 genes showed functional polymorphisms among eight parents, including frameshift variations or premature stop codon variations, which provides the potential to map almost all genes of the MAGIC population. Principal component analysis results showed that the MAGIC population had a weak population structure. A high-density bin map of 24 414 bins was constructed. Segregation distortion occurred in the regions possessing the genes underlying genetic incompatibility and gamete development. SNP-based association analysis and bin-based linkage analysis identified 25 significant loci and 47 QTLs for heading date, including 14 known heading date genes. The mapping resolution of genes is dependent on genetic effects with offset distances of <55 kb for major effect genes and <123 kb for moderate effect genes. Four causal variants and noncoding structure variants were identified to be associated with heading date. Three to four types of alleles with strong, intermediate, weak, and no genetic effects were identified from eight parents, providing flexibility for the improvement of rice heading date. In most cases, japonica rice carries weak alleles, and indica rice carries strong alleles and nonfunctional alleles. These results confirm that the MAGIC population provides the exceptional opportunity to detect QTLs, and its use is encouraged for mapping genes and mining favorable alleles for breeding. [ABSTRACT FROM AUTHOR]

Biased sex ratios among reproductive individuals are common in plants, but the underlying mechanisms, as well as the evolutionary consequences, are not well understood. The classical theory of Düsing and Fisher predicts an equal primary sex ratio at seed production, based on the selective advantage of the rare sex. Biased sex ratios among reproductive plants can arise from sexual dimorphism in survival and flowering. Sex ratio biases can also be present from the seed stage; in these cases, assumptions of Düsing's and Fisher's theory, for example, random mating or demographic equilibrium, are thought to be violated.We investigated mechanisms leading to female‐biased sex ratios in the arctic‐alpine dwarf willow Salix herbacea L. We studied sex ratios in three natural populations over 3 years as well as in 29 crosses (full‐sib families) under controlled conditions over four growth periods. We tested whether sex ratio was associated with habitat parameters (elevation and snowmelt time), or with germination, survival or flowering, and whether females and males differed in size or flowering that may cause observation bias.We detected a strong and consistent female bias, both in natural populations (sex ratio [proportion of females]: 0.71–0.82) and in our controlled experiment (overall sex ratio: 0.70–0‐72). Female bias became more pronounced with increasing elevation. Our data did not support sexual dimorphism in size or flowering. Family sex ratios varied largely (from 0.25 to 1), including many female‐biased families, unbiased families and two male‐biased families. Families with lower germination, seedling establishment, survival or flowering did not have stronger female bias, indicating that intrinsically higher survival or flowering in females does not explain overall female bias.Synthesis. Our results suggest that sex ratio bias in S. herbacea is already present in seeds and does not arise through intrinsic differences between sexes. Candidate mechanisms that can lead to both overall female bias and variation in sex ratio among families are meiotic drive or cyto‐nuclear interactions. The pioneer habit of Salix may lead to non‐equilibrium population dynamics that allow for the long‐term persistence of variable genetic sex ratio distortion systems that arise from genetic conflict. [ABSTRACT FROM AUTHOR]

We calculated the found and expected frequencies of metacentrics in polymorphic populations of the Dnieper basin common rodent, resulting from hybridization of local populations with acrocentric karyotype and four chromosomal races (Neroosa, Kiev, Białowieża, and Western Dvina) with 3–5 diagnostic metacentrics in each. We have previously shown an increased frequency of acrocentric karyotype compared to that expected according to Hardy–Weinberg. The low frequency (less than 0.5) of most metacentrics of the four chromosomal races and the disappearance of some of them from the populations can be explained by the increased fitness of the acrocentric karyotype and the absence of meiotic drive. On the contrary, the preservation of high frequency (more than 0.5) of such metacentrics as gm, hk (races of Western Dvina), hi (races of Kiev), hn, ik (races of Białowieża), and, especially, the fixation of metacentric hi (races of Neroosa) in polymorphic populations can be explained by meiotic drive. The fixation of Rb compounds in the range of the common rodent may be a consequence not only of gene drift but also of meiotic drive. Most likely, meiotic drive is able to maintain the frequency of Rb compounds with the largest acrocentrics g, h, and i, which contributed to the widespread distribution of such compounds throughout the range of the common rodent. [ABSTRACT FROM AUTHOR]

Plant breeders utilize marker-assisted selection (MAS) to identify favorable or unfavorable alleles in seedlings early. In this task, they need methods that provide maximum information with minimal input of time and economic resources. Grape breeding aimed at producing cultivars resistant to pathogens employs several resistance loci (Rpv, Ren, and Run) that are ideal for implementing MAS. In this work, a sustainable MAS protocol was developed based on non-purified DNA (crude), multiplex PCR of SSR markers, and capillary electrophoresis, and its application on grapevine seedlings to follow some main resistance loci was described. The optimized protocol was utilized on 8440 samples and showed high efficiency, reasonable throughput (2–3.2 min sample), easy handling, flexibility, and tolerable costs (reduced by at least 3.5 times compared to a standard protocol). The Rpv, Ren, and Run allelic data analysis did not show limitations to loci combination and pyramiding, but segregation distortions were frequent and displayed both low (undesired) and high rates of inheritance. The protocol and results presented are useful tools for grape breeders and beyond, and they can address sustainable changes in MAS. Several progenies generated have valuable pyramided resistance and will be the subject of new studies and implementation in the breeding program. [ABSTRACT FROM AUTHOR]

Haploid induction (HI) holds great promise in expediting the breeding process in onion, a biennial cross-pollinated crop. We used the CENH3-based genome elimination technique in producing a HI line in onion. Here, we downregulated AcCENH3 using the RNAi approach without complementation in five independent lines. Out of five events, only three could produce seeds upon selfing. The progenies showed poor seed set and segregation distortion, and we were unable to recover homozygous knockdown lines. The knockdown lines showed a decrease in accumulation of AcCENH3 transcript and protein in leaf tissue. The decrease in protein content in transgenic plants was correlated with poor seed set. When the heterozygous knockdown lines were crossed with wild-type plants, progenies showed HI by genome elimination of the parental chromosomes from AcCENH3 knockdown lines. The HI efficiency observed was between 0 and 4.63% in the three events, and it was the highest (4.63%) when E1 line was crossed with wildtype. Given the importance of doubled haploids in breeding programmes, the findings from our study are poised to significantly impact onion breeding. [ABSTRACT FROM AUTHOR]

