Segregation Distortion Research Articles

Identification and characterization of genes related to salt stress tolerance within segregation distortion regions of genetic map in F2 population of upland cotton.

Segregation distortion (SD) is a genetic mechanism commonly found in segregating or stable populations. The principle behind this puzzles many researchers. The F2 generation developed from wild Gossypium darwinii and G. hirsutum CCRI12 species was used to investigate the possible transcription factors within the segregation distortion regions (SDRs). The 384 out of 2763 markers were distorted in 29 SDRs on 18 chromosomes. Good collinearity was observed among genetic and physical maps of G. hirsutum and G. barbadense syntenic blocks. Total 568 genes were identified from SDRs of 18 chromosomes. Out of these genes, 128 belonged to three top-ranked salt-tolerant gene families. The DUF597 contained 8 uncharacterized genes linked to Pkinase (PF00069) gene family in the phylogenetic tree, while 15 uncharacterized genes clustered with the zinc finger gene family. Two hundred thirty four miRNAs targeted numerous genes, including ghr-miR156, ghr-miR399 and ghr-miR482, while others targeted top-ranked stress-responsive transcription factors. Moreover, these genes were involved in the regulation of numerous stress-responsive cis-regulatory elements. The RNA sequence data of fifteen upregulated genes were verified through the RT-qPCR. The expression profiles of two highly upregulated genes (Gh_D01G2015 and Gh_A01G1773) in salt-tolerant G. darwinii showed antagonistic expression in G. hirsutum. The results indicated that salt-tolerant genes have been possibly transferred from the wild G. darwinii species. A detailed functional analysis of these genes can be carried out which might be helpful in the future for gene cloning, transformation, gene editing and the development of salt-resistant cotton varieties.

A high-density genetic linkage map for Chinese perch (Siniperca chuatsi) using 2.3K genotyping-by-sequencing SNPs.

Chinese perch, Siniperca chuatsi (Basilewsky), is one of the most commercially important cultured fishes in China. In the present study, a high-density genetic linkage map of Chinese perch was constructed by genotyping-by-sequencing technique with an F1 mapping panel containing 190 progenies. A total of 2328 SNPs were assigned to 24 linkage groups (LGs), agreeing with the chromosome haploid number in this species (n=24). The sex-averaged map covered 97.9% of the Chinese perch genome, with the length of 1694.3cM and a marker density of 0.7cM/locus. The number of markers per LG ranged from 57 to 222, with a mean of 97. The length of LGs varied from 43.2 to 108.2cM, with a mean size of 70.6cM. The recombination rate of females was 1.5:1, which was higher than that of males. To better understand the distribution pattern of segregation distortion between the two sexes of Chinese perch, the skewed markers were retained and used to reconstruct the sex-specific maps. The 16 segregation distortion regions were identified on 10 LGs of the female map, while 12 segregation distortion regions on eight LGs of the male map. Among these LGs, six LGs matched between the sex-specific maps. This high-density linkage map could provide a solid basis for identifying QTL associated with economically important traits, and for implementing marker-assisted selection breeding of Chinese perch.

Major locus for spontaneous haploid genome doubling detected by a case-control GWAS in exotic maize germplasm.

A major locus for spontaneous haploid genome doubling was detected by a case-control GWAS in an exotic maize germplasm. The combination of double haploid breeding method with this locus leads to segregation distortion on genomic regions of chromosome five. Temperate maize (Zea mays L.) breeding programs often rely on limited genetic diversity, which can be expanded by incorporating exotic germplasm. The aims of this study were to perform characterization of inbred lines derived from the tropical BS39 population using different breeding methods, to identify genomic regions showing segregation distortion in lines derived by the DH process using spontaneous haploid genome doubling (SHGD), and use case-control association mapping to identify loci controlling SHGD. Four different sets were used: BS39_DH and BS39_SSD were derived from the BS39 population by DH and single-seed descendent (SSD) methods, and BS39 × A427_DH and BS39 × A427_SSD from the cross between BS39 and A427. A total of 663 inbred lines were genotyped. The analyses of gene diversity and genetic differentiation for the DH sets provided evidence of the presence of a SHGD locus near the centromere of chromosome 5. The case-control GWAS for the DH set also pinpointed this locus. Haplotype sharing analysis showed almost 100% exclusive contribution of the A427 genome in the same region on chromosome 5 of BS39 × A427_DH, presumably due to an allele in this region affecting SHGD. This locus enables DH line production in exotic populations without colchicine or other artificial haploid genome doubling.

