Haplotype diversity in the endosperm specific β-amylase gene Bmy1 of cultivated barley (Hordeum vulgare L.)

Five single nucleotide polymorphism (SNP) sites corresponding to substitutions in the protein sequence of the β-amylase gene Bmy1 at amino acid (AA) positions 115, 165, 233, 347 and 430 were genotyped in 493 cultivated barley accessions by Pyrosequencing and a CAPS assay. A total of 6 different haplotypes for the Bmy1 gene were discovered of which 4 haplotypes were identified as previously described alleles Bmy1-Sd1, Bmy1-Sd2L, Bmy1-Sd2H and Bmy1-Sd3, while 2 haplotypes were new. A broad spectrum of haplotypes was found in spring barleys, while the winter barleys were dominated by the newly described haplotype Bmy1-Sd4. Individual haplotype frequencies varied between the geographic regions.Three pairs of SNP loci within the gene showed highly significant (P<0.0001) elevated values of linkage disequilibrium (LD) with r ² > 0.6. In the European and Asian subpopulations different loci were in linkage disequilibrium due to the differences in haplotype frequency distributions. By applying LD data to select haplotype tagging SNPs, three SNP sites corresponding to AA positions 115, 233 and 347 were identified that allowed to discriminate 4 haplotypes and to capture 91.6% of the available diversity by distinguishing 452 out of 493 accessions. In a subset of 2-rowed German spring barley varieties 4 SNPs and 2 haplotypes had a significant association with the malting quality parameter final attenuation limit which is related to the total amylolytic enzymatic activity.     

A first insight into population structure and linkage disequilibrium in the US peanut minicore collection

Knowledge of genetic diversity, population structure, and degree of linkage disequilibrium (LD) in target association mapping populations is of great importance and is a prerequisite for LD-based mapping. In the present study, 96 genotypes comprising 92 accessions of the US peanut minicore collection, a component line of the tetraploid variety Florunner, diploid progenitors A. duranensis (AA) and A. ipaënsis (BB), and synthetic amphidiploid accession TxAG-6 were investigated with 392 simple sequence repeat (SSR) marker bands amplified using 32 highly-polymorphic SSR primer pairs. Both distance- and model-based (Bayesian) cluster analysis revealed the presence of structured diversity. In general, the wild-species accessions and the synthetic amphidiploid grouped separately from most minicore accessions except for COC155, and were eliminated from most subsequent analyses. UPGMA analysis divided the population into four subgroups, two major subgroups representing subspecies fastigiata and hypogaea, a third group containing individuals from each subspecies or possibly of mixed ancestry, and a fourth group, either consisting of COC155 alone if wild species were excluded, or of COC155, the diploid species, and the synthetic amphidiploid. Model-based clustering identified four subgroups- one each for fastigiata and hypogaea subspecies, a third consisting of individuals of both subspecies or of mixed ancestry predominantly from Africa or Asia, and a fourth group, consisting of individuals predominantly of var fastigiata, peruviana, and aequatoriana accessions from South America, including COC155. Analysis of molecular variance (AMOVA) revealed statistically-significant (P < 0.0001) genetic variance of 16.87% among subgroups. A total of 4.85% of SSR marker pairs revealed significant LD (at r² ≥ 0.1). Of the syntenic marker pairs separated by distances < 10 cM, 11–20 cM, 21–50 cM, and > 50 cM, 19.33, 5.19, 6.25 and 5.29% of marker pairs were found in strong LD (P ≤ 0.01), in accord with LD extending to great distances in self pollinated crops. A threshold value of r² > 0.035 was found to distinguish mean r² values of linkage distance groups statistically from the mean r² values of unlinked markers; LD was found to extend to 10 cM over the entire minicore collection by this criterion. However, there were large differences in r² values among marker pairs even among tightly-linked markers. The implications of these findings with regard to the possibility of using association mapping for detection of genome-wide SSR marker-phenotype association are discussed.     