Species frequently differ in the number and structure of chromosomes they harbor, but individuals that are heterozygous for chromosomal rearrangements may suffer from reduced fitness. Chromosomal rearrangements like fissions and fusions can hence serve as a mechanism for speciation between incipient lineages, but their evolution poses a paradox. How can rearrangements get fixed between populations if heterozygotes have reduced fitness? One solution is that this process predominantly occurs in small and isolated populations, where genetic drift can override natural selection. However, fixation is also more likely if a novel rearrangement is favored by a transmission bias, such as meiotic drive. Here, we investigate chromosomal transmission distortion in hybrids between two wood white (Leptidea sinapis) butterfly populations with extensive karyotype differences. Using data from two different crossing experiments, we uncover that there is a transmission bias favoring the ancestral chromosomal state for derived fusions, a result that shows that chromosome fusions actually can fix in populations despite being counteracted by meiotic drive. This means that meiotic drive not only can promote runaway chromosome number evolution and speciation, but also that it can be a conservative force acting against karyotypic change and the evolution of reproductive isolation. Based on our results, we suggest a mechanistic model for why chromosome fusion mutations may be opposed by meiotic drive and discuss factors contributing to karyotype evolution in Lepidoptera. [ABSTRACT FROM AUTHOR]

Exaggerated ornaments provide opportunities to understand how selection can operate at different levels to shape the evolution of a trait. While these features aid their bearer in attracting mates or fending off competitors, they can also be costly and influenced by the environment and genetic variation. The eyestalks of the stalk-eyed fly, Teleopsis dalmanni, are of interest because eyestalk length is the target of both intra- and intersexual selection and is also reduced by loci on a highly-divergent sex ratio X chromosome (XSR), a meiotic driver accounting for up to 30% of wild X chromosomes. Male stalk-eyed flies fight to control access to females and over food using a combination of low-intensity displays and high-intensity physical fights. We staged, filmed, and scored contests between pairs of eyespan-matched males to evaluate whether X chromosome type impacts the behavior and outcome of aggressive interactions. While our results broadly match expectations from previous studies, we found that XSR males used more high-intensity behaviors than males carrying a non-driving, standard X chromosome (XST), particularly when their eyestalks were of similar size or smaller than their opponents. Additionally, we found that when XSR males use high-intensity behaviors, they win more bouts than when they use low-intensity behaviors. Taken together, these results suggest that XSR impacts male aggressive behavior to compensate for the shorter eyestalks of XSR males and may help to explain how this selfish chromosome is maintained.

Simple Summary: A new interspecific backcross ([(Crassostrea hongkongensis ♀ × C. gigas ♂) ♂ × C. hongkongensis ♀]) variety was bred by the South China Sea Institute of Oceanology and named "South China No. 1". This study aims to explore the effects of stocking density on the growth performance of "South China No. 1", and compare the growth performance and genetic diversity to that of C. hongkongensis in Beibu Gulf. The results showed that oysters bred under a stocking density of 20 oysters/substrate had better growth manifestation. It was found that the shell height and total weight of "South China No. 1" cultured in Fangchenggang were significantly higher than that of those in Beihai and Qinzhou from September 2018 to November 2018. In addition, the shell height and shell width of "South China No. 1" were significantly higher than that of C. hongkongensis. In the Hardy–Weinberg equilibrium test, for the seven populations and ten microsatellites, in 10 of the 70 groups, the segregation distortion was significant. These results suggest that a stocking density of 20 oysters/substrate can promote the shell height, shell width and total weight of "South China No. 1". Fangchenggang is a suitable place to cultivate the "South China No. 1" breed according to the total weight and sum of all algal genus abundances. Crassostrea hongkongensis is an economically important bivalve found in various parts of the South China Sea. A new interspecific backcross ([(Crassostrea hongkongensis ♀ × C. gigas ♂) ♂ × C. hongkongensis ♀]) variety was bred by the South China Sea Institute of Oceanology which named "South China No. 1". This study aims to explore the effects of stocking density on the growth performance of "South China No. 1", compared their growth performance and genetic diversity to C. hongkongensis, and found the best place breeding site for "South China No. 1" in Beibu Gulf. The results showed that stocking a density of 20 oysters/substrate can significantly increase the shell height, shell width, total weight, survival rate, daily shell height gain and daily body mass gain. It was found that the shell height and total weight of "South China No. 1" cultured in Fangchenggang were significantly higher than that of those in Beihai and Qinzhou from September 2018 to November 2018. Similarly, the shell width of oysters in Fangchenggang and Qinzhou was also significantly higher in September 2018, and the interaction between site and stocking density had significant effects on the shell width in March 2018 and November 2018. In addition, the shell height and shell width of "South China No. 1" were significantly higher than that of C. hongkongensis in all three sites. At all three sites, the phytoplankton community structure was mostly dominated by Bacillariophyta. In the Hardy–Weinberg equilibrium test, for the seven populations and ten microsatellites, in 10 of the 70 groups, the segregation distortion was significant. These results suggest that a stocking density of 20 oysters/substrate can promote the shell height, shell width and total weight of "South China No. 1" in Beibu Gulf, China. "South China No. 1" has better growth performance compared with C. hongkongensis. Fangchenggang is a suitable place to cultivate the "South China No. 1" breed according to the total weight and sum of all algal genus abundances. The results of this study can be used as a reference to further understand the stocking density and genetic diversity of the "South China No. 1" breed in Beibu Gulf, China. [ABSTRACT FROM AUTHOR]

In filamentous fungi, vegetative cell fusion occurs within and between individuals. These fusions of growing hyphae (anastomosis) from two individuals produce binucleated cells with mixed cytoplasm known as heterokaryons. The fate of heterokaryotic cells was genetically controlled with delicacy by specific loci named het (heterokaryon) or vic (vegetative incompatibility) as a part of self-/nonself-recognition system. When het loci of two individuals are incompatible, the resulting heterokaryotic cells underwent programmed cell death or showed severely impaired fungal growth. In Podospora anserina, het-s is one of at least nine alleles that control heterokaryon incompatibility and the altered protein conformation [Het-s] prion. The present study describes the [Het-s] prion in terms of (1) the historical discovery based on early genetic and physiological studies, (2) architecture built on its common and unique nature compared with other prions, and (3) functions related to meiotic drive and programmed cell death. [ABSTRACT FROM AUTHOR]