Development of sub-tropically adapted diverse provitamin-A rich maize inbreds through marker-assisted pedigree selection, their characterization and utilization in hybrid breeding.

Malnutrition has emerged as one of the major health problems worldwide. Traditional yellow maize has low provitamin-A (proA) content and its genetic base in proA biofortification breeding program of subtropics is extremely narrow. To diversify the proA rich germplasm, 10 elite low proA inbreds were crossed with a proA rich donor (HP702-22) having mutant crtRB1 gene. The F2 populations derived from these crosses were genotyped using InDel marker specific to crtRB1. Severe marker segregation distortion was observed. Seventeen crtRB1 inbreds developed through marker-assisted pedigree breeding and seven inbreds generated using marker-assisted backcross breeding were characterized using 77 SSRs. Wide variation in gene diversity (0.08 to 0.79) and dissimilarity coefficient (0.28 to 0.84) was observed. The inbreds were grouped into three major clusters depicting the existing genetic diversity. The crtRB1-based inbreds possessed high β-carotene (BC: 8.72μg/g), β-cryptoxanthin (BCX: 4.58μg/g) and proA (11.01μg/g), while it was 2.35μg/g, 1.24μg/g and 2.97μg/g in checks, respectively. Based on their genetic relationships, 15 newly developed crtRB1-based inbreds were crossed with five testers (having crtRB1 gene) using line × tester mating design. 75 experimental hybrids with crtRB1 gene were evaluated over three locations. These experimental hybrids possessed higher BC (8.02μg/g), BCX (4.69μg/g), proA (10.37μg/g) compared to traditional hybrids used as check (BC: 2.36 μg/g, BCX: 1.53μg/g, proA: 3.13μg/g). Environment and genotypes × environment interaction had minor effects on proA content. Both additive and dominance gene action were significant for proA. The mean proportion of proA to total carotenoids (TC) was 44% among crtRB1-based hybrids, while 11% in traditional hybrids. BC was found to be positively correlated with BCX (r = 0.68) and proA (r = 0.98). However, no correlation was observed between proA and grain yield. Several hybrids with >10.0 t/ha grain yield with proA content >10.0 μg/g were identified. This is the first comprehensive study on development of diverse proA rich maize hybrids through marker-assisted pedigree breeding approach. The findings provides sustainable and cost-effective solution to alleviate vitamin-A deficiency.

Mapping QTLs for Alternaria blight in Linseed (Linum usitatissimum L.).

A SSR-based linkage map of linseed constructed based on 154 individual lines of F 2 mapping population derived from JRF-4 (disease-resistant) and Chambal (disease susceptible) genotypes. QTLs for Alternaria blight and other yield related traits identified. Out of 1720 SSRs, 216 SSRs were found polymorphic among the parents but due to segregation distortion 18 SSRs could not be used for linkage map construction. Total 191 SSRs were used to construct the linkage map and distributed in 15 linkage groups covering genome length of 1802.4cM. A total of 10 QTLs were identified for 4 phenotypic traits including 4 QTLs for capsules/plant, 2 for capsule weight/plant, 2 for seed weight/plant and 2 for Alternaria blight resistance. This study laid a foundation for further validation and fine mapping with more advance and large set of marker for different QTL identification and marker-assisted selection in linseed.

Coconut genome assembly enables evolutionary analysis of palms and highlights signaling pathways involved in salt tolerance

Coconut (Cocos nucifera) is the emblematic palm of tropical coastal areas all around the globe. It provides vital resources to millions of farmers. In an effort to better understand its evolutionary history and to develop genomic tools for its improvement, a sequence draft was recently released. Here, we present a dense linkage map (8402 SNPs) aiming to assemble the large genome of coconut (2.42 Gbp, 2n = 32) into 16 pseudomolecules. As a result, 47% of the sequences (representing 77% of the genes) were assigned to 16 linkage groups and ordered. We observed segregation distortion in chromosome Cn15, which is a signature of strong selection among pollen grains, favouring the maternal allele. Comparing our results with the genome of the oil palm Elaeis guineensis allowed us to identify major events in the evolutionary history of palms. We find that coconut underwent a massive transposable element invasion in the last million years, which could be related to the fluctuations of sea level during the glaciations at Pleistocene that would have triggered a population bottleneck. Finally, to better understand the facultative halophyte trait of coconut, we conducted an RNA-seq experiment on leaves to identify key players of signaling pathways involved in salt stress response. Altogether, our findings represent a valuable resource for the coconut breeding community.

