GWAS of soybean seed protein and oil, using 12,000 accessions from the USDA soybean collection and the SoySNP50K BeadChip.
Genotyping Platform:
SoySNP50K
Genotypes:
USDA Soybean Collection
Description:
In this research, we conducted the first comprehensive analysis of population structure on the collection of 14,000 soybean accessions [Glycine max (L.) Merr. and G. soja Siebold & Zucc.] using a 50KSNP chip. Accessions originating from Japan were relatively homogenous and distinct from the Korean accessions. As a whole, both Japanese and Korean accessions diverged from the Chinese accessions. The ancestry of founders of the American accessions derived mostly from two Chinese subpopulations, which reflects the composition of the American accessions as a whole. A 12,000 accession GWAS conducted on seed protein and oil is the largest reported to date in plants and identified single nucleotide polymorphisms (SNPs) with strong signals on chromosomes 20 and 15. A chromosome 20 region previously reported to be important for protein and oil content was further narrowed and now contains only three plausible candidate genes. The haplotype effects show a strong negative relationship between oil and protein at this locus, indicating negative pleiotropic effects or multiple closely linked loci in repulsion phase linkage. The vast majority of accessions carry the haplotype allele conferring lower protein and higher oil.
GWAS of soybean sudden death syndrome (SDS), based on 282 breeding lines, genotyped with the 1536-SNP USLP1.0 chip.
Genotyping Platform:
1536_USLP1
Genotypes:
282 soybean breeding lines from the University of Minnesota soybean breeding program
Description:
Sudden death syndrome (SDS), caused by Fusarium virguliforme, has spread to northern soybean growing regions in the US causing significant yield losses. The objectives of this study were to identify loci underlying variation in plant responses to SDS through association mapping (AM) and to assess prediction accuracy of genomic selection (GS) in a panel of early maturing soybean germplasm. A set of 282 soybean breeding lines was selected from the University of Minnesota soybean breeding program and then genotyped using a genome-wide panel of 1536 single-nucleotide polymorphism markers. Four resistance traits, root lesion severity (RLS), foliar symptom severity (FSS), root retention (RR), and dry matter reduction (DMR), were evaluated using soil inoculation in the greenhouse. AM identified significant peaks in genomic regions of known SDS resistance quantitative trait loci cqSDS001, cqRfs4, and SDS11-2. Additionally, two novel loci, one on chromosome 3 and another on chromosome 18, were tentatively identified. A ninefold cross-validation scheme was used to assess the prediction accuracy of GS for SDS resistance. The prediction accuracy of single-trait GS (ST-GS) was 0.64 for RLS, but less than 0.30 for RR, DMR, and FSS. Compared to STGS, none of multi-trait GS (MT-GS) models significantly improved the prediction accuracy due to weak correlations between the four traits. This study suggests both AM and GS hold promise for implementation in genetic improvement of SDS resistance in existing soybean breeding programs.
282 representative accessions from the University of Minnesota soybean breeding program using a genome-wide panel of 1536 single nucleotide polymorphism (SNP) markers and evaluated plant responses to SCN HG type 0
Genotyping Platform:
1536_USLP1
Genotypes:
282 representative accessions from the University of Minnesota soybean breeding program
Description:
DNA samples were genotyped using an Illumina GoldenGate SNP assay with the Universal Soy Linkage Panel 1.0 of 1536 single nucleotide polymorphism (SNP) markers. The SNPs with >5% minor allele frequency (MAF) and a missing data rate < 50% were retained, followed by imputation of missing SNP data based on population mean of each marker. Total 1247 SNP markers passed the filters and were used in the subsequent analysis.
GWAS and QTL study of soybean seed oil, conducted on 279 lines from a Chinese breeding population, genotyped with 59,845 SNPs.
Genotyping Platform:
Li_Guo_2016
Genotypes:
279 lines from a Chinese breeding population
Description:
We used both a linkage and association mapping methodology to dissect the genetic basis of seed oil content of Chinese soybean cultivars in various environments in the Jiang-Huai River Valley. One recombinant inbred line (RIL) population (NJMN-RIL), with 104 lines developed from a cross between M8108 and NN1138-2, was planted in five environments to investigate phenotypic data, and a new genetic map with 2,062 specific-locus amplified fragment markers was constructed to map oil content QTLs. A derived F2 population between MN-5 (a line of NJMN-RIL) and NN1138-2 was also developed to confirm one major QTL. A soybean breeding germplasm population (279 lines) was established to perform a genome-wide association study (GWAS) using 59,845 high-quality single nucleotide polymorphism markers. In the NJMN-RIL population, 8 QTLs were found that explained a range of phenotypic variance from 6.3 to 26.3% in certain planting environments. Among them, qOil-5-1, qOil-10-1, and qOil-14-1 were detected in different environments, and qOil-5-1 was further confirmed using the secondary F2 population. Three loci located on chromosomes 5 and 20 were detected in a 2-year long GWAS, and one locus that overlapped with qOil-5-1 was found repeatedly and treated as the same locus. qOil-5-1 was further localized to a linkage disequilibrium block region of approximately 440 kb. These results will not only increase our understanding of the genetic control of seed oil content in soybean, but will also be helpful in marker-assisted selection for breeding high seed oil content soybean and gene cloning to elucidate the mechanisms of seed oil content.