Robertsonian chromosomes form by fusion of two chromosomes that have centromeres located near their ends, known as acrocentric or telocentric chromosomes. This fusion creates a new metacentric chromosome and is a major mechanism of karyotype evolution and speciation. Robertsonian chromosomes are common in nature and were first described in grasshoppers by the zoologist W. R. B. Robertson more than 100 years ago. They have since been observed in many species, including catfish, sheep, butterflies, bats, bovids, rodents and humans, and are the most common chromosomal change in mammals. Robertsonian translocations are particularly rampant in the house mouse, Mus musculus domesticus, where they exhibit meiotic drive and create reproductive isolation. Recent progress has been made in understanding how Robertsonian chromosomes form in the human genome, highlighting some of the fundamental principles of how and why these types of fusion events occur so frequently. Consequences of these fusions include infertility and Down's syndrome. In this Hypothesis, I postulate that the conditions that allow these fusions to form are threefold: (1) sequence homology on non-homologous chromosomes, often in the form of repetitive DNA; (2) recombination initiation during meiosis; and (3) physical proximity of the homologous sequences in threedimensional space. This Hypothesis highlights the latest progress in understanding human Robertsonian translocations within the context of the broader literature on Robertsonian chromosomes. [ABSTRACT FROM AUTHOR]

The cell cycle is ordered by a controlled network of kinases and phosphatases. To generate gametes via meiosis, two distinct and sequential chromosome segregation events occur without an intervening S phase. How canonical cell cycle controls are modified for meiosis is not well understood. Here, using highly synchronous budding yeast populations, we reveal how the global proteome and phosphoproteome change during the meiotic divisions. While protein abundance changes are limited to key cell cycle regulators, dynamic phosphorylation changes are pervasive. Our data indicate that two waves of cyclin-dependent kinase (Cdc28Cdk1) and Polo (Cdc5Polo) kinase activity drive successive meiotic divisions. These two distinct phases of phosphorylation are ensured by the meiosis-specific Spo13 protein, which rewires the phosphoproteome. Spo13 binds to Cdc5Polo to promote phosphorylation in meiosis I, particularly of substrates containing a variant of the canonical Cdc5Polo motif. Overall, our findings reveal that a master regulator of meiosis directs the activity of a kinase to change the phosphorylation landscape and elicit a developmental cascade. Synopsis: Meiosis is a specialized cell cycle, where two consecutive divisions occur. This study quantifies the dynamics of thousands of phosphorylation events across the meiotic divisions in budding yeast, and reveals how a meiosis-specific regulator changes phosphorylation patterns. Two rounds of phosphorylation of strict Cdc28Cdk1 and Cdc5Polo kinase consensus motifs occur during the meiotic divisions. The meiosis-specific protein Spo13 promotes Cdc28Cdk1 and Cdc5Polo consensus phosphorylation at metaphase I. Spo13 promotes phosphorylation of sites with the modified Cdc5Polo motif [DEN]x[ST]*F. Master meiosis regulator Spo13 modulates Cdc5Polo kinase activity/specificity to ensure the occurrence of two successive divisions without an intervening S-phase. [ABSTRACT FROM AUTHOR]

Anther culture is a promising technique used in rice (Oryza sativa L.) breeding, although the genetic mechanisms associated with anther culturability remain elusive. In the process of in vitro anther culture, favorable alleles for anther culture are preferentially transmitted to doubled haploid (DH) populations, resulting in biased segregation of DH populations. Therefore, the segregation distortion (SD) method is an ideal approach for mapping the genetic loci controlling anther culturability. Performing a SD analysis using a genetic map consisting of 666 single nucleotide polymorphism markers, we identified five potential loci (logarithm of odds [LOD] > 3.5) that may be associated with anther culturability, including SDL2 and SDL3, which are overrepresented in japonica alleles, and SDL7, SDL9, and SDL11, which are overrepresented in indica alleles. In addition, nine pairs of epistatic interactions (EPIs) that contribute significantly (p < 0.05) to SD in the DH population were identified. Among them, the interaction between SDL2 and SDL3 is particularly noteworthy. These findings suggest that anther culturability in rice is governed by complex genetic mechanisms involving multiple nuclear genes and EPIs. This study provides insights into the genetic control underlying anther culturability in rice and lays the foundation for future research aimed at identifying causal genes associated with anther culturability. Core Ideas: A segregation distortion loci (SDLs) analysis was conducted on a doubled haploid (DH) population comprising 154 lines.Five SDLs (logarithm of odds [LOD] > 3.5) that may be associated with anther culturability were identified.Nine pairs of epistatic interactions that contribute significantly to SD in the DH population were identified.Rice culturability may be governed by complex genetic mechanisms with multiple genes and epistatic interactions. [ABSTRACT FROM AUTHOR]

The filamentous fungus Podospora anserina is a model organism used extensively in the study of molecular biology, senescence, prion biology, meiotic drive, mating-type chromosome evolution, and plant biomass degradation. It has recently been established that P. anserina is a member of a complex of 7 closely related species. In addition to P. anserina , high-quality genomic resources are available for 2 of these taxa. Here, we provide chromosome-level annotated assemblies of the 4 remaining species of the complex, as well as a comprehensive data set of annotated assemblies from a total of 28 Podospora genomes. We find that all 7 species have genomes of around 35 Mb arranged in 7 chromosomes that are mostly collinear and less than 2% divergent from each other at genic regions. We further attempt to resolve their phylogenetic relationships, finding significant levels of phylogenetic conflict as expected from a rapid and recent diversification. [ABSTRACT FROM AUTHOR]

Drosophila ananassae was originally described by Doleschall in 1858 from Ambon Island in Indonesia. This species came into notice when Morgan, Bridges and Sturtevant compiled data in a volume entitled 'The Genetics of Drosophila' in 1925 as D. caribbea Sturtevant in the chapter 'other species of Drosophila'. Kikkawa in 1935 verified D. caribbea as D. ananassae. The first mutation in this species was curved wing, an autosomal recessive gene on II chromosome reported by Sturtevant in 1921. Since then D. ananassae has been utilized extensively for different kinds of studies and results of these studies conducted during the last hundred years have clearly revealed that D. ananassae is genetically unique species and stands distinct from other species of the genus Drosophila. The important unusual features of this species are: spontaneous meiotic male recombination, presence of chiasmata in males, high mutability, optic morphology hyper mutability system, absence of genetic coadaptation, Y-4 linkage of nucleolus organizer, high frequency of pericentric inversions and translocations, population substructing, parthenogenesis, extra chromosomal inheritance, incipient sexual isolation, inversion karyotypes and mate recognition system, spontaneous genetic mosaic, segregation distortion, lack of correlation between crossing-over and chromosome distance between inversions, rare male mating advantage, trait and sex specific fluctuating asymmetry, female and male remating and sperm displacement, speciation in south Pacific populations, association with a bacterium Wolbachia, variation in resistance to environmental stress, nutrition regulated stress resistance, correlation between inversion karyotypes and mating propensity and phylogenetic relationship with its sibling D. pallidosa which is in statu nascendi. [ABSTRACT FROM AUTHOR]

