Efficiency of genome-wide association studies in random cross populations

Genome-wide association studies (GWAS) with plant species have employed inbred lines panels. We evaluated the efficiency of GWAS in non-inbred and inbred populations and assessed factors affecting GWAS. Fifty samples of 800 individuals from populations with linkage disequilibrium were simulated. Individuals were genotyped for 10,000 single nucleotide polymorphisms (SNPs) and phenotyped for traits controlled by ten quantitative trait loci (QTLs) and 90 minor genes, assuming different degrees of dominance and broad sense heritabilities of 40 and 80%. The average SNP density was 0.1 centiMorgan (cM) and the QTL heritabilities ranged from 3.2 to 11.8%. The results for random cross populations evidenced that to increase the QTL detection power, the additive-dominance model must be fitted for traits controlled by dominance effects but must not be fitted for traits showing no dominance. The power of detection was maximized by increasing the sample size to 400 and the false discovery rate (FDR) to 5%. The average power of detection for the low, intermediate, and high heritability QTLs achieved 52.4, 87.0, and 100.0%, respectively. Assuming sample sizes of 400 and 800, the observed FDR was equal to or lower than the specified level of significance. The association mapping was highly precise, since at least 97% of the declared QTLs were detected by the SNP inside it (average bias of 0.4 cM). Besides controlling the FDR, relatedness (and identity by state) efficiently controls the number of significant associations outside the QTL interval (not all false positive associations). The analysis of the inbred random cross population provided essentially the same results as the non-inbred populations.     

Effect of population structure corrections on the results of association mapping tests in complex maize diversity panels

Association mapping of sequence polymorphisms underlying the phenotypic variability of quantitative agronomical traits is now a widely used method in plant genetics. However, due to the common presence of a complex genetic structure within the plant diversity panels, spurious associations are expected to be highly frequent. Several methods have thus been suggested to control for panel structure. They mainly rely on ad hoc criteria for selecting the number of ancestral groups; which is often not evident for the complex panels that are commonly used in maize. It was thus necessary to evaluate the effect of the selected structure models on the association mapping results. A real maize data set (342 maize inbred lines and 12,000 SNPs) was used for this study. The panel structure was estimated using both Bayesian and dimensional reduction methods, considering an increasing number of ancestral groups. Effect on association tests depends in particular on the number of ancestral groups and on the trait analyzed. The results also show that using a high number of ancestral groups leads to an over-corrected model in which all causal loci vanish. Finally the results of all models tested were combined in a meta-analysis approach. In this way, robust associations were highlighted for each analyzed trait.     

Associations between quantitative traits and enzyme loci in the F2 population of a maize hybrid

Summary Univariate and multivariate analyses were used to identify associations between eight enzyme marker loci and 11 quantitative traits of maize (Zea mays L.). The material analyzed included inbred lines Wf9 and Pa405, single-cross hybrid Wf9 X Pa405, and the F2 generation of the selfed single-cross hybrid. Each enzyme locus assayed was associated with at least one quantitative trait, and all quantitative traits were associated with genotypes at particular enzyme loci. Significant associations also were found between the level of heterozygosity per individual and nine of 11 quantitative traits. The total contribution to heterosis, for seed yield per plant, of genes linked with the eight enzyme loci, was 27% of the F2 mean and 18% of the difference in mean between the F1 hybrid and the inbred parents. Genes linked with Glu1 accounted for nearly one third of the total dominance effect detected by the eight enzyme loci. The chromosome segments marked by loci with significant effects on seed yield were markedly overdominant. The large heterotic effects of chromosome segments marked by particular loci suggest that enzyme loci could be used to help transfer genes responsible for heterosis to inbred lines. We conclude that analyses of additional inbred lines, F1 hybrids, and F2 populations in more environments will halp identify specific associations between enzyme loci, or chromosome segments which they mark, and important agronomic traits.Cooperative investigations of the USDA, ARS and Dept. of Plant Sciences, South Dakota State Univ. (SDSU), Brookings, Journal Series No. 2039; and the Institute of Animal Resource Ecology, Univ. of British Columbia, Vancouver, B.C. V6T 1W5, Canada     