Molecular diversity and association mapping of fiber quality traits in exotic G. hirsutum L. germplasm

The narrow genetic base of cultivated cotton germplasm is hindering the cotton productivity worldwide. Although potential genetic diversity exists in Gossypium genus, it is largely ‘underutilized’ due to photoperiodism and the lack of innovative tools to overcome such challenges. The application of linkage disequilibrium (LD)-based association mapping is an alternative powerful molecular tool to dissect and exploit the natural genetic diversity conserved within cotton germplasm collections, greatly accelerating still ‘lagging’ cotton marker-assisted selection (MAS) programs. However, the extent of genome-wide linkage disequilibrium (LD) has not been determined in cotton. We report the extent of genome-wide LD and association mapping of fiber quality traits by using a 95 core set of microsatellite markers in a total of 285 exotic Gossypium hirsutum accessions, comprising of 208 landrace stocks and 77 photoperiodic variety accessions. We demonstrated the existence of useful genetic diversity within exotic cotton germplasm. In this germplasm set, 11–12% of SSR loci pairs revealed a significant LD. At the significance threshold (r² ≥ 0.1), a genome-wide average of LD declines within the genetic distance at < 10 cM in the landrace stocks germplasm and > 30 cM in variety germplasm. Genome wide LD at r² ≥ 0.2 was reduced on average to  1–2 cM in the landrace stock germplasm and 6–8 cM in variety germplasm, providing evidence of the potential for association mapping of agronomically important traits in cotton. We observed significant population structure and relatedness in assayed germplasm. Consequently, the application of the mixed liner model (MLM), considering both kinship (K) and population structure (Q) detected between 6% and 13% of SSR markers associated with the main fiber quality traits in cotton. Our results highlight for the first time the feasibility and potential of association mapping, with consideration of the population structure and stratification existing in cotton germplasm resources. The number of SSR markers associated with fiber quality traits in diverse cotton germplasm, which broadly covered many historical meiotic events, should be useful to effectively exploit potentially new genetic variation by using MAS programs.     

Polymorphism of the cultivated barley (<Emphasis Type="Italic">Hordeum vulgare</Emphasis> L.) of South Arabia at hordein-coding loci

Electrophoresis in starch gel was used to study the polymorphism of hordeins controlled by loci Hrd A, Hrd B, and Hrd F in 89 accessions of the local barleys from South Arabia (Yemen). Overall, 36 alleles were detected for locus Hrd A; 48 alleles, for Hrd B; and 5 alleles, for Hrd F. The existence of the blocks of hordein components controlled by loci Hrd A and Hrd B was demonstrated. Calculation of genetic distances allows us to conclude that the barley populations from Yemen and Ethiopia are more similar compared with the populations from Egypt. This confirms the hypothesis of Bakhteev on the origin of Ethiopian barleys.     

Genetic diversity and linkage disequilibrium analysis in elite sugar beet breeding lines and wild beet accessions

Key message

Linkage disequilibrium decay in sugar beet is strongly affected by the breeding history, and varies extensively between and along chromosomes, allowing identification of known and unknown signatures of selection.

Abstract

Genetic diversity and linkage disequilibrium (LD) patterns were investigated in 233 elite sugar beet breeding lines and 91 wild beet accessions, using 454 single nucleotide polymorphisms (SNPs) and 418 SNPs, respectively. Principal coordinate analysis suggested the existence of three groups of germplasm, corresponding to the wild beets, the seed parent and the pollen parent breeding pool. LD was investigated in each of these groups, with and without correction for genetic relatedness. Without correction for genetic relatedness, in the pollen as well as the seed parent pool, LD persisted beyond 50 centiMorgan (cM) on four (2, 3, 4 and 5) and three chromosomes (2, 4 and 6), respectively; after correction for genetic relatedness, LD decayed after <6 cM on all chromosomes in both pools. In the wild beet accessions, there was a strong LD decay: on average LD disappeared after 1 cM when LD was calculated with a correction for genetic relatedness. Persistence of LD was not only observed between distant SNPs on the same chromosome, but also between SNPs on different chromosomes. Regions on chromosomes 3 and 4 that harbor disease resistance and monogermy loci showed strong genetic differentiation between the pollen and seed parent pools. Other regions, on chromosomes 8 and 9, for which no a priori information was available with respect to their contribution to the phenotype, still contributed to clustering of lines in the elite breeding material.     