Summary: Although intrinsic postzygotic reproductive barriers can play a fundamental role in speciation, their underlying evolutionary causes are widely debated. One hypothesis is that incompatibilities result from genomic conflicts. Here, I synthesize the evidence that conflict generates incompatibilities in plants, thus playing a creative role in plant biodiversity. While much evidence supports a role for conflict in several classes of incompatibility, integrating knowledge of incompatibility alleles with natural history can provide further essential tests. Moreover, comparative work can shed light on the relative importance of conflict in causing incompatibilities, including the extent to which their evolution is repeatable. Together, these approaches can provide independent lines of evidence that conflict causes incompatibilities, cementing its role in plant speciation. Jenn Coughlan is a finalist of the 2023 New Phytologist Tansley Medal competition for excellence in plant science. See Slater & Dolan (2023, 240: 2171–2172) for more details. [ABSTRACT FROM AUTHOR]

X chromosome meiotic drive (XCMD) kills Y‐bearing sperm during spermatogenesis, leading to the biased transmission of the selfish X chromosome. Despite this strong transmission, some natural XCMD systems remain at low and stable frequencies, rather than rapidly spreading through populations. The reason may be that male carriers can have reduced fitness, as they lose half of their sperm, only produce daughters, and may carry deleterious alleles associated with XCMD. Thus, females may benefit from avoiding mating with male carriers, yielding a further reduction in fitness. Genetic suppressors of XCMD, which block the killing of Y sperm and restore fair Mendelian inheritance, are also common and could prevent the spread of XCMD. However, whether suppressed males are as fit as a wild‐type male remains an open question, as the effect that genetic suppressors may have on a male's mating success is rarely considered. Here, we investigate the mating ability of XCMD males and suppressed XCMD males in comparison to wild‐type males in the fruit fly Drosophila subobscura, where drive remains at a stable frequency of 20% in wild populations where it occurs. We use both competitive and non‐competitive mating trials to evaluate male mating success in this system. We found no evidence that unsuppressed XCMD males were discriminated against. Remarkably, however, their suppressed XCMD counterparts had a higher male mating success compared to wild‐type controls. Unsuppressed XCMD males suffered 12% lower offspring production in comparison to wild‐type males. This cost appears too weak to counter the transmission advantage of XCMD, and thus the factors preventing the spread of XCMD remain unclear. [ABSTRACT FROM AUTHOR]

Sex chromosomes are havens for intragenomic conflicts. The absence of recombination between sex chromosomes creates the opportunity for the evolution of segregation distorters: selfish genetic elements that hijack different aspects of an individual's reproduction to increase their own transmission. Biased (non-Mendelian) segregation, however, often occurs at a detriment to their host's fitness, and therefore can trigger evolutionary arms races that can have major consequences for genome structure and regulation, gametogenesis, reproductive strategies and even speciation. Here, we review an emerging feature from comparative genomic and sex chromosome evolution studies suggesting that meiotic drive is pervasive: the recurrent evolution of paralogous sex-linked gene families. Sex chromosomes of several species independently acquire and co-amplify rapidly evolving gene families with spermatogenesis-related functions, consistent with a history of intragenomic conflict over transmission. We discuss Y chromosome features that might contribute to the tempo and mode of evolution of X/Y co-amplified gene families, as well as their implications for the evolution of complexity in the genome. Finally, we propose a framework that explores the conditions that might allow for recurrent bouts of fixation of drivers and suppressors, in a dosage-sensitive fashion, and therefore the co-amplification of multigene families on sex chromosomes. [ABSTRACT FROM AUTHOR]

Meiotic drive biases the transmission of alleles in heterozygous individuals, such that Mendel's law of equal segregation is violated. Most examples of meiotic drive have been discovered over the past century based on causing sex ratio distortion or the biased transmission of easily scoreable genetic markers that were linked to drive alleles. More recently, several approaches have been developed that attempt to identify distortions of Mendelian segregation genome wide. Here, we test a candidate female meiotic drive locus in Drosophila melanogaster, identified previously as causing a ~54:46 distortion ratio using sequencing of large pools of backcross progeny. We inserted fluorescent visible markers near the candidate locus and scored transmission in thousands of individual progeny. We observed a small but significant deviation from the Mendelian expectation; however, it was in the opposite direction to that predicted based on the original experiments. We discuss several possible causes of the discrepancy between the 2 approaches, noting that subtle viability effects are particularly challenging to disentangle from potential small-effect meiotic drive loci. We conclude that pool sequencing approaches remain a powerful method to identify candidate meiotic drive loci but that genotyping of individual progeny at early developmental stages may be required for robust confirmation. [ABSTRACT FROM AUTHOR]

Context: Broadening the gene pool of staple food crops by incorporating desirable genes from wild/relative species is way to achieve higher genetic gains. The African rice species Oryza glaberrima Steud. is a source of genes for genetic improvement of Oryza sativa L. to various biotic and abiotic stresses. Aim: The study was undertaken to identify genomic regions associated with yield and yield-related traits in interspecific backcross mapping populations derived from variety IR64 (O. sativa indica) × O. glaberrima. Methods: The BC1F2 and BC1F2:3 populations were phenotyped for days to 50% flowering, plant height, number of tillers, number of productive tillers, panicle length, spikelet fertility and grain yield under irrigated conditions. The BC1F2 population was genotyped with 99 genome-wide polymorphic SSR markers. Quantitative trait loci (QTLs) associated with yield-enhancing traits were identified through single marker analysis. Key results: Significant genetic variability was observed with moderate to high heritability in mapping populations. Genotyping revealed the presence of segregation distortion and skewed genome composition. Single marker analysis identified 20 QTLs linked to the studied traits. A QTL linked to grain yield, qGY-4.1 , derived from O. glaberrima was found in both populations with high phenotypic variance. The chromosome region around marker RM510 was identified as a QTL hotspot and putative candidate genes were identified. Conclusions: Our study demonstrates that O. glaberrima can serve as a valuable genetic resource for genetic improvement of yield-enhancing traits in O. sativa cultivars. Implications: The identified QTLs regions can be employed in molecular breeding. The promising introgression lines identified can be used as pre-breeding lines in future breeding programs. African rice species Oryza glaberrima as a source of genes for improvement of Oryza sativa is well established for various biotic and abiotic stresses. In this study, yield and yield-related QTLs derived from O. glaberrima were mapped in backcross mapping populations of IR64 × O. glaberrima. The outcomes of the study will help in harnessing useful genomic regions from O. glaberrima for genetic improvement of O. sativa. [ABSTRACT FROM AUTHOR]