Gene and QTL detection in a three-way barley cross under selection by a mixed model with kinship information using SNPs

Quantitative trait locus (QTL) detection is commonly performed by analysis of designed segregating populations derived from two inbred parental lines, where absence of selection, mutation and genetic drift is assumed. Even for designed populations, selection cannot always be avoided, with as consequence varying correlation between genotypes instead of uniform correlation. Akin to linkage disequilibrium mapping, ignoring this type of genetic relatedness will increase the rate of false-positives. In this paper, we advocate using mixed models including genetic relatedness, or ‘kinship’ information for QTL detection in populations where selection forces operated. We demonstrate our case with a three-way barley cross, designed to segregate for dwarfing, vernalization and spike morphology genes, in which selection occurred. The population of 161 inbred lines was screened with 1,536 single nucleotide polymorphisms (SNPs), and used for gene and QTL detection. The coefficient of coancestry matrix was estimated based on the SNPs and imposed to structure the distribution of random genotypic effects. The model incorporating kinship, coancestry, information was consistently superior to the one without kinship (according to the Akaike information criterion). We show, for three traits, that ignoring the coancestry information results in an unrealistically high number of marker–trait associations, without providing clear conclusions about QTL locations. We used a number of widely recognized dwarfing and vernalization genes known to segregate in the studied population as landmarks or references to assess the agreement of the mapping results with a priori candidate gene expectations. Additional QTLs to the major genes were detected for all traits as well.     

Quantitative genetic variation of metabolism in the nymphs of the sand cricket, Gryllus firmus, inferred from an analysis of inbred-lines

Compared with morphological and life history traits, quantitative genetic variation of metabolic and related traits in animals has been poorly studied. We used flow-through VCO(2) respirometry and simultaneous activity measurement on nymphs of the sand cricket (Gryllus firmus) from inbred lines to estimate broad-sense heritability of four metabolic variables. In addition, we measured a number of linear dimensions in the adults from the same inbred lines. There were significant multivariate effects of inbred lines for all traits and broad-sense heritability for physiological traits was 4.5%, 5.2%, 10.3% and 8.5% for average, resting, minimum and maximum CO(2) production in nymphs, respectively. Though the MANOVA indicated significant genetic variation among inbred lines in adult morphology, the broad-sense heritabilities were relatively low ranging from 0-18%. Our results indicate that the heritabilities of metabolic measures are large enough to potentially respond to selection.     

Heterosis for viability,fecundity, and male fertility in Drosophila melanogaster: comparison of mutational and standing variation.

If genetic variation for fitness traits in natural populations ("standing" variation) is maintained by recurrent mutation, then quantitative-genetic properties of standing variation should resemble those of newly arisen mutations. One well-known property of standing variation for fitness traits is inbreeding depression, with its converse of heterosis or hybrid vigor. We measured heterosis for three fitness traits, pre-adult viability, female fecundity, and male fertility, among a set of inbred Drosophilia melanogaster lines recently derived from the wild, and also among a set of lines that had been allowed to accumulate spontaneous mutations for over 200 generations. The inbred lines but not the mutation-accumulation (MA) lines showed heterosis for pre-adult viability. Both sets of lines showed heterosis for female fecundity, but heterosis for male fertility was weak or absent. Crosses among a subset of the MA lines showed that they were strongly differentiated for male fertility, with the differences inherited in autosomal fashion; the absence of heterosis for male fertility among the MA lines was therefore not caused by an absence of mutations affecting this trait. Crosses among the inbred lines also gave some, albeit equivocal, evidence for male fertility variation. The contrast between the results for female fecundity and those for male fertility suggests that mutations affecting different fitness traits may differ in their average dominance properties, and that such differences may be reflected in properties of standing variation. The strong differentiation among the MA lines in male fertility further suggests that mutations affecting this trait occur at a high rate.     