Resequencing the<Emphasis Type="Italic">Vrs1</Emphasis> gene in Spanish barley landraces revealed reversion of six-rowed to two-rowed spike

Six-rowed spike 1 (Vrs1) is a gene of major importance for barley breeding and germplasm management as it is the main gene determining spike row-type (2-rowed vs. 6-rowed). This is a widely used DUS trait, and has been often associated to phenotypic traits beyond spike type. Comprehensive re-sequencing Vrs1 revealed three two-rowed alleles (Vrs1.b2; Vrs1.b3; Vrs1.t1) and four six-rowed (vrs1.a1; vrs1.a2; vrs1.a3; vrs1.a4) in the natural population. However, the current knowledge about Vrs1 alleles and its distribution among Spanish barley subpopulations is still underexploited. We analyzed the gene in a panel of 215 genotypes, made of Spanish landraces and European cultivars. Among 143 six-rowed accessions, 57 had the vrs1.a1 allele, 83 were vrs1.a2, and three showed the vrs1.a3 allele. Vrs1.b3 was found in most two-rowed accessions, and a new allele was observed in 7 out of 50 two-rowed Spanish landraces. This allele, named Vrs1.b5, contains a ‘T’ insertion in exon 2, originally proposed as the causal mutation giving rise to the six-row vrs1.a2 allele, but has an additional upstream deletion that results in the change of 15 amino acids and a potentially functional protein. We conclude that eight Vrs1 alleles (Vrs1.b2, Vrs1.b3, Vrs1.b5, Vrs1.t1, vrs1.a1, vrs1.a2, vrs1.a3, vrs1.a4) discriminate two and six-rowed barleys. The markers described will be useful for DUS identification, plant breeders, and other crop scientists.     

Polymorphisms of caprine <Emphasis Type="Italic">GnRHR</Emphasis> gene and their association with litter size in West African Dwarf goats

Gonadotropin-releasing hormone receptor (GnRHR) gene is considered a candidate gene for litter size due to its critical role in regulating the activities of hypothalamo-pituitary-gonadal axis which synthesizes and releases gonadotropins. This study was designed to identify mutations within the caprine GnRHR gene and investigate their association with litter size at various parities. Polymorphisms scanning and genotyping of GnRHR gene in West African Dwarf (WAD) goats (n?=?226) revealed three single nucleotide polymorphisms (SNPs), one mutation (g.-29T?>?G) was detected within 5′UTR region while two others (g.48G?>?A and g.209T?>?G) were identified in exon 1. Mutation at g.209T?>?G locus resulted in amino acid change from Methionine to Arginine at position 70 on the polypeptide residue. Based on heterozygosity and polymorphism information content (PIC), WAD goat population diversity at the SNP loci was moderate. Strong linkage disequilibrium (LD) (r²?>?0.98) existed among the detected mutations resulting in three observed haplotypes, two (T-G-T and G-A-G) had cumulative frequency of >?97%. The mutation within 5′UTR region of GnRHR gene (g.-29T?>?G) is novel, being reported in goats for the first time. Association analysis revealed a significant (p?<?0.05) association between allele G at g.-29T?>?G with higher mean litter size for homozygous (GG) mutant does compared with heterozygotes (GT) or homozygotes (TT), while the relationship between SNPs at the two loci detected in exon 1 and litter size was not significant.     

Patterns of genetic diversity and linkage disequilibrium in a highly structured Hordeum vulgare association-mapping population for the Mediterranean basin