Genetic factors associated with favourable pollinator traits in the wheat cultivar Piko.

Hybrid breeding in wheat has the potential to boost yields. An efficient hybrid seed production system requires elite pollinators; however, such germplasm is limited among modern cultivars. Piko, a winter wheat (Triticum aestivum L.) cultivar, has been identified as a superior pollinator and has been used in Europe. Piko has favourable pollinator traits for anther extrusion, anther length, pollen mass and hybrid seed set. However, the genetic factors responsible for Piko's favourable traits are largely unknown. Here, we report on the genetic analysis of a Piko-derived F2 mapping population. We confirmed that Piko's Rht-D1a allele for tall stature is associated with large anthers and high anther extrusion. However, Rht-D1 was not found to be associated with anther filament length, confirmed by near isogenic lines. Piko's photoperiod sensitive Ppd-B1b allele shows an association with increased spike length, more spikelets and spike architecture traits, while the insensitive Ppd-B1a allele is linked with high anther extrusion and larger anthers. We identified an anther extrusion quantitative trait locus (QTL) on chromosome 6A that showed significantly biased transmission of the favourable Piko allele amongst F2 progenies. The Piko allele is completely absent in the distal 6AS region and the central 6A region revealed a significantly lower ratio (<8%) of F2 with homozygous Piko alleles. Our study provided further evidence for the effects of Rht-D1 and Ppd-B1 loci on multiple pollinator traits and a novel anther extrusion QTL that exhibits segregation distortion.

Selective forces acting on spinocerebellar ataxia type 3/Machado-Joseph disease recurrency: A systematic review and meta-analysis.

Spinocerebellar ataxia type 3/Machado-Joseph disease (SCA3/MJD) is a dominant neurodegenerative disease caused by the expansion of a CAG repeat tract in ATXN3. Anticipation and worsening of clinical picture in subsequent generations were repeatedly reported, but there is no indication that SCA3/MJD frequency is changing. Thus, we performed a systematic review and meta-analysis on phenomena with potential effect on SCA3/MJD recurrency in populations: instability of CAG repeat transmissions, anticipation, fitness, and segregation of alleles. Transmission of the mutant allele was associated with an increase of 1.23 CAG repeats in the next generation, and the average change in age at onset showed an anticipation of 7.75 years per generation; but biased recruitments cannot be ruled out. Affected SCA3/MJD individuals had 45% more children than related controls. Transmissions from SCA3/MJD carriers showed that the expanded allele was segregated in 64% of their children. In contrast, transmissions from normal subjects showed that the minor allele was segregated in 54%. The present meta-analysis concluded that there is a segregation distortion favoring the expanded allele, among children of carriers. Therefore, further studies on transmissions and anticipation phenomena as well as more observations about fertility are required to clarify these selective forces over SCA3/MJD.

Segregation distortion: high genetic load suggested by a Chinese shrimp family under high-intensity selection

Segregation distortion is a common phenomenon found in most genetic mapping studies and is an important resource to dissect the mechanism of action in gene loci that cause deviation. Marine animals possess high genetic diversity and genomic heterozygosity, they therefore are ideal model organisms to study segregation distortion induced by selection. In the present study, we constructed a full-sib family of Fenneropenaeus chinensis and exerted high-intensity selection on 10,000 incipient progenies. 2b-RAD method was employed in remaining 273 individuals to develop genome-wide SNPs for segregating analysis and 41,612 SNPs were developed. 50.77% of 32,229 high-quality representative markers deviated from the expected Mendelian ratio. Results showed that most of these distorted markers (91.57%) were influenced at zygotic level. Heterozygote excess (53.07%) and homozygous deletions (41.96%) may both play an important role, sum of which explained 95.03% of distortion after fertilization. However, further results identified highly probable linkage among deleterious alleles, which may account for a considerable portion of heterozygote excess rather than single locus with heterozygote advantage. Results of this study support a major role of deleterious alleles in genetic load, thus in favor of partial dominance hypothesis. It would also offer necessary recommendations for the formulation of breeding strategy in shrimps.