GWAS of Tobacco ringspot virus (TRSV) conducted on 19,652 lines in the USDA Soybean Collection, genotyped with the SoySNP50K BeadChip.
Genotyping Platform:
SoySNP50K
Genotypes:
USDA Soybean Collection
Description:
TRSV-induced disease sensitivities of the 697 soybean PIs were rated on a one to five scale with plants rated as one exhibiting mild symptoms and plants rated as five displaying terminal bud necrosis (i.e., bud blight). The GWAS identified a single locus on soybean chromosome 2 strongly associated with TRSV sensitivity. Crossvalidation showed a correlation of 0.55 (P < 0.01) to TRSV sensitivity without including the most significant SNP marker from the GWAS as a covariate, which was a better estimation compared to the mean separation by using significant SNPs. The genomic estimated breeding values for the remaining 18,955 unscreened soybean PIs in the USDA Soybean Germplasm Collection were obtained using the GAPIT R package. To evaluate the prediction accuracy, an additional 55 soybean accessions were evaluated for sensitivity to TRSV, which resulted in a correlation of 0.67 (P < 0.01) between actual and predicted severities.
GWAS of Soybean mosaic virus (SMV), conducted on 165 lines from parents with differing susceptibility, genotyped with the NJAU 355K Soy SNP assay.
Genotyping Platform:
NJAU355K
Genotypes:
93 mutants from Nannong 86-4 and 72 mutants from Nannong 94-16
Description:
A genome-wide association study was conducted to accelerate molecular breeding for the improvement of resistance to SMV in soybean. A population of 165 soybean mutants derived from two soybean parents was used in this study. There were 104 SNPs identified significantly associated with resistance to SC7, some of which were located within previous reported quantitative trait loci. Three putative genes on chromosome 1, 9, and 12 were homologous to WRKY72, eEF1Bβ, and RLP9, which were involved in defense response to insect and disease in Arabidopsis.
GWAS of soybean chlorophyll traits based on canopy spectral reflectance and leaf extracts.
Genotyping Platform:
SoySNP50K
Genotypes:
385 maturity group IV soybean genotypes
Description:
A genome-wide associating mapping approach was employed using 31,253 single nucleotide polymorphisms (SNPs) to identify loci associated with the extract based eChl_A, eChl_B, eChl_R and eChl_T measurements and the two canopy spectral reflectance-based methods (tChl_T and iChl_T). A total of 23 (14 loci), 15 (7 loci) and 14 SNPs (10 loci) showed significant association with eChl_A, eChl_B and eChl_R respectively. A total of 52 unique SNPs were significantly associated with total chlorophyll content based on at least one of the three approaches (eChl_T, tChl_T and iChl_T) and likely tagged 27 putative loci for total chlorophyll content, four of which were indicated by all three approaches.
GWAS of 84 agronomic traits, conducted on 809 soybean accessions, with genotyping by resequencing.
Genotyping Platform:
Fang_Ma_2017
Genotypes:
809 soybean accessions
Description:
To understand the genetic networks underlying phenotypic correlations, we collected 809 soybean accessions worldwide and phenotyped them for two years at three locations for 84 agronomic traits. Genome-wide association studies identified 245 significant genetic loci, among which 95 genetically interacted with other loci. We determined that 14 oil synthesis-related genes are responsible for fatty acid accumulation in soybean and function in line with an additive model. Network analyses demonstrated that 51 traits could be linked through the linkage disequilibrium of 115 associated loci and these links reflect phenotypic correlations. We revealed that 23 loci, including the known Dt1, E2, E1, Ln, Dt2, Fan, and Fap loci, as well as 16 undefined associated loci, have pleiotropic effects on different traits.
440 soybean landraces and elite cultivars were screened for resistance to SCN HG Type 0 and HG Type 1.2.3.5.7; GWAS relative to Wm82.gnm2
Genotyping Platform:
Han_Zhao_2015
Genotypes:
440 diverse soybean landraces and elite cultivars mostly collected in China.
Description:
The Genomic DNA of the 440 accessions were partially sequenced using specific-locus amplified fragment sequencing (SLAF-seq) approach by Illumina Genome Analyzer II. The 347 million paired-end reads with 45 bp read length were mapped to the reference soybean gen- ome (Wm82.a2.v1) and a mean of 57,418 high quality tags were identified from paired-end reads for each accession. A data set of 36,976 SNPs at Minor Allele Fre- quency (MAF)≥4 % was generated from 57,418 high quality tags. The rate of missing data was controlled at less than 10 % for each accession. The set of SNPs covered 20 chromosomes of soybean. The resulting SNP density of one SNP per 27 Kbp was available in the present study.
