A Novel Segregation Distortion in Intraspecific Population of Asian Cotton(Gossypium arboretum L.)Detected by Molecular Markers

The segregation ratio of markers in an F2 population derived from Rudongjijiaoyaguo （Rdjjyg） and Zhongmian971 （Zm971） was studied using 3 morphological markers, 20 SSR markers, and ll SRAP markers. Totally, 24 markers （77.42%） showed a distorted segregation and all of them skewed toward the female genotype, which was peculiar in recent cotton research. All the three types of SSR markers and SRAP marker showed distorted segregation, but the morphological markers （Purple stem, Okra leaf, and Red spot color） were normally segregated. This indicated that such a novel segregation distortion phenomenon resulted from interior genetic factors, The allele frequency and the distribution of different genotype frequencies in the F2 population were analyzed in codominant markers, to find out factors attributed to distorted segregation. Most of them implied distorted allele frequency, but it was normal genotype frequency, which showed that these markers were influenced at the gamete level.

A SSR Linkage Map of Maizex Teosinte F_2 Population and Analysis of Segregation Distortion

In this study,a linkage genetic map was constructed using a F2 population derived from a cross between a elite maize inbred,B73,and its progenitor,Teosinte（Z.mays ssp.mexicana）,through 205 simple sequence repeat（SSR） markers and one morphological marker.By Mapmaker 3.0,polymorphic markers were clustered into 10 groups,covering 10 chromosomes of maizexteosinte,with a total length of 2 002.4 cM and an average interval of 9.7 cM.Genotyping errors were detected using R/QTL（LOD=2.0） in 109 markers referring to 176 individuals,distributed across all 10 chromosomes with a ratio 1.2%.Projected error loci were re-run and 304 out of the 460 were confirmed as errors and replaced.A new linkage map was constructed,in which markers maintained the same order but the total map length decreased to 1 947.8 cM,with an average interval of 9.4 cM between markers.In total,25.2%（P0.05） markers were identified to have segregation distortion,in which 34.6% deviated towards the pollination parent（B73）,30.8% deviated towards Teosinte,32.7% deviated towards heterozygote and 1.9% deviated towards both parents.This map was also compared with published maizexteosinte and maize IBM map.

Genome-wide search for segregation distortion loci associated with the expression of complex traits in Populus tomentosa

Segregation distortion of molecular markers has been reported in a broad range of organisms. It has been detected in an interspecific BC1 Populus pedigree established by controlled crossing between clone ＂LM50＂ （Populus tomentosa） and its hybrid clone ＂TB01＂ （P. tomentosa × p. bolleana）. The study with a total of 150 AFLP markers （approximately 18.9% of the total loci） exhibited significant deviation from the Mendelian ratio （1：1） （p〈0.01）. Twenty-five percent of the markers were mapped on the parental specific genetic linkage maps of clones ＂LM50＂ and ＂TB01＂ with a pseudo-test-cross mapping strategy. Twelve linkage groups had markers with skewed segregation ratios, but the major regions were on linkage groups TLG2, TLG4 and TLG6 in the linkage map of clone ＂LM50＂. We also analyzed the association between distorted loci and expression of complex traits with Mapmaker/QTL software. A total of 16 putative QTLs affecting 12 traits were identified in the distorted regions on seven linkage groups. Therefore we could detect the distribution of skewed loci along the entire genome and identify the association between quantitative traits and segregation loci via genetic mapping in an interspecific BC1 P. tomentosa family. Furthermore, the genetic nature and possible causes of these segregation distortions for differentiation between female and male parents were also discussed.

Genetic Analysis of Segregation Distortion of Molecular Markers in Maize RIL Population

A RIL population was used in this study, which was derived from a cross between a temperate maize germplasm inbred line B31-1 and a tropical maize germplasm inbred lines Huangzao 4. A genetic linkage map was constructed comprising of 153 polymorphic markers. Among the 153 polymorphic markers, 82 markers showed the significantly segregation distortion（P〈0.05）, favoring either the marker alleles of female parent 1331-1（62.50%） or male parent Huangzao 4（37.50%）. Segregation distortion marker distribution along the present molecular maps of maize was far from uniform, with clusters of tightly linked loci and single marker. Nine segregation distortion regions were detected on 10 chromosomes, indicating that possible causes for segregation deviation of molecular markers are genetic selection.

Genetic map construction and functional characterization of genes within the segregation distortion regions(SDRs)in the F_(2:3) populations derived from wild cotton species of the D genome

Background:Segregation 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.Results:The consensus linkage map had 1492 markers across the 13 linkage groups with a map size of 1467.445 cM and an average marker distance of 1.0370 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 D507,2308 and 3730 genes were mined,respectively,and were found to belong to 1117 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,gramiR5207,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.Conclusion:The results indicated the critical role of the SDRs in the evolution of the key regulatory genes in plants.

Recurrent breakdown and rebalance of segregation distortion in the genomes: battle for the transmission advantage

Mendel’s laws state that each of the two alleles would segregate during gamete formation and show the same transmission ratio in the next generation.However,an unexpected biased allele transmission was first detected in Drosophila a century ago,and was subsequently observed in other animals,plants,and microorganisms.Such segregation distortion(SD)shows substantial effects in population structure and fitness of the progenies,which would ultimately lead to reproductive isolation and speciation.Here,we trace the early investigations on the violation of Mendelian genetic principle,which appears as a wideexistence phenomenon rather than a case of exception.The occurence of SD in the whole genome was observed in a number of plant species at the single-and multi-locus level.Biased transmission ratio might occur at meiosis stage due to asymmetric movement of the chromosome;transmission ratio advantage is also caused by interaction and battle between the alleles from respective genomes at the genetic and molecular level.The origin of a SD system is likely to be determined by coevolution of the killer and protector via recurrent breakdown or rebalance loop.These updated understandings also promote genetic improvement of hybrid crops.

Genetic Analysis of Distorted Segregation Ratio of Mating Types AmongBasidiospores in Lentinula edodes

This study prepared 17 strains of Lentinula edodes, including wild and cultivated strains as materials, and statistically analyzed the ratios of spores from different aspects via mating types＇ analysis and the OWE-SOJ technique. The results from this study first systematically identified skewed expected distribution of mating-type factors segregation in Lentinula edodes spores has commonly statistical meanings in wild and cultivated strains. Genetic analysis of positive and negative parental-recombined fruiting showed that the nuclear type of F1 progeny spores among those strains segregated through theoretical distribution mainly depended on the combined state of parental dikaryons, and the predominant spores were those with the mating type identical to the dikaryotic parent, indicating that the genetic basis of segregation distortion of spores is different from that of protoplast monokaryons in which the B factor takes predominant responsibility for that phenomenon, and it cooperates A factor with B factor to influence the ratio of spores.

Optimization of a Reaction System of Sequence Related Amplified Polymorphism and Segregation of Polymorphic Loci in an F_2 Population of Rice

An effective PCR protocol for detecting the sequence related amplified polymorphism （SRAP） in rice was developed. One hundred and ten pairs of SRAP primers were used for segregation analysis in an F2 population derived from a cross between Shennong 606 and Lijiangxintuanheigu. Among the 110 primer pairs, 35 pairs generated 143 polymorphic bands with an average of 4.09 polymorphic bands per primer pair, and 24 pairs （16.78%） showed the genetic distortion （P〈0.05）. Of the 24 primer pairs, 12 pairs deviated toward the male parent Shennong 606 and 11 pairs toward the female parent Lijiangxintuanheigu, only one toward heterozygote. It was found that the segregation distortion might be caused by the joint gametic and zygotic effects.

Detection of Distorted Segregation in Genotype of Pollen Calli Derived from Hybrid F_1 of Cultivated Rice (Oryza sativa L.) Using SSR Markers

S-a, S-b and S-c are three loci for F1 pollen sterility in cultivated rice （Oryza sativa L.）. Taichung 65 （T65） is all Sj/Sj at these three loci, while its F1 pollen sterile near-isogenic lines, TISL2 （S-b）, TISL4 （S-a） and TISL5 （S-c） is Sj/Sj according to their respective sterility locus. Using SSR molecular marker to detect the segregation of the allele Si and Sj in pollen calli population induced from different hybrid F1, which have different pollen sterility locus, showed that the segregation of allele Si and Sj was distorted. The distorted direction of pollen calli population in vitro was not the same as F2 population in vivo. The quantities of pollen callus carrying Sj were much more than that of carrying Siat S-a and S-c locus, the ratio of Si and Sj were 1：4.81 and 1：1.96 respectively. But the opposite tendency was observed at S-b locus, the ratio of Si and Sj being 1：0.35. At the same time, all these results were undisturbed by either culture medium or culture period.

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.

The genetic basis and process of inbreeding depression in an elite hybrid rice

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

QTL Scanning for Rice Yield Using a Whole Genome SNP Array

High-throughput SNP genotyping is widely used for plant genetic studies. Recently, a RICE6K SNP array has been developed based on the Illumina Bead Array platform and Infinium SNP assay technology for genome-wide evaluation of allelic variations and breeding applications. In this study, the RICE6K SNP array was used to genotype a recombinant inbred line （RIL） population derived from the cross between the indica variety, Zhenshan 97, and the japonica variety, Xizang 2. A total of 3324 SNP markers of high quality were identified and were grouped into 1495 recombination bins in the RIL population. A high-density linkage map, consisting of the 1495 bins, was developed, covering 1591.2 cM and with average length ofl.1 cM per bin. Segregation distortions were observed in 24 regions of the 11 chromosomes in the RILs. One half of the distorted regions contained fertility genes that had been previously reported. A total of 23 QTLs were identified for yield. Seven QTLs were firstly detected in this study. The positive alleles from about half of the identified QTLs came from Zhenshan 97 and they had lower phenotypic values than Xizang 2. This indicated that favorable alleles for breeding were dispersed in both parents and pyramiding favorable alleles could develop elite lines. The size of the mapping population for QTL analysis using high throughput SNP genotyping platform is also discussed.

Genetic load in marine animals： a review

Marine invertebrates and fish are well known for their remarkable genetic diversity, which is commonly explained by large population size and the characteristic dispersive nature of their early, planktonic life history. Other potential sources of diversity in marine animals, such as a higher mutation rate, have been much less considered, though evidence for a high genetic load in marine bivalves has been accumulating for nearly half a century. In this review, I examine evidence for a higher genetic load in marine animals from studies of molecular marker segregation and linkage over the last 40 years, and survey recent work examining mutational load with molecular evolution approaches. Overall, marine animals appear to have higher genetic load than terrestrial animals （higher dn/ds ratios, inbreeding load, and segregation dis＇tortion）, though results are mixed for marine fish and data are lacking for many marine animal groups. Bivalves （oysters） have the highest loads observed among marine animals, comparable only to long-lived plants; however, more data is needed from other bivalves and more marine invertebrate taxa generally. For oysters, a higher load may be related to a chronically lower effective population size that, in concert with a higher mutational rate, elevate the number of deleterious mutations observed. I suggest that future studies use high-throughput sequencing approaches to examine （1） polymorphism in genomescale datasets across a wider range of marine animals at the population level and （2） intergenerational mutational changes between parents and offspring in crosses of aquaculture species to quantify mutation rates.

No evidence for female discrimination against male house mice carrying a selfish genetic element

Meiotic drivers distort transmission to the next generation in their favor, with detrimental effects on the fitness of their homologues and the rest of the genome. Male carriers of meiotic drivers commonly inflict costs on their mates through genetic incompatibility, reduced fecundity, or biased brood sex ratios. Given these costs, evidence for female discrimination against male carriers is surprisingly rare. One of few examples is the t haplotype in house mice, a meiotic driver that shows strong transmission distortion in males and is typically homozygote lethal. As a consequence, mating between 2 t heterozygous （＋/t） mice leads to high embryo mortality. Previous experiments showing that＋/t females avoid this incompatibility cost by preferring ＋/＋ versus ＋/t males have inferred preference based on olfactory cues or brief social interactions. Evidence from mating contexts in laboratory settings and semi-natural populations has been inconclusive. Here, we investigated female choice from a large number of no-choice mating trials. We found no evidence for discrimination against＋/t males based on mating, remating, and copulatory behavior. Further, we found no evidence for avoidance of incompatibility through selective interactions between game- tes. The likelihood of mating showed significant effects of female weight and genotype, suggesting that our test paradigm enabled females to exhibit mate choice. We discuss the strengths and limitations of our approach. By explicitly considering selection at both the individual and gene level, we argue why precopulatory female discrimination by＋/t females may be less evolutionarily stable than discrimination by all females based on postcopulatory mechanisms.