Anther culture (AC) is a valuable technique in rice breeding. However, the genetic mechanisms underlying anther culturability remain elusive, which has hindered its widespread adoption in rice breeding programs. During AC, microspores carrying favorable alleles for AC are selectively regenerated, leading to segregation distortion (SD) of chromosomal regions linked to these alleles in the doubled haploid (DH) population. Using the AC method, a DH population was generated from the japonica hybrid rice Shenyou 26. A genetic map consisting of 470 SNPs was constructed using this DH population, and SD analysis was performed at both the single- and two-locus levels to dissect the genetic basis underlying anther culturability. Five segregation distortion loci (SDLs) potentially linked to anther culturability were identified. Among these, SDL5 exhibited an overrepresentation of alleles from the female parent, while SDL1.1, SDL1.2, SDL2, and SDL7 displayed an overrepresentation of alleles from the male parent. Furthermore, six pairs of epistatic interactions (EPIs) that influenced two-locus SDs in the DH population were discovered. A cluster of genetic loci, associated with EPI-1, EPI-3, EPI-4, and EPI-5, overlapped with SDL1.1, indicating that the SDL1.1 locus may play a role in regulating anther culturability via both additive and epistatic mechanisms. These findings provide valuable insights into the genetic control of anther culturability in rice and lay the foundation for future research focused on identifying the causal genes associated with anther culturability. [ABSTRACT FROM AUTHOR]

In all species, new chromosomal inversions are constantly being formed by spontaneous rearrangement and then stochastically eliminated from natural populations. In Drosophila, when new chromosomal inversions overlap with a preexisting inversion in the population, their rate of elimination becomes a function of the relative size, position, and linkage phase of the gene rearrangements. These altered dynamics result from complex meiotic behavior wherein overlapping inversions generate asymmetric dyads that cause both meiotic drive/drag and segmental aneuploidy. In this context, patterns in rare inversion polymorphisms of a natural population can be modeled from the fundamental genetic processes of forming asymmetric dyads via crossing-over in meiosis I and preferential segregation from asymmetric dyads in meiosis II. Here, a mathematical model of crossover-dependent female meiotic drive is developed and parameterized with published experimental data from Drosophila melanogaster laboratory constructs. This mechanism is demonstrated to favor smaller, distal inversions and accelerate the elimination of larger, proximal inversions. Simulated sampling experiments indicate that the paracentric inversions directly observed in natural population surveys of D. melanogaster are a biased subset that both maximizes meiotic drive and minimizes the frequency of lethal zygotes caused by this cytogenetic mechanism. Incorporating this form of selection into a population genetic model accurately predicts the shift in relative size, position, and linkage phase for rare inversions found in this species. The model and analysis presented here suggest that this weak form of female meiotic drive is an important process influencing the genomic distribution of rare inversion polymorphisms. [ABSTRACT FROM AUTHOR]

Grifola frondosa is a valuable edible fungus with high nutritional and medicinal values. The mating systems of fungi not only offer practical strategies for breeding, but also have far-reaching effects on genetic variability. Grifola frondosa has been considered as a sexual species with a tetrapolar mating system based on little experimental data. In the present study, one group of test crosses and six groups of three-round mating experiments from two parental strains were conducted to determine the mating system in G. frondosa. A chi-squared test of the results of the test-cross mating experiments indicated that they satisfied Mendelian segregation, while a series of three-round mating experiments showed that Mendelian segregation was not satisfied, implying a segregation distortion phenomenon in G. frondosa. A genomic map of the G. frondosa strain, y59, grown from an LMCZ basidiospore, with 40.54 Mb and 12 chromosomes, was generated using genome, transcriptome and Hi-C sequencing technology. Based on the genomic annotation of G. frondosa, the mating-type loci A and B were located on chromosomes 1 and 11, respectively. The mating-type locus A coded for the β-fg protein, HD1, HD2 and MIP, in that order. The mating-type locus B consisted of six pheromone receptors (PRs) and five pheromone precursors (PPs) in a crossed order. Moreover, both HD and PR loci may have only one sublocus that determines the mating type in G. frondosa. The nonsynonymous SNP and indel mutations between the A1B1 and A2B2 mating-type strains and the reference genome of y59 only occurred on genes HD2 and PR1/2, preliminarily confirming that the mating type of the y59 strain was A1B2 and not A1B1. Based on the genetic evidence and the more reliable molecular evidence, the results reveal that the mating system of G. frondosa is tetrapolar. This study has important implications for the genetics and hybrid breeding of G. frondosa. [ABSTRACT FROM AUTHOR]

Male X-linked meiotic drive systems, which cause the degeneration of Y-bearing sperm, are common in the Diptera. Sperm killing is typically associated with fitness costs that arise from the destruction of wildtype sperm and collateral damage to maturing drive sperm, resulting in poor success under sperm competition. We investigate X-linked meiotic drive fertility in the stalk-eyed fly, Teleopsis dalmanni. Drive male paternity was measured in double mating trials under sperm competition against a wildtype male. Drive males sired the same number of offspring as wildtype males, both when mated first or second. This is the first evidence that drive males can compete equally with non-drive males in double matings, challenging the assumption that drive males inevitably suffer reduced fertility. The finding is in accord with previous work showing that the number of sperm per ejaculate transferred to females during non-competitive single matings does not differ between drive and wildtype males, which is likely due to the adaptive evolution of enlarged testes in drive males. Future experiments will determine whether the competitive ability of drive males is maintained under higher rates of female remating likely to be experienced in nature. [ABSTRACT FROM AUTHOR]

Abstract X chromosome meiotic drive (XCMD) kills Y‐bearing sperm during spermatogenesis, leading to the biased transmission of the selfish X chromosome. Despite this strong transmission, some natural XCMD systems remain at low and stable frequencies, rather than rapidly spreading through populations. The reason may be that male carriers can have reduced fitness, as they lose half of their sperm, only produce daughters, and may carry deleterious alleles associated with XCMD. Thus, females may benefit from avoiding mating with male carriers, yielding a further reduction in fitness. Genetic suppressors of XCMD, which block the killing of Y sperm and restore fair Mendelian inheritance, are also common and could prevent the spread of XCMD. However, whether suppressed males are as fit as a wild‐type male remains an open question, as the effect that genetic suppressors may have on a male's mating success is rarely considered. Here, we investigate the mating ability of XCMD males and suppressed XCMD males in comparison to wild‐type males in the fruit fly Drosophila subobscura, where drive remains at a stable frequency of 20% in wild populations where it occurs. We use both competitive and non‐competitive mating trials to evaluate male mating success in this system. We found no evidence that unsuppressed XCMD males were discriminated against. Remarkably, however, their suppressed XCMD counterparts had a higher male mating success compared to wild‐type controls. Unsuppressed XCMD males suffered 12% lower offspring production in comparison to wild‐type males. This cost appears too weak to counter the transmission advantage of XCMD, and thus the factors preventing the spread of XCMD remain unclear.