Effects of inbreeding on aversive learning in Drosophila

Inbreeding adversely affects life history traits as well as various other fitness‐related traits, but its effect on cognitive traits remains largely unexplored, despite their importance to fitness of many animals under natural conditions. We studied the effects of inbreeding on aversive learning (avoidance of an odour previously associated with mechanical shock) in multiple inbred lines of Drosophila melanogaster derived from a natural population through up to 12 generations of sib mating. Whereas the strongly inbred lines after 12 generations of inbreeding (0.75 < F < 0.93) consistently showed reduced egg‐to‐adult viability (on average by 28%), the reduction in learning performance varied among assays (average = 18% reduction), being most pronounced for intermediate conditioning intensity. Furthermore, moderately inbred lines (F = 0.38) showed no detectable decline in learning performance, but still had reduced egg‐to‐adult viability, which indicates that overall inbreeding effects on learning are mild. Learning performance varied among strongly inbred lines, indicating the presence of segregating variance for learning in the base population. However, the learning performance of some inbred lines matched that of outbred flies, supporting the dominance rather than the overdominance model of inbreeding depression for this trait. Across the inbred lines, learning performance was positively correlated with the egg‐to‐adult viability. This positive genetic correlation contradicts a trade‐off observed in previous selection experiments and suggests that much of the genetic variation for learning is owing to pleiotropic effects of genes affecting functions related to survival. These results suggest that genetic variation that affects learning specifically (rather than pleiotropically through general physiological condition) is either low or mostly due to alleles with additive (semi‐dominant) effects.     

不结球白菜自交不亲和S单元型的鉴定研究

依据甘蓝SRK基因保守序列设计SRK特异引物并进行验证,通过PCR-RFLP法分析16份不结球白菜自交系材料的SRK基因的多态性,根据其差异鉴定不结球白菜S单元型及自交不亲和性.结果表明:16个不结球白菜自交系SRK基因共产生6种不同的带型,其中有1个是强自交不亲和系,4个是弱自交不亲和系,且与田间测定的亲和指数相符,说明利用SRK基因的多态性鉴定不结球白菜纯合自交系的自交不亲和性和S单元型是可行的.同时对部分材料的SRK基因的核苷酸序列进行分析验证,表明相同类型SRK基因序列一致性较高,且SRK基因存在明显的单核苷酸多态性,为进一步自交不亲和性的研究奠定了基础.     

Development and mapping of SSR markers for maize

Microsatellite or simple sequence repeat (SSR) markers have wide applicability for genetic analysis in crop plant improvement strategies. The objectives of this project were to isolate, characterize, and map a comprehensive set of SSR markers for maize (Zea mays L.). We developed 1051 novel SSR markers for maize from microsatellite-enriched libraries and by identification of microsatellite-containing sequences in public and private databases. Three mapping populations were used to derive map positions for 978 of these markers. The main mapping population was the intermated B73 × Mo17 (IBM) population. In mapping this intermated recombinant inbred line population, we have contributed to development of a new high-resolution map resource for maize. The primer sequences, original sequence sources, data on polymorphisms across 11 inbred lines, and map positions have been integrated with information on other public SSR markers and released through MaizeDB at URL:www.agron.missouri.edu. The maize research community now has the most detailed and comprehensive SSR marker set of any plant species.     

The Collaborative Cross, a groundbreaking tool to tackle complex traits

Complex traits, like the susceptibility to common diseases, are controlled by numerous genomic regions which individual effect is generally weak. These observations led geneticists to develop an experimental system to dissect the genetic of complex traits in the mouse. The Collaborative Cross (CC) is a genetic reference population of over 300 inbred lines derived from eight inbred strains of three Mus musculus sub-species that captures 90% of the genetic variation known in the mouse genome. We present here the generation and the characteristics of the CC and we report the results of the first experiments with partially inbred CC lines.     

Dent and Flint maize diversity panels reveal important genetic potential for increasing biomass production

Key message

Genetic and phenotypic analysis of two complementary maize panels revealed an important variation for biomass yield. Flowering and biomass QTL were discovered by association mapping in both panels.