Genetic map construction and functional characterization of genes within the segregation distortion regions (SDRs) in the F2:3 populations derived from wild cotton species of the D genome

BackgroundSegregation distortion (SD) is a common phenomenon among stable or segregating populations, and the principle behind it still puzzles many researchers. The F2:3 progenies developed from the wild cotton species of the D genomes were used to investigate the possible plant transcription factors within the segregation distortion regions (SDRs). A consensus map was developed between two maps from the four D genomes, map A derived from F2:3 progenies of Gossypium klotzschianum and G. davidsonii while Map B from G. thurberi and G. trilobum F2:3 generations. In each map, 188 individual plants were used.ResultsThe consensus linkage map had 1 492 markers across the 13 linkage groups with a map size of 1 467.445 cM and an average marker distance of 1.037 0 cM. Chromosome D502 had the highest percentage of SD with 58.6%, followed by Chromosome D507 with 47.9%. Six thousand and thirty-eight genes were mined within the SDRs on chromosome D502 and D507 of the consensus map. Within chromosome D502 and D507, 2 308 and 3 730 genes were mined, respectively, and were found to belong to 1 117 gourp out of which 622 groups were common across the two chromosomes. Moreover, genes within the top 9 groups related to plant resistance genes (R genes), whereas 188 genes encoding protein kinase domain (PF00069) comprised the largest group. Further analysis of the dominant gene group revealed that 287 miRNAs were found to target various genes, such as the gra-miR398, gra-miR5207, miR164a, miR164b, miR164c among others, which have been found to target top-ranked stress-responsive transcription factors such as NAC genes. Moreover, some of the stress- responsive cis-regulatory elements were also detected. Furthermore, RNA profiling of the genes from the dominant family showed that higher numbers of genes were highly upregulated under salt and osmotic stress conditions, and also they were highly expressed at different stages of fiber development.ConclusionThe results indicated the critical role of the SDRs in the evolution of the key regulatory genes in plants.

47 Distortion of Mendelian segregation across Angus cattle genome reveal novel lethal haplotype affecting reproduction

Abstract The rapid development of DNA technologies, together with the adoption and daily routine use of commercial SNP arrays in livestock industries, provided a valuable resource of large and powerful data that can be explored for innovative applications for animal breeding purposes. Thus, the current availability of trios (i.e., sire-dam-offspring) of genotyped families enables the implementation of the transmission ratio distortion (TRD) approach to discover lethal alleles. Lethal alleles, which are crucial genetic determinants for reproduction, do not follow Mendelian principles but deviate from inheritance expectations, displaying signals of TRD. In this research, TRD was characterized using allelic (specific- and unspecific-parent TRD) and genotypic parameterizations (additive- and dominance-TRD) using both SNP- and haplotype-based methods. The analyses were performed using 258,140 Angus animals with 92,942 autosomal SNP genotypes, including 7,486 sires, 72,688 dams and 205,966 offspring. Across the whole genome, 852 regions displaying TRD were identified with different statistical significance. Among these findings, 19 haplotypes with recessive patterns (potential lethality for homozygote individuals) and 52 genomic regions with allelic patterns exhibiting complete or quasi-complete absence for homozygous individuals in addition to under-representation (potentially reduced viability) of heterozygous offspring were found. The average number of under-represented offspring (i.e., expected but not observed) across 52 allelic TRD regions ranged from 5,000 to 41,008. In contrast, the number of non-observed homozygous offspring for the 19 regions with recessive pattern ranges from 10 to 564. In addition, 64 and 20 genomic regions with TRD showed significant effects on the trait heifer pregnancy P &amp;lt; 0.05 and P &amp;lt; 0.01, respectively, reducing the progeny rate up to 15%. These novel findings in Angus present new candidate genomic regions putatively carrying lethal and semi-lethal alleles providing opportunities to reduce the rates of embryonic losses or death of offspring which could improve fertility and fitness in beef cattle populations.

A 36 Mb terminal deletion of chromosome 2BL is responsible for a wheat semi-dwarf mutation

Reduced plant height is one of the most important traits related to lodging resistance and crop yield. The use of reduced height genes has been one of the main features in breeding modern high-yielding wheat varieties with less lodging. A spontaneous dwarf mutant DD399 was identified in a high yielding, gibberellic acid (GA)-insensitive, lodging-resistant variety Nongda 399 (ND399). Significant differences in upper internode lengths between mutant DD399 and wild type ND399 were caused by reduced cell elongation. The plant height of ND399 × DD399 F1 hybrids was intermediate between the parents, indicating incomplete dominance or a dose–response effect of a reduced height gene. Plant height showed continuous distribution in the F2 population, and segregation distortion was observed among the 2292 F2:3 progenies. The reduced height mutation was characterized by Illumina 90 K iSelect SNP genotyping and bulked segregant RNA-Seq (BSR-Seq) analysis of the segregating population. A concentrated cluster of polymorphic SNPs associated with the reduced height phenotype was detected in the distal region of chromosome arm 2BL. Co-segregation of reduced height phenotype with the clustered markers revealed a 36 Mb terminal deletion of chromosome 2BL in mutant DD399.

Alien genomic introgressions enhanced fiber strength in upland cotton (Gossypium hirsutum L.)

Cotton (Gossypium) is a worldwide natural fiber crop. Fiber quality improvement lags far behind that of fiber yield. Although interspecific hybridization contributes significantly to improve fiber quality, the mechanism of alien genomic introgression to improve fiber quality has rarely been reported. In this study, a superior fiber-strength line (J02−508) derived from interspecific hybridization was used to dissect the genetic and genomic bases for fiber quality by forward-genetics technologies. Both F2 and F2:5 populations were developed from a cross between superior line J02−508 and a weak fiber-quality line (ZRI015). Based on the linkage map constructed from the F2:5 population, 27 stable quantitative trait loci (QTL) were detected for fiber yield and quality. Unexpectedly, an abnormally high segregation distortion ratio was found for all chromosomes (reaching an average of 83.13 % for each chromosome), and the highest ratio of segregation distortion markers (SDMs) was on chromosome D08, reaching 99.39 %. Taking the SDMs into account, a distinct genome region on chromosome D08 was identified, which had a sizeable physical interval (∼53 Mb length) with low recombination frequency and was significantly associated with fiber strength (named qFS_D08, LOD value = 11.49). Additionally, by integrating different approaches, we initially confirmed that this region was an alien fragment introgressed from wild diploid cotton, G. thurberi (D1), accounting for nearly 77 % of the length of chromosome D08 in the J02−508 genome. We provided molecular evidence for fiber strength improvement caused by introgression. This study is also beneficial to understand the importance of interspecific hybridization for improving fiber strength during cotton breeding.

Genetic and comparative mapping of Lupinus luteus L. highlight syntenic regions with major orthologous genes controlling anthracnose resistance and flowering time

Anthracnose susceptibility and ill-adapted flowering time severely affect Lupinus luteus yield, which has high seed protein content, is excellent for sustainable agriculture, but requires genetic improvement to fulfil its potential. This study aimed to (1) develop a genetic map; (2) define collinearity and regions of synteny with Lupinus angustifolius; and (3) map QTLs/candidate genes for anthracnose resistant and flowering time. A few linkage groups/genomic regions tended to be associated with segregation distortion, but did not affect the map. The developed map showed collinearity, and syntenic regions with L. angustifolius. Major QTLs were mapped in syntenic regions. Alleles from the wild parent and cultivar, explained 75% of the phenotypic variance for anthracnose resistance and 83% for early flowering, respectively. Marker sequences flanking the QTLs showed high homology with the Lanr1 gene and Flowering-locus-T of L. angustifolius. This suggests orthologous genes for both traits in the L. luteus genome. The findings are remarkable, revealing the potential to combine early flowering/anthracnose resistant in fulfilling yield capacity in L. luteus, and can be a major strategy in the genetic improvement and usage of this species for sustainable protein production. Allele sequences and PCR-marker tagging of these genes are being applied in marker assisted selection.

A cross-eyed geneticist’s view VI. Segregation distortion in Drosophila melanogaster: Recent progress in solving ‘an esoteric puzzle’

Segregation distortion refers to an unusual genetic phenomenon in diploid organisms by which the two alleles at a locus in a parent are not recovered in the classical 1:1 Mendelian ratio in its offspring. The Drosophila melanogaster neogene Sd was created by a duplication breakpoint on the left arm of chromosome 2 (2L), and encodes a truncated RanGAP protein with normal GTPase activity but which mis-localizes to the nucleus and disrupts Ran gradients. Male flies carrying Sd exhibit segregation distortion for the Rsp locus on the right arm of chromosome 2 (2R). Specifically, spermatids inheriting chromosome 2 with the Sd+ Rsps(s) genotype, in heterozygous males of genotype Sd Rspi/ Sd+ Rsps(s), fail to develop properly so that the majority of progeny (approaching 100%) carry just the Sd Rspichromosome. One recent paper reported novel RNAi-expressing transgenes with Sd-mimicking properties; and another reported localization of an X-linked suppressor which restores Mendelian transmission. This article highlights how Drosophila genetics resources made this possible, and the significance of these findings to nucleus-cytoplasm transactions of interest to the wider cell biology community.

Genetic analysis of some morphological traits in synthetic $$\times $$ naturally polyploid cotton derivatives

Cotton has received attention of geneticists since more than a century. Gossypium hirsutum, the predominantly cultivated cotton species worldwide, has a narrow genetic base. It is important to broaden its genetic base through introgression of novel alleles from related species. Here, we report the development and characterization of a backcross population derived from the hybridization of a 'synthetic' (derived by crossing and chromosomal doubling of nonprogenitor Gossypium species) and natural tetraploid upland cotton. 'Synthetic' was observed to be male-sterile and thus, was used as the female parent. A total of 7434 flowers were pollinated to obtain 1868 BC1F1 seeds by direct and reciprocal crosses. Characterization of the experimental plant material was conducted in the field for several morphological traits such as pubescence on the stem, leaf, petiole and bract, presence/absence of petal spot, petal margin colouration and stamen filament colouration. Genetic analysis revealed that petal margin colouration phenotype was governed by a single dominant gene, whereas the petal spot and filament colouration phenotypes manifested segregation distortion. None of the BC1F1 plants was devoid of trichomes thus demonstrating that presence of trichomes is dominant over their absence. Modern upland cotton cultivars are usually devoid of petal spot, petal margin colouration and stamen filament colouration. These floral anthocyanin pigmentation characteristics, if fixed in the cotton germplasm, may serve as diagnostic features for the identification of cultivars during DUS testing as well as in the maintenance breeding programmes.

Extensive Recombination Suppression and Epistatic Selection Causes Chromosome-Wide Differentiation of a Selfish Sex Chromosome in Drosophila pseudoobscura.

Sex-Ratio (SR) chromosomes are selfish X-chromosomes that distort Mendelian segregation and are commonly associated with inversions. These chromosomal rearrangements suppress recombination with Standard (ST) X-chromosomes and are hypothesized to maintain multiple alleles important for distortion in a single large haplotype. Here, we conduct a multifaceted study of the multiply inverted Drosophila pseudoobscura SR chromosome to understand the evolutionary history, genetic architecture, and present-day dynamics that shape this enigmatic selfish chromosome. The D.pseudoobscura SR chromosome has three nonoverlapping inversions of the right arm of the metacentric X-chromosome: basal, medial, and terminal. We find that 23 of 29Mb of the D.pseudoobscuraX-chromosome right arm is highly differentiated between the Standard and SR arrangements, including a 6.6Mb collinear region between the medial and terminal inversions. Although crossing-over is heavily suppressed on this chromosome arm, we discover it is not completely eliminated, with measured rates indicating recombination suppression alone cannot explain patterns of differentiation or the near-perfect association of the three SR chromosome inversions in nature. We then demonstrate the ancient basal and medial inversions of the SR chromosome contain genes sufficient to cause weak distortion. In contrast, the younger terminal inversion cannot distort by itself, but contains at least one modifier gene necessary for full manifestation of strong sex chromosome distortion. By parameterizing population genetic models for chromosome-wide linkage disequilibrium with our experimental results, we infer that strong selection acts to maintain the near-perfect association of SR chromosome inversions in present-day populations. Based on comparative genomic analyses, direct recombination experiments, segregation distortion assays, and population genetic modeling, we conclude the combined action of suppressed recombination and strong, ongoing, epistatic selection shape the D.pseudoobscura SR arrangement into a highly differentiated chromosome.

A new genetic locus for self-compatibility in the outcrossing grass species perennial ryegrass (Lolium perenne).

BackgroundSelf-incompatibility (SI) is a physiological mechanism that many flowering plants employ to prevent self-fertilization and maintain heterozygosity. In the grass family this is known to be controlled by a two locus (S-Z) system; however, the SI system is intrinsically leaky. Modifier genes of both the S and Z loci and a further locus, T, are known to override SI leading to self-fertilization and self-seed production. This has implications for the ecological and evolutionary success as well as the commercial breeding of grasses. Here we report a study where the genetic control of self-compatibility (SC) was determined from the results of self-pollinating an F2 population of perennial ryegrass from two independently derived inbred lines produced by single-seed descent.Methods In vitro self-pollinations of 73 fertile plants were analysed. A genetic association analysis was made with a panel of 1863 single-nucleotide polymorphism (SNP) markers, generated through genotype-by-sequencing methodology. Markers were placed on a recombination map of seven linkage groups (LGs) created using Joinmap v.5. The seed set on self- and open-pollinated inflorescences was determined on 143 plants, including the 73 plants analysed for self-pollination response.Key ResultsSelf-pollinations revealed a bimodal distribution of percentage SC with peaks at 50 and 100 %. A single quantitative trait locus (QTL) was identified with peak association for marker 6S14665z17875_11873 that mapped to LG 6. Peak position was associated with maximum marker segregation distortion. The self-compatible plants were equally fecund after self- and open pollination.ConclusionsThis is the first report in the Poaceae family of an SC locus located on LG 6. This new SC QTL discovery, as well as indicating the complex nature of the pollen–stigma recognition process and its evolutionary significance, provides an additional source of SC for breeding perennial ryegrass.

The Genetic Architecture of Post-Zygotic Reproductive Isolation Between Anopheles coluzzii and An. quadriannulatus.

The Anopheles gambiae complex is comprised of eight morphologically indistinguishable species and has emerged as a model system for the study of speciation genetics due to the rapid radiation of its member species over the past two million years. Male hybrids between most An. gambiae complex species pairs are sterile, and some genotype combinations in hybrid males cause inviability. We investigated the genetic basis of hybrid male inviability and sterility between An. coluzzii and An. quadriannulatus by measuring segregation distortion and performing a QTL analysis of sterility in a backcross population. Hybrid males were inviable if they inherited the An. coluzzii X chromosome and were homozygous at one or more loci in 18.9 Mb region of chromosome 3. The An. coluzzii X chromosome has a disproportionately large effect on hybrid sterility when introgressed into an An. quadriannulatus genetic background. Additionally, an epistatic interaction between the An. coluzzii X and a 1.12 Mb, pericentric region of the An. quadriannulatus 3L chromosome arm has a statistically significant contribution to the hybrid sterility phenotype. This same epistatic interaction occurs when the An. coluzzii X is introgressed into the genetic background of An. arabiensis, the sister species of An. quadriannulatus, suggesting that this may represent one of the first Dobzhansky–Muller incompatibilities to evolve early in the radiation of the Anopheles gambiae species complex. We describe the additive effects of each sterility QTL, epistatic interactions between them, and genes within QTL with protein functions related to mating behavior, reproduction, spermatogenesis, and microtubule morphogenesis, whose divergence may contribute to post-zygotic reproductive isolation between An. coluzzii and An. quadriannulatus.

A hybrid sterile locus leads to the linkage drag of interspecific hybrid progenies

Interspecific hybridization plays an important role in rice breeding by broadening access to desirable traits such as disease resistance and improving yields. However, interspecific hybridization is often hindered by hybrid sterility, linkage drag, and distorted segregation. To mine for favorable genes from Oryza glaberrima, we cultivated a series of BC4 introgression lines (ILs) of O. glaberrima in the japonica rice variety background (Dianjingyou 1) in which the IL-2769 (BC4F10) showed longer sterile lemmas, wider grains and spreading panicles compared with its receptor parent, suggesting that linkage drag may have occurred. Based on the BC5F2 population, a hybrid sterility locus, S20, a long sterile lemma locus, G1-g, and a new grain width quantitative trait locus (QTL), qGW7, were mapped in the linkage region about 15 centimorgan (cM) from the end of the short arm of chromosome 7. The hybrid sterility locus S20 from O. glaberrima eliminated male gametes of Oryza sativa, and male gametes carrying the alleles of O. sativa in the heterozygotes were aborted completely. In addition, the homozygotes presented a genotype of O. glaberrima, and homozygous O. sativa were not produced. Surprisingly, the linked traits G1-g and qGW7 showed similar segregation distortion. These results indicate that S20 was responsible for the linkage drag. As a large number of detected hybrid sterility loci are widely distributed on rice chromosomes, we suggest that hybrid sterility loci are the critical factors for the linkage drag in interspecific and subspecific hybridization of rice.