Nowadays, the availability of genotyped trios (sire-dam-offspring) in the livestock industry enables the implementation of the transmission ratio distortion (TRD) approach to discover deleterious alleles in the genome. Various biological mechanisms at different stages of the reproductive cycle such as gametogenesis, embryo development and postnatal viability can induce signals of TRD (i.e., deviation from Mendelian inheritance expectations). In this study, TRD was evaluated using both SNP-by-SNP and sliding windows of 2-, 4-, 7-, 10- and 20-SNP across 92,942 autosomal SNPs for 258,140 genotyped Angus cattle including 7,486 sires, 72,688 dams and 205,966 offspring. Transmission ratio distortion was characterized using allelic (specific- and unspecific-parent TRD) and genotypic parameterizations (additive- and dominance-TRD). Across the Angus autosomal chromosomes, 851 regions were clearly found with decisive evidence for TRD. Among these findings, 19 haplotypes with recessive patterns (potential lethality for homozygote individuals) and 52 regions with allelic patterns exhibiting complete or quasi-complete absence for homozygous individuals in addition to under-representation (potentially reduced viability) of the carrier (heterozygous) offspring were found. In addition, 64 (12) and 20 (4) regions showed significant influence on the trait heifer pregnancy at p-value < 0.05 (after chromosome-wise false discovery rate) and 0.01, respectively, reducing the pregnancy rate up to 15%, thus, supporting the biological importance of TRD phenomenon in reproduction. [ABSTRACT FROM AUTHOR]

Experimental evolution provides an integrative method for revealing complex interactions among evolutionary processes. One such interaction involves sex-linked selfish genetic elements and sexual selection. X-linked segregation distorters, a type of selfish genetic element, influence sperm transmission to increase in frequency and consequently alter the population sex ratio and the opportunity for sexual selection, while sexual selection may impact the spread of X-linked distorters. Here we manipulated sexual selection by controlling female mating opportunities and the presence of a distorting X chromosome in experimental lines of the stalk-eyed fly, Teleopsis dalmanni, over 11 generations. We find that removal of sexual selection leads to an increase in the frequency of the X-linked distorter and sex ratio across generations and that post-copulatory sexual selection alone is sufficient to limit the frequency of distorters. In addition, we find that male eyestalk length, a trait under pre-copulatory sexual selection, evolves in response to changes in the strength of sexual selection with the magnitude of the response dependent on X chromosome type and the frequency of distorting X chromosomes. These results reveal how a selfish X can interact with sexual selection to influence the evolution of sexually selected traits in multiple ways. [ABSTRACT FROM AUTHOR]

Stalk-eyed flies in the genus Teleopsis carry selfish genetic elements that induce sex ratio (SR) meiotic drive and impact the fitness of male and female carriers. Here, we assemble and describe a chromosome-level genome assembly of the stalk-eyed fly, Teleopsis dalmanni , to elucidate patterns of divergence associated with SR. The genome contains tens of thousands of transposable element (TE) insertions and hundreds of transcriptionally and insertionally active TE families. By resequencing pools of SR and ST males using short and long reads, we find widespread differentiation and divergence between XSR and XST associated with multiple nested inversions involving most of the SR haplotype. Examination of genomic coverage and gene expression data revealed seven X-linked genes with elevated expression and coverage in SR males. The most extreme and likely drive candidate involves an XSR-specific expansion of an array of partial copies of JASPer, a gene necessary for maintenance of euchromatin and associated with regulation of TE expression. In addition, we find evidence for rapid protein evolution between XSR and XST for testis expressed and novel genes, that is, either recent duplicates or lacking a Dipteran ortholog, including an X-linked duplicate of maelstrom , which is also involved in TE silencing. Overall, the evidence suggests that this ancient XSR polymorphism has had a variety of impacts on repetitive DNA and its regulation in this species. [ABSTRACT FROM AUTHOR]

Achieving high-yield potential is always the ultimate objective of any breeding program. However, various abiotic stresses such as salinity, drought, cold, flood, and heat hampered rice productivity tremendously. Salinity is one of the most important abiotic stresses that adversely affect rice grain yield. The present investigation was undertaken to dissect new genetic loci, which are responsible for salt tolerance at the early seedling stage in rice. A bi-parental mapping population (F2:3) was developed from the cross between BRRI dhan28/Akundi, where BRRI dhan28 (BR28) is a salt-sensitive irrigated (boro) rice mega variety and Akundi is a highly salinity-tolerant Bangladeshi origin indica rice landrace that is utilized as a donor parent. We report reliable and stable QTLs for salt tolerance from a common donor (Akundi) irrespective of two different genetic backgrounds (BRRI dhan49/Akundi and BRRI dhan28/Akundi). A robust 1k-Rice Custom Amplicon (1k-RiCA) SNP marker genotyping platform was used for genome-wide analysis of this bi-parental population. After eliminating markers with high segregation distortion, 886 polymorphic SNPs built a genetic linkage map covering 1526.5 cM of whole rice genome with an average SNP density of 1.72 cM for the 12 genetic linkage groups. A total of 12 QTLs for nine different salt tolerance-related traits were identified using QGene and inclusive composite interval mapping of additive and dominant QTL (ICIM-ADD) under salt stress on seven different chromosomes. All of these 12 new QTLs were found to be unique, as no other map from the previous study has reported these QTLs in the similar chromosomal location and found them different from extensively studied Saltol, SKC1, OsSalT, and salT locus. Twenty-eight significant digenic/epistatic interactions were identified between chromosomal regions linked to or unlinked to QTLs. Akundi acts like a new alternate donor source of salt tolerance except for other usually known donors such as Nona Bokra, Pokkali, Capsule, and Hasawi used in salt tolerance genetic analysis and breeding programs worldwide, including Bangladesh. Integration of the seven novel, reliable, stable, and background independent salinity-resilient QTLs (qSES1, qSL1, qRL1, qSUR1, qSL8, qK8, qK1) reported in this investigation will expedite the cultivar development that is highly tolerant to salt stress. [ABSTRACT FROM AUTHOR]

The recent evolutionary history of the Y chromosome in Drosophila simulans , a worldwide species of Afrotropical origin, is closely linked to that of X-linked meiotic drivers (Paris system). The spread of the Paris drivers in natural populations has elicited the selection of drive-resistant Y chromosomes. To infer the evolutionary history of the Y chromosome in relation to the Paris drive, we sequenced 21 iso-Y lines, each carrying a Y chromosome from a different location. Among them, 13 lines carry a Y chromosome that is able to counteract the effect of the drivers. Despite their very different geographical origins, all sensitive Y's are highly similar, suggesting that they share a recent common ancestor. The resistant Y chromosomes are more divergent and segregate in four distinct clusters. The phylogeny of the Y chromosome confirms that the resistant lineage predates the emergence of Paris drive. The ancestry of the resistant lineage is further supported by the examination of Y-linked sequences in the sister species of D. simulans , Drosophila sechellia and Drosophila mauritiana. We also characterized the variation in repeat content among Y chromosomes and identified multiple simple satellites associated with resistance. Altogether, the molecular polymorphism allows us to infer the demographic and evolutionary history of the Y chromosome and provides new insights on the genetic basis of resistance. [ABSTRACT FROM AUTHOR]