Abstract

The high whole plant biomass productivity of maize makes it a potential source of energy in animal feeding and biofuel production. The variability and the genetic determinism of traits related to biomass are poorly known. We analyzed two highly diverse panels of Dent and Flint lines representing complementary heterotic groups for Northern Europe. They were genotyped with the 50 k SNP-array and phenotyped as hybrids (crossed to a tester of the complementary pool) in a western European field trial network for traits related to flowering time, plant height, and biomass. The molecular information revealed to be a powerful tool for discovering different levels of structure and relatedness in both panels. This study revealed important variation and potential genetic progress for biomass production, even at constant precocity. Association mapping was run by combining genotypes and phenotypes in a mixed model with a random polygenic effect. This permitted the detection of significant associations, confirming height and flowering time quantitative trait loci (QTL) found in literature. Biomass yield QTL were detected in both panels but were unstable across the environments. Alternative kinship estimator only based on markers unlinked to the tested SNP increased the number of significant associations by around 40 % with a satisfying control of the false positive rate. This study gave insights into the variability and the genetic architectures of biomass-related traits in Flint and Dent lines and suggests important potential of these two pools for breeding high biomass yielding hybrid varieties.     

Relationship of restriction fragment length polymorphisms to single-cross hybrid performance of maize

Summary Isozymes and restriction fragment length polymorphisms (RFLPs) have been proposed for use in varietal identification and selection for agronomic traits. Although the use of isozymes for these purposes has been well documented, evaluation of the efficacy of RFLP technology as applied to crop improvement is far from complete. This investigation was conducted to study the relationship between RFLP-derived genotypes and heterotic patterns of a group of maize (Zea mays L.) inbred lines. A total of 22 inbreds was crossed to four testers (B73, B76, Mo17, and Va26) in combinations that minimized crossing within heterotic groups. Forty-seven single-cross progeny were subsequently evaluated for several agronomic traits (including grain yield and moisture, ear height, and root lodging) over 2–4 consecutive years at two to four Iowa locations in a randomized complete-block design. The inbred lines were subjected to RFLP analysis, which involved 47 genomic clones and the restriction enzymes EcoRI and HindIII. Hybrid RFLP patterns were predicted from their inbred parents. Modified Roger's distances were computed to estimate genetic distance among the inbred lines. Principal component analysis facilitated ascertainment of relative dispersion of the inbreds based on the frequency of variants at specific RFLP loci. Evident associations of variants with genes affecting agronomic traits were identified by principal component regression analysis, in which adjusted hybrid means were regressed on the matrix of hybrid variants frequencies. The hybrid means were adjusted by removing environmental effects, using residuals as dependent variables in the regression analysis. Results from this study suggest that RFLP analysis may be of value in allocating maize inbreds to heterotic groups, but no relationship between RFLP-based genetic distance and hybrid performance was apparent. Principal component regression identified variants potentially linked to genes that control specific agronomic traits.Joint contribution: USDA-ARS and Journal Paper No. J-13590 of the Iowa Agriculture and Home Economics Experiment Station, Ames, IA 50011, USA. Projects No. 2818 and 2778     

Efficiency of selection, as measured by single nucleotide polymorphism variation, is dependent on inbreeding rate in Drosophila melanogaster

It is often hypothesized that slow inbreeding causes less inbreeding depression than fast inbreeding at the same absolute level of inbreeding. Possible explanations for this phenomenon include the more efficient purging of deleterious alleles and more efficient selection for heterozygote individuals during slow, when compared with fast, inbreeding. We studied the impact of inbreeding rate on the loss of heterozygosity and on morphological traits in Drosophila melanogaster. We analysed five noninbred control lines, 10 fast inbred lines and 10 slow inbred lines; the inbred lines all had an expected inbreeding coefficient of approximately 0.25. Forty single nucleotide polymorphisms in DNA coding regions were genotyped, and we measured the size and shape of wings and counted the number of sternopleural bristles on the genotyped individuals. We found a significantly higher level of genetic variation in the slow inbred lines than in the fast inbred lines. This higher genetic variation was resulting from a large contribution from a few loci and a smaller effect from several loci. We attributed the increased heterozygosity in the slow inbred lines to the favouring of heterozygous individuals over homozygous individuals by natural selection, either by associative over‐dominance or balancing selection, or a combination of both. Furthermore, we found a significant polynomial correlation between genetic variance and wing size and shape in the fast inbred lines. This was caused by a greater number of homozygous individuals among the fast inbred lines with small, narrow wings, which indicated inbreeding depression. Our results demonstrated that the same amount of inbreeding can have different effects on genetic variance depending on the inbreeding rate, with slow inbreeding leading to higher genetic variance than fast inbreeding. These results increase our understanding of the genetic basis of the common observation that slow inbred lines express less inbreeding depression than fast inbred lines. In addition, this has more general implications for the importance of selection in maintaining genetic variation.     