GWAS study of control of flowering time in soybean, genotyped with the 180k Axiom SoyaSNP array.
Genotyping Platform:
SoyaSNP180K
Genotypes:
Williams 82
Description:
This study reports on the identification of candidate markers associated with flower time in soybean (Glycine max). A large population of 2,662 cultivated soybean accessions was genotyped using the 180k Axiom SoyaSNP array, and the genomic architecture of these accessions was investigated to confirm the population structure. Then, GWAS was conducted to evaluate the association between SNP markers and flower ytime. A tyyotal of 93 significant SNP markers were detected within 59 significant genes, including E1 and E3, which are the main determinants of flower time. Based on the GWAS results, multilocus epistatic interactions were examined between the significant and non-significant SNP markers. Two significant and 16 non-significant SNP markers were discovered as candidate markers affecting flower time via interactions with each other. These 18 candidate SNP markers mapped to 18 candidate genes including E1 and E3, and the 18 candidate genes were involved in six major flower pathways.
GWAS study of soybean seed protein and oil, conducted on 298 accessions, genotyped with a panel of 1536 SNPs.
Genotyping Platform:
Li_Zhao_2019
Genotypes:
185 soybean accessions from China and across the northern hemisphere
Description:
A GWAS study of seed protein and oil content using a population of 185 soybean (Glycine max) accessions from China and across the northern hemisphere. Specific length amplified fragment sequencing (SLAF-seq) tecyyhnology detected 12,072 SNPs across 20 chromosomes showing a marker density of 78.7 kbp. Thirty-one SNPs, and their 31 beneficial alleles, placed on 12 of the chromosomes represented QTLs associateyd with protein and oil. In both 2015 and 2016, the SNPs rs15774585 and rs15783346 (Chr 7) were correlated with seed oil, and the SNPs rs53140888 (Chr 01), rs19485676 (Chr 13), and rs24787338 (Chr 20) with seed protein.
GWAS study of iron deficiency chlorosis (IDC) in soybean, conducted on two populations (n=143, n=141), genotyped with the 1536 SNP USLP1 array.
Genotyping Platform:
1536_USLP1
Genotypes:
two independent populations, each consisting of a unique set of advanced soybean breeding lines
Description:
The objective of this analysis was to employ single nucleotide polymorphism (SNP)-based genome-wide association mapping to uncover genomic regions associated with IDC tolerance. Two populations [2005 (n = 143) and 2006 (n = 141)] were evaluated in replicated, multilocation IDC trials. After controlling for population structure and individual relatedness, and selecting statistical models that minimized false positives, 42 and 88 loci, with minor allele frequency >10%, were significant in 2005 and 2006, respectively. The loci accounted for 74.5% of the phenotypic variation in IDC in2005 and 93.8% of the variation in 2006. Nine loci from seven genomic locations were significant in both years. These loci accounted for 43.7% of the variation in 2005 and 47.6% in 2006. A number of the loci discovered here mapped at or near previously discovered IDC quantitative trait loci (QTL). A total of 15 genes known to be involved in iron metabolism mapped in the vicinity (<500 kb) of significant markers in one or both populations.
Utilizing an innovative GWAS in CSLRP, 44 QTL 199 alleles with 72.2 % contribution to SIFC variation were detected and organized into a QTL-allele matrix for cross design and gene annotation.
Genotyping Platform:
Meng_He_2016
Genotypes:
366 landraces from the Chinese soybean landrace population (CSLRP)
Description:
The seed isoflavone content (SIFC) of soybeans is of great importance to health care. The Chinese soybean landrace population (CSLRP) as a genetic reservoir was studied for its whole-genome quantitative trait loci (QTL) system of the SIFC using an innovative restricted twostage multi-locus genome-wide association study procedure (RTM-GWAS). A sample of 366 landraces was tested under four environments and sequenced using RAD-seq (restriction-site-associated DNA sequencing) technique to obtain 116,769 single nucleotide polymorphisms (SNPs) then organized into 29,119 SNP linkage disequilibrium blocks (SNPLDBs) for GWAS. The detected 44 QTL 199 alleles on 16 chromosomes (explaining 72.2 % of the total phenotypic variation) with the allele effects (92 positive and 107 negative) of the CSLRP were organized into a QTL-allele matrix showing the SIFC population genetic structure. Additional differentiation among eco-regions due to the SIFC in addition to that of genome-wide markers was found. All accessions comprised both positive and negative alleles, implying a great potential for recombination within the population. The optimal crosses were predicted from the matrices, showing transgressive potentials in the CSLRP. From the detected QTL system, 55 candidate genes related to 11 biological processes were χ2 -tested as an SIFC candidate gene system. The present study explored the genome-wide SIFC QTL/gene system with the innovative RTM-GWAS and found the