Although the biological utilities of endogenous RNAi (endo-RNAi) have been largely elusive, recent studies reveal its critical role in the non-model fruitfly Drosophila simulans to suppress selfish genes, whose unchecked activities can severely impair spermatogenesis. In particular, hairpin RNA (hpRNA) loci generate endo-siRNAs that suppress evolutionary novel, X-linked, meiotic drive loci. The consequences of deleting even a single hpRNA (Nmy) in males are profound, as such individuals are nearly incapable of siring male progeny. Here, comparative genomic analyses of D. simulans and D. melanogaster mutants of the core RNAi factor dcr-2 reveal a substantially expanded network of recently-emerged hpRNA-target interactions in the former species. The de novo hpRNA regulatory network in D. simulans provides insight into molecular strategies that underlie hpRNA emergence and their potential roles in sex chromosome conflict. In particular, our data support the existence of ongoing rapid evolution of Nmy/Dox-related networks, and recurrent targeting of testis HMG Box loci by hpRNAs. Importantly, the impact of the endo-RNAi network on gene expression flips the convention for regulatory networks, since we observe strong derepression of targets of the youngest hpRNAs, but only mild effects on the targets of the oldest hpRNAs. These data suggest that endo-RNAi are especially critical during incipient stages of intrinsic sex chromosome conflicts, and that continual cycles of distortion and resolution may contribute to speciation. Author summary: Selfish meiotic drive loci promote their own transmission at the cost of host reproductive fitness. Therefore, their existence and activity places strong pressure to innovate genetic suppressors that can return gametogenesis to a normal Mendelian state. Because such genetic battles are typically kept in a silenced, cryptic state, the identity of underlying meiotic drivers and suppressors is often hidden. We find that endo-siRNAs generated by the hairpin RNA (hpRNA) substrates of the RNA interference (RNAi) pathway evolve rapidly, and strongly repress specific genes in the male germline that exhibit signatures of genetic conflict. This indicates that genetic analysis of RNAi-suppressed target networks is a new forward strategy to uncover loci with candidate meiotic drivers. More generally, these data flip the convention for gene regulatory strategies for the paralogous miRNA pathway. Whereas only the oldest miRNAs typically have gained high expression levels and substantial target repression, it is the very youngest hpRNA-siRNA loci that exhibit highest expression and most overt effects on gene silencing. [ABSTRACT FROM AUTHOR]

Y chromosomes are typically viewed as genetic wastelands with few intact genes. Recent genomic analyses in Drosophila, however, show that gene gain is prominent on young Y chromosomes. Meiosis- and RNAi-related genes often coamplify on recently formed X and Y chromosomes, are testis-expressed, and produce antisense transcripts and short RNAs. RNAi pathways are also involved in suppressing sex ratio drive in Drosophila. These observations paint a dynamic picture of sex chromosome differentiation, suggesting that rapidly evolving genomic battles over segregation are rampant on young sex chromosomes and utilize RNAi to defend the genome against selfish elements that manipulate fair meiosis. Recurrent sex chromosome drive can have profound ecological, evolutionary, and cellular impacts and account for unique features of sex chromosomes.

Haploid gametes are produced from diploid parents through meiosis, a process inherent to all sexually reproducing eukaryotes. Faithful chromosome segregation in meiosis is essential for reproductive success, although it is less clear how the meiotic spindle achieves this compared to the mitotic spindle. It is becoming increasingly clear that tubulin post-translational modifications (PTMs) play critical roles in regulating microtubule functions in many biological processes, and meiosis is no exception. Here, I review recent advances in the understanding of tubulin PTMs in meiotic spindles, especially focusing on their roles in spindle integrity, oocyte aging, and non-Mendelian transmission. [ABSTRACT FROM AUTHOR]

Wheat yield is highly correlated with plant height, heading date, spike characteristics, and kernel traits. In this study, we used the wheat55K single nucleotide polymorphism array to genotype a recombinant inbred line population of 165 lines constructed by crossing two tetraploid wheat materials, Icaro and Y4. A genetic linkage map with a total length of 6244.51 cM was constructed, covering 14 chromosomes of tetraploid wheat. QTLs for 12 important agronomic traits, including plant height (PH), heading date (HD), awn color (AC), spike-branching (SB), and related traits of spike and kernel, were mapped in multiple environments, while combined QTL-by-environment interactions and epistatic effects were analyzed for each trait. A total of 52 major or stable QTLs were identified, among which may be some novel loci controlling PH, SB, and kernel length-width ratio (LWR), etc., with LOD values ranging from 2.51 to 54.49, thereby explaining 2.40–66.27% of the phenotypic variation. Based on the 'China Spring' and durum wheat reference genome annotations, candidate genes were predicted for four stable QTLs, QPH.nwafu-2B.2 (165.67–166.99 cM), QAC.nwafu-3A.1 (419.89–420.52 cM), QAC.nwafu-4A.1 (424.31–447.4 cM), and QLWR.nwafu-7A.1 (166.66–175.46 cM). Thirty-one QTL clusters and 44 segregation distortion regions were also detected, and 38 and 18 major or stable QTLs were included in these clusters and segregation distortion regions, respectively. These results provide QTLs with breeding application potential in tetraploid wheat that broadens the genetic basis of important agronomic traits such as PH, HD, AC, SB, etc., and benefits wheat breeding. [ABSTRACT FROM AUTHOR]

Many animal species employ sperm nuclear basic proteins (SNBPs) or protamines to package sperm genomes tightly. SNBPs vary across animal lineages and evolve rapidly in mammals. We used a phylogenomic approach to investigate SNBP diversification in Drosophila species. We found that most SNBP genes in Drosophila melanogaster evolve under positive selection except for genes essential for male fertility. Unexpectedly, evolutionarily young SNBP genes are more likely to be critical for fertility than ancient, conserved SNBP genes. For example, CG30056 is dispensable for male fertility despite being one of three SNBP genes universally retained in Drosophila species. We found 19 independent SNBP gene amplification events that occurred preferentially on sex chromosomes. Conversely, the montium group of Drosophila species lost otherwise-conserved SNBP genes, coincident with an X-Y chromosomal fusion. Furthermore, SNBP genes that became linked to sex chromosomes via chromosomal fusions were more likely to degenerate or relocate back to autosomes. We hypothesize that autosomal SNBP genes suppress meiotic drive, whereas sex-chromosomal SNBP expansions lead to meiotic drive. X-Y fusions in the montium group render autosomal SNBPs dispensable by making X-versus-Y meiotic drive obsolete or costly. Thus, genetic conflicts between sex chromosomes may drive SNBP rapid evolution during spermatogenesis in Drosophila species. [ABSTRACT FROM AUTHOR]

Columbianetin acetate (CE) is one of the effective components of Angelica pubescens. So far, the specific role and molecular mechanism of CE in pancreatic cancer are not clear. Thus, this study aimed to explore the specific mechanism of CE on pancreatic cancer. The target genes combined with CE were predicted through the PharmMapper database and the 3D molecular structure of CE. Then, the Cancer Genome Atlas (TCGA) and Cistrome data browser (DB) databases were used to screen Meiotic nuclear divisions 1 (MND1)-related genes, transcription factors, and transcription factor data sets, and the intersection of the above data sets. The "limma" package in the R and gene expression profiling interactive analysis (GEPIA) databases were used to analyze the correlation and survival difference between the target genes and MND1 to predict the degree of association between CE and MND1. Western blotting and RT-PCR experiments revealed the regulatory relationship among CE, E2F1, and MND1 at the cellular level. The specific effects of CE on pancreatic cancer cells were explored through CCK8, wound healing, migration, and flow cycle experiments. E2F1, also the predictive transcription factor of MND1, was also the predictive target protein of CE. At the same time, E2F1 and MND1 were closely related in pancreatic tissue. In the cell function experiment, CE and interference with E2F1 expression could reduce the gene and protein expression of MND1, which was closely associated with cell proliferation, migration, and cycle development. Similarly, interfering with the expression of mnd1 can also inhibit the further development of tumor cells. CE may inhibit the development of pancreatic cancer cells by reducing the expression of MND1. This implies that CE may be a potential novel agent for the treatment of pancreatic cancer. [ABSTRACT FROM AUTHOR]

Haldane's rule is one of the 'two rules of speciation'. It states that if one sex is 'absent, rare or sterile' in a hybrid population, then that sex will be heterogametic. Since Haldane first made this observation, 100 years have passed and still questions arise over how many independent examples exist and what the underlying causes of Haldane's rule are. This review aims to examine research that has occurred over the last century. It seeks to do so by discussing possible causes of Haldane's rule, as well as gaps in the research of these causes that could be readily addressed today. After 100 years of research, it can be concluded that Haldane's rule is a complicated one, and much current knowledge has been accrued by studying the model organisms of speciation. This has led to the primacy of dominance theory and faster‐male theory as explanations for Haldane's rule. However, some of the most interesting findings of the 21st century with regard to Haldane's rule have involved investigating a wider range of taxa emphasizing the need to continue using comparative methods, including ever more taxa as new cases are discovered. [ABSTRACT FROM AUTHOR]

Mendel's law of segregation states that the two alleles at a diploid locus should be transmitted equally to the progeny. A genetic segregation distortion, also referred to as transmission ratio distortion (TRD), is a statistically significant deviation from this rule. TRD has been observed in several mammal species and may be due to different biological mechanisms occurring at diverse time points ranging from gamete formation to lethality at post-natal stages. In this review, we describe examples of TRD and their possible mechanisms in mammals based on current knowledge. We first focus on the differences between TRD in male and female gametogenesis in the house mouse, in which some of the most well studied TRD systems have been characterized. We then describe known TRD in other mammals, with a special focus on the farmed species and in the peculiar common shrew species. Finally, we discuss TRD in human diseases. Thus far, to our knowledge, this is the first time that such description is proposed. This review will help better comprehend the processes involved in TRD. A better understanding of these molecular mechanisms will imply a better comprehension of their impact on fertility and on genome evolution. In turn, this should allow for better genetic counseling and lead to better care for human families. [ABSTRACT FROM AUTHOR]

Mechanisms that safeguard mitochondrial DNA (mtDNA) limit the accumulation of mutations linked to mitochondrial and agerelated diseases. Yet, pathways that repair double-strand breaks (DSBs) in animal mitochondria are poorly understood. By performing a candidate screen for mtDNA repair proteins, we identify that REC—an MCM helicase that drives meiotic recombination in the nucleus—also localizes to mitochondria in Drosophila. We show that REC repairs mtDNA DSBs by homologous recombination in somatic and germline tissues. Moreover, REC prevents age-associated mtDNA mutations. We further show that MCM8, the human ortholog of REC, also localizes to mitochondria and limits the accumulation of mtDNA mutations. This study provides mechanistic insight into animal mtDNA recombination and demonstrates its importance in safeguarding mtDNA during ageing and evolution. [ABSTRACT FROM AUTHOR]

Background Genotyping-by-sequencing (GBS) provides affordable methods for genotyping hundreds of individuals using millions of markers. However, this challenges bioinformatic procedures that must overcome possible artifacts such as the bias generated by polymerase chain reaction duplicates and sequencing errors. Genotyping errors lead to data that deviate from what is expected from regular meiosis. This, in turn, leads to difficulties in grouping and ordering markers, resulting in inflated and incorrect linkage maps. Therefore, genotyping errors can be easily detected by linkage map quality evaluations. Results We developed and used the Reads2Map workflow to build linkage maps with simulated and empirical GBS data of diploid outcrossing populations. The workflows run GATK, Stacks, TASSEL , and Freebayes for single-nucleotide polymorphism calling and updog, polyRAD , and SuperMASSA for genotype calling, as well as OneMap and GUSMap to build linkage maps. Using simulated data, we observed which genotype call software fails in identifying common errors in GBS sequencing data and proposed specific filters to better handle them. We tested whether it is possible to overcome errors in a linkage map using genotype probabilities from each software or global error rates to estimate genetic distances with an updated version of OneMap. We also evaluated the impact of segregation distortion, contaminant samples, and haplotype-based multiallelic markers in the final linkage maps. Through our evaluations, we observed that some of the approaches produce different results depending on the dataset (dataset dependent) and others produce consistent advantageous results among them (dataset independent). Conclusions We set as default in the Reads2Map workflows the approaches that showed to be dataset independent for GBS datasets according to our results. This reduces the number of required tests to identify optimal pipelines and parameters for other empirical datasets. Using Reads2Map , users can select the pipeline and parameters that best fit their data context. The Reads2MapApp shiny app provides a graphical representation of the results to facilitate their interpretation. [ABSTRACT FROM AUTHOR]