Natural variation in GA1 associates with floral morphology in Arabidopsis thaliana

? The genetic architecture of floral traits is evolutionarily important due to the fitness consequences of quantitative variation in floral morphology. Yet, little is known about the genes underlying these traits in natural populations. Using Arabidopsis thaliana, we examine molecular variation at GIBBERELLIC ACID REQUIRING 1 (GA1) and test for associations with floral morphology. ? We examined full-length sequence in 32 accessions and describe two haplotypes (comprising four nonsynonymous polymorphisms) in GA1 that segregate at intermediate frequencies. In 133 A. thaliana accessions, we test for genotype-phenotype associations and corroborate these findings in segregating progenies. ? The two common GA1 haplotypes were associated with the length of petals, stamens, and to a lesser extent style-stigma length. Associations were confirmed in a segregating progeny developed from 19 accessions. We find analogous results in recombinant inbred lines of the Bayreuth × Shahdara cross, which differ only at one of 4 SNPs, suggesting that this SNP may contribute to the observed association. ? Assuming GA1 causally affects floral organ size, it is interesting that adjacent petal and stamen whorls are most strongly affected. This pattern suggests that GA1 could contribute to the greater strength of petal-stamen correlations relative to other floral-length correlations observed in some Brassicaceous species.     

Identification of associations between SSR markers and fiber traits in an exotic germplasm derived from multiple crosses among Gossypium tetraploid species

Genetic improvement in yield and fiber quality is needed for worldwide cotton production. Identification of molecular markers associated with fiber-related traits can facilitate selection for these traits in breeding. This study was designed to identify associations between SSR markers and fiber traits using an exotic germplasm population, species polycross (SP), derived from multiple crosses among Gossypium tetraploid species. The SP population underwent 11 generations of mixed random mating and selfing followed by 12 generations of selfing. A total of 260 lines were evaluated for fiber-related traits under three environments in 2005 and 2006. Large genotypic variance components in traits were identified relative to components of genotype × environment. Eighty-six primer pairs amplified a total of 314 polymorphic fragments among 260 lines. A total of 202 fragments with above 6% allele frequency were analyzed for associations. Fifty-nine markers were found to have a significant (P < 0.05, 0.01, or 0.001) association with six fiber traits. There were six groups identified within the population using structure analysis. Allele frequency divergence among six groups ranged from 0.11 to 0.27. Of the 59 marker–trait associations, 39 remained significant after correction for population structure and kinship using a mixed linear model. The effect of population sub-structure on associations was most significant in boll weight among the traits analyzed. The sub-structure among the SP lines may be caused by natural selection, the breeding method applied during development of inbred lines, and unknown factors. The identified marker–trait associations can be useful in breeding and help determine genetic mechanisms underlying interrelationships among fiber traits. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

SSR analysis of genetic diversity among maize inbred lines adapted to cold regions of Japan