Population structure and genome-wide linkage disequilibrium (LD) were investigated in 192 Hordeum vulgare accessions providing a comprehensive coverage of past and present barley breeding in the Mediterranean basin, using 50 nuclear microsatellite and 1,130 DArT^® markers. Both clustering and principal coordinate analyses clearly sub-divided the sample into five distinct groups centred on key ancestors and regions of origin of the germplasm. For given genetic distances, large variation in LD values was observed, ranging from closely linked markers completely at equilibrium to marker pairs at 50 cM separation still showing significant LD. Mean LD values across the whole population sample decayed below r ² of 0.15 after 3.2 cM. By assaying 1,130 genome-wide DArT^® markers, we demonstrated that, after accounting for population substructure, current genome coverage of 1 marker per 1.5 cM except for chromosome 4H with 1 marker per 3.62 cM is sufficient for whole genome association scans. We show, by identifying associations with powdery mildew that map in genomic regions known to have resistance loci, that associations can be detected in strongly stratified samples provided population structure is effectively controlled in the analysis. The population we describe is, therefore, shown to be a valuable resource, which can be used in basic and applied research in barley.     

Extent and consistency of linkage disequilibrium and identification of DNA markers for production and egg quality traits in commercial layer chicken populations

Background

The genome sequence and a high-density SNP map are now available for the chicken and can be used to identify genetic markers for use in marker-assisted selection (MAS). Effective MAS requires high linkage disequilibrium (LD) between markers and quantitative trait loci (QTL), and sustained marker-QTL LD over generations. This study used data from a 3,000 SNP panel to assess the level and consistency of LD between single nucleotide polymorphisms (SNPs) over consecutive years in two egg-layer chicken lines, and analyzed one line by two methods (SNP-wise association and genome-wise Bayesian analysis) to identify markers associated with egg-quality and egg-production phenotypes.

Results

The LD between markers pairs was high at short distances (r² > 0.2 at < 2 Mb) and remained high after one generation (correlations of 0.80 to 0.92 at < 5 Mb) in both lines. Single- and 3-SNP regression analyses using a mixed model with SNP as fixed effect resulted in 159 and 76 significant tests (P < 0.01), respectively, across 12 traits. A Bayesian analysis called BayesB, that fits all SNPs simultaneously as random effects and uses model averaging procedures, identified 33 SNPs that were included in the model >20% of the time (φ > 0.2) and an additional ten 3-SNP windows that had a sum of φ greater than 0.35. Generally, SNPs included in the Bayesian model also had a small P-value in the 1-SNP analyses.

Conclusion

High LD correlations between markers at short distances across two generations indicate that such markers will retain high LD with linked QTL and be effective for MAS. The different association analysis methods used provided consistent results. Multiple single SNPs and 3-SNP windows were significantly associated with egg-related traits, providing genomic positions of QTL that can be useful for both MAS and to identify causal mutations.

     

Resistance to <Emphasis Type="Italic">Rhynchosporium commune</Emphasis> in a collection of European spring barley germplasm

Key message

Association analyses of resistance to Rhynchosporium commune in a collection of European spring barley germplasm detected 17 significant resistance quantitative trait loci. The most significant association was confirmed as Rrs1.

Abstract

Rhynchosporium commune is a fungal pathogen of barley which causes a highly destructive and economically important disease known as rhynchosporium. Genome-wide association mapping was used to investigate the genetic control of host resistance to R. commune in a collection of predominantly European spring barley accessions. Multi-year disease nursery field trials revealed 8 significant resistance quantitative trait loci (QTL), whilst a separate association mapping analysis using historical data from UK national and recommended list trials identified 9 significant associations. The most significant association identified in both current and historical data sources, collocated with the known position of the major resistance gene Rrs1. Seedling assays with R. commune single-spore isolates expressing the corresponding avirulence protein NIP1 confirmed that this locus is Rrs1. These results highlight the significant and continuing contribution of Rrs1 to host resistance in current elite spring barley germplasm. Varietal height was shown to be negatively correlated with disease severity, and a resistance QTL was identified that co-localised with the semi-dwarfing gene sdw1, previously shown to contribute to disease escape. The remaining QTL represent novel resistances that are present within European spring barley accessions. Associated markers to Rrs1 and other resistance loci, identified in this study, represent a set of tools that can be exploited by breeders for the sustainable deployment of varietal resistance in new cultivars.

     

Single-nucleotide polymorphism,linkage disequilibrium and geographic structure in the malaria parasite <Emphasis Type="Italic">Plasmodium vivax</Emphasis>: prospects for genome-wide association studies

Background

The ideal malaria parasite populations for initial mapping of genomic regions contributing to phenotypes such as drug resistance and virulence, through genome-wide association studies, are those with high genetic diversity, allowing for numerous informative markers, and rare meiotic recombination, allowing for strong linkage disequilibrium (LD) between markers and phenotype-determining loci. However, levels of genetic diversity and LD in field populations of the major human malaria parasite P. vivax remain little characterized.

Results

We examined single-nucleotide polymorphisms (SNPs) and LD patterns across a 100-kb chromosome segment of P. vivax in 238 field isolates from areas of low to moderate malaria endemicity in South America and Asia, where LD tends to be more extensive than in holoendemic populations, and in two monkey-adapted strains (Salvador-I, from El Salvador, and Belem, from Brazil). We found varying levels of SNP diversity and LD across populations, with the highest diversity and strongest LD in the area of lowest malaria transmission. We found several clusters of contiguous markers with rare meiotic recombination and characterized a relatively conserved haplotype structure among populations, suggesting the existence of recombination hotspots in the genome region analyzed. Both silent and nonsynonymous SNPs revealed substantial between-population differentiation, which accounted for ~40% of the overall genetic diversity observed. Although parasites clustered according to their continental origin, we found evidence for substructure within the Brazilian population of P. vivax. We also explored between-population differentiation patterns revealed by loci putatively affected by natural selection and found marked geographic variation in frequencies of nucleotide substitutions at the pvmdr-1 locus, putatively associated with drug resistance.

Conclusion

These findings support the feasibility of genome-wide association studies in carefully selected populations of P. vivax, using relatively low densities of markers, but underscore the risk of false positives caused by population structure at both local and regional levels.See commentary: http://www.biomedcentral.com/1741-7007/8/90

     

Linkage disequilibrium and association analysis of stripe rust resistance in wild emmer wheat (Triticum turgidum ssp. dicoccoides) population in Israel

Key Message

Rapid LD decay in wild emmer population from Israel allows high-resolution association mapping. Known and putative new stripe rust resistance genes were found.

Abstract

Genome-wide association mapping (GWAM) is becoming an important tool for the discovery and mapping of loci underlying trait variation in crops, but in the wild relatives of crops the use of GWAM has been limited. Critical factors for the use of GWAM are the levels of linkage disequilibrium (LD) and genetic diversity in mapped populations, particularly in those of self-pollinating species. Here, we report LD estimation in a population of 128 accessions of self-pollinating wild emmer, Triticum turgidum ssp. dicoccoides, the progenitor of cultivated wheat, collected in Israel. LD decayed fast along wild emmer chromosomes and reached the background level within 1 cM. We employed GWAM for the discovery and mapping of genes for resistance to three isolates of Puccinia striiformis, the causative agent of wheat stripe rust. The wild emmer population was genotyped with the wheat iSelect assay including 8643 gene-associated SNP markers (wheat 9K Infinium) of which 2,278 were polymorphic. The significance of association between stripe rust resistance and each of the polymorphic SNP was tested using mixed linear model implemented in EMMA software. The model produced satisfactory results and uncovered four significant associations on chromosome arms 1BS, 1BL and 3AL. The locus on 1BS was located in a region known to contain stripe rust resistance genes. These results show that GWAM is an effective strategy for gene discovery and mapping in wild emmer that will accelerate the utilization of this genetic resource in wheat breeding.     

Genetic diversity and population structure of trifoliate yam (<Emphasis Type="Italic">Dioscorea dumetorum</Emphasis> Kunth) in Cameroon revealed by genotyping-by-sequencing (GBS)

Background

Yams (Dioscorea spp.) are economically important food for millions of people in the humid and sub-humid tropics. Dioscorea dumetorum (Kunth) is the most nutritious among the eight-yam species, commonly grown and consumed in West and Central Africa. Despite these qualities, the storage ability of D. dumetorum is restricted by severe postharvest hardening of the tubers that can be addressed through concerted breeding efforts. The first step of any breeding program is bound to the study of genetic diversity. In this study, we used the Genotyping-By-Sequencing of Single Nucleotide Polymorphism (GBS-SNP) to investigate the genetic diversity and population structure of 44 accessions of D. dumetorum in Cameroon. Ploidy was inferred using flow cytometry and gbs2ploidy.

Results

We obtained on average 6371 loci having at least information for 75% accessions. Based on 6457 unlinked SNPs, our results demonstrate that D. dumetorum is structured into four populations. We clearly identified, a western/north-western, a western, and south-western populations, suggesting that altitude and farmers-consumers preference are the decisive factors for differential adaptation and separation of these populations. Bayesian and neighbor-joining clustering detected the highest genetic variability in D. dumetorum accessions from the south-western region. This variation is likely due to larger breeding efforts in the region as shown by gene flow between D. dumetorum accessions from the south-western region inferred by maximum likelihood. Ploidy analysis revealed diploid and triploid levels in D. dumetorum accessions with mostly diploid accessions (77%). Male and female accessions were mostly triploid (75%) and diploid (69%), respectively. The 1C genome size values of D. dumetorum accessions were on average 0.333?±?0.009?pg and 0.519?±?0.004?pg for diploids and triploids, respectively.

Conclusions

Germplasm characterization, population structure and ploidy are an essential basic information in a breeding program as well as for conservation of intraspecific diversity. Thus, results obtained in this study provide valuable information for the improvement and conservation of D. dumetorum. Moreover, GBS appears as an efficient powerful tool to detect intraspecific variation.

     

Evaluation of LD decay and various LD-decay estimators in simulated and SNP-array data of tetraploid potato

Key message

The number of SNPs required for QTL discovery is justified by the distance at which linkage disequilibrium has decayed. Simulations and real potato SNP data showed how to estimate and interpret LD decay.

Abstract

The magnitude of linkage disequilibrium (LD) and its decay with genetic distance determine the resolution of association mapping, and are useful for assessing the desired numbers of SNPs on arrays. To study LD and LD decay in tetraploid potato, we simulated autotetraploid genotypes and used it to explore the dependence on: (1) the number of haplotypes in the population (the amount of genetic variation) and (2) the percentage of haplotype specific SNPs (hs-SNPs). Several estimators for short-range LD were explored, such as the average r ², median r ², and other percentiles of r ² (80, 90, and 95 %). For LD decay, we looked at LD_½,90, the distance at which the short-range LD is halved when using the 90 % percentile of r ² at short range, as estimator for LD. Simulations showed that the performance of various estimators for LD decay strongly depended on the number of haplotypes, although the real value of LD decay was not influenced very much by this number. The estimator LD_½,90 was chosen to evaluate LD decay in 537 tetraploid varieties. LD_½,90 values were 1.5 Mb for varieties released before 1945 and 0.6 Mb in varieties released after 2005. LD_½,90 values within three different subpopulations ranged from 0.7 to 0.9 Mb. LD_½,90 was 2.5 Mb for introgressed regions, indicating large haplotype blocks. In pericentromeric heterochromatin, LD decay was negligible. This study demonstrates that several related factors influencing LD decay could be disentangled, that no universal approach can be suggested, and that the estimation of LD decay has to be performed with great care and knowledge of the sampled material.

     

Microsatellite based linkage disequilibrium analyses reveal <Emphasis Type="Italic">Saltol</Emphasis> haplotype fragmentation and identify novel QTLs for seedling stage salinity tolerance in rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.)

A set of 84 diverse rice genotypes were assessed for seedling stage salt tolerance and their genetic diversity using 41 polymorphic SSR markers comprising of 19 Saltol QTL linked and 22 random markers. Phenotypic screening under hydroponics identified three indica landraces (Badami, Shah Pasand and Pechi Badam), two Oryza rufipogon accessions (NKSWR2 and NKSWR17) and one each of Basmati rice (Seond Basmati) and japonica cultivars (Tompha Khau) as salt tolerant, having similar tolerance as of Pokkali and FL478. Among the salt tolerant genotypes, biomass showed positive correlation with shoot fresh weight and negative association with root and shoot Na⁺ content. The results indicated repression of Na⁺ loading within the tolerant plants. Linkage disequilibrium (LD) of the Saltol linked markers was weak, suggestive of high fragmentation of Pokkali haplotype, a result of evolutionary active recombination events. Poor haplotype structure of the Saltol region, may reduce its usefulness in marker assisted breeding programmes, if the target foreground markers chosen are wide apart. LD mapping identified eight robust marker-trait associations (QTLs), of which RM10927 was found linked to root and shoot Na⁺ content and RM10871 with shoot Na⁺/K⁺ ratio. RM271 on chromosome 10, an extra Saltol marker, was found associated to root Na⁺/K⁺ ratio. This marker showed a distinct allele among O. rufipogon accessions. There were also other novel loci detected on chromosomes 2, 5 and 10 influencing salt tolerance in the tested germplasm. Although Saltol remained as the key locus, the role of other genomic regions cannot be neglected in tailoring seedling stage salt tolerance in rice.     

Genome-wide association study for soybean cyst nematode resistance in Chinese elite soybean cultivars

Soybean cyst nematode (SCN) (Heterodera glycines Ichinohe) is a highly recalcitrant endoparasite of soybean roots, causing more yield loss than any other pest. To identify quantitative trait loci (QTL) controlling resistance to SCN (HG type 2.5.7, race 1), a genome-wide association study (GWAS) was performed. The association panel, consisting of 120 Chinese soybean cultivars, was genotyped with 7189 single nucleotide polymorphism (SNPs). A total of 6204 SNPs with minor allele frequency >0.05 were used to estimate linkage disequilibrium (LD) and population structure. The mean level of LD measured by r ² declined very rapidly to half its maximum value (0.51) at 220 kb. The overall population structure was approximately coincident with geographic origin. The GWAS results identified 13 SNPs in 7 different genomic regions significantly associated with SCN resistance. Of these, three SNPs were localized in previously mapped QTL intervals, including rhg1 and Rhg4. The GWAS results also detected 10 SNPs in 5 different genomic regions associated with SCN resistance. The identified loci explained an average of 95.5% of the phenotypic variance. The proportion of phenotypic variance was due to additive genetic variance of the validated SNPs. The present study identified multiple new loci and refined chromosomal regions of known loci associated with SCN resistance. The loci and trait-associated SNPs identified in this study can be used for developing soybean cultivars with durable resistance against SCN.     

Association mapping utilizing diverse barley lines reveals net form net blotch seedling resistance/susceptibility loci

Key message

A diverse collection of barley lines was phenotyped with three North American Pyrenophora teres f. teres isolates and association analyses detected 78 significant marker-trait associations at 16 genomic loci.

Abstract

Pyrenophora teres f. teres is a necrotrophic fungal pathogen and the causal agent of the economically important foliar disease net form net blotch (NFNB) of barley. The deployment of effective and durable resistance against P. teres f. teres has been hindered by the complexity of quantitative resistance and susceptibility. Several bi-parental mapping populations have been used to identify QTL associated with NFNB disease on all seven barley chromosomes. Here, we report the first genome-wide association study (GWAS) to detect marker-trait associations for resistance or susceptibility to P. teres f. teres. Geographically diverse barley genotypes from a world barley core collection (957) were genotyped with the Illumina barley iSelect chip and phenotyped with three P. teres f. teres isolates collected in two geographical regions of the USA (15A, 6A and LDNH04Ptt19). The best of nine regression models tested were identified for each isolate and used for association analysis resulting in the identification of 78 significant marker-trait associations (MTA; ?log10p value?>3.0). The MTA identified corresponded to 16 unique genomic loci as determined by analysis of local linkage disequilibrium between markers that did not meet a correlation threshold of R ²?≥?0.1, indicating that the markers represented distinct loci. Five loci identified represent novel QTL and were designated QRptts-3HL, QRptts-4HS, QRptts-5HL.1, QRptts-5HL.2, and QRptts-7HL.1. In addition, 55 of the barley lines examined exhibited a high level of resistance to all three isolates and the SNP markers identified will provide useful genetic resources for barley breeding programs.