Information regarding diversity and relationships among breeding material is necessary for hybrid maize (Zea mays L.) breeding. Simple-sequence repeat (SSR) analysis of the 60 loci distributed uniformly throughout the maize genome was carried out for 65 inbred lines adapted to cold regions of Japan in order to assess genetic diversity among the inbred lines and to assign them to heterotic groups. The mean value (0.69) of the polymorphic-index content (PIC) for the SSR loci provided sufficient discrimination-ability for the assessment of genetic diversity among the inbred lines. The correlation between the genetic-similarity (GS) estimates and the coancestry coefficient was significant (r = 0.70). The average-linkage (UPGMA) cluster analysis and principal-coordinate analysis (PCOA) for a matrix of the GS estimates showed that the Northern flint inbred lines bred in Japan were similar to a Canadian Northern flint inbred line CO12 and a European flint inbred line F283, and that dent inbred lines bred in Japan were similar to BSSS inbred lines such as B73. These associations correspond to the known pedigree records of these inbred lines. The results indicate that SSR analysis is effective for the assessment of genetic diversity among maize inbred lines and for the assignment of inbred lines to heterotic groups.     

Performance of recombinant inbred lines in Brussels sprouts (Brassica oleracea var. gemmifera)

Summary Performance of a random array of recombinant inbred lines derived by single seed descent from five different source populations of Brussels sprouts (Brassica oleracea var. gemmifera) is presented. A total of 2,356 lines were tested in trials during 1985 and 1986. Three of the source populations were derived from double crosses between F₁ hybrids. These hybrids show a considerable heterotic advantage over their inbred parents for the most important agronomic traits. The recombinant inbred lines performed, on average, less well than the parental inbred material, indicating that additive x additive genie interactions may make a significant contribution to the performance of current inbred material. Nevertheless, the very large variation among the recombinant inbred lines permitted many lines to be identified which outperformed the best parental inbred for all traits. Two lines outperformed the reference F₁ hybrid, Gower, for an index that included marketable yield and quality. Consideration was also given to the dangers of misinterpreting phenotypically based proportions. Accordingly, response equations were used to ascertain the real genetic progress that was made. Advance seemed small when compared with the large heterotic effect, which is consistent with the segregation of a large number of loci. The distribution of the recombinant inbred lines was compared to predictions made from early generation trials. There was broad agreement but significant discrepancies existed which, it is suggested, may arise from the effects of genotype-environment interactions.     

240份玉米自交系纹枯病抗性鉴定与评价

在人工接种条件下,连续3年对240份玉米自交系纹枯病抗性进行鉴定和评价,分析了玉米纹枯病抗性与主要农艺性状的相关性。结果表明,玉米纹枯病抗性资源较为缺乏,240份自交系中无免疫或高抗的材料,有中抗自交系4份、感病自交系18份、高感自交系218份。旅大红骨、Reid、PA和塘四平头类群自交系中未发现玉米纹枯病抗源,PB类群和Lancaster类群自交系纹枯病抗性相对较好,今后应主要从这两类种质中寻找玉米纹枯病抗源。玉米纹枯病病情指数与株高、穗位高、穗位高/株高、穗下节间数和穗下平均节间长均呈极显著负相关,这些表型可以作为非接种条件下筛选抗玉米纹枯病种质的参考指标。     

Association mapping for yield and grain quality traits in rice (Oryza sativa L.)

Association analysis was applied to a panel of accessions of Embrapa Rice Core Collection (ERiCC) with 86 SSR and field data from two experiments. A clear subdivision between lowland and upland accessions was apparent, thereby indicating the presence of population structure. Thirty-two accessions with admixed ancestry were identified through structure analysis, these being discarded from association analysis, thus leaving 210 accessions subdivided into two panels. The association of yield and grain-quality traits with SSR was undertaken with a mixed linear model, with markers and subpopulation as fixed factors, and kinship matrix as a random factor. Eight markers from the two appraised panels showed significant association with four different traits, although only one (RM190) maintained the marker-trait association across years and cultivation. The significant association detected between amylose content and RM190 was in agreement with previous QTL analyses in the literature. Herein, the feasibility of undertaking association analysis in conjunction with germplasm characterization was demonstrated, even when considering low marker density. The high linkage disequilibrium expected in rice lines and cultivars facilitates the detection of marker-trait associations for implementing marker assisted selection, and the mining of alleles related to important traits in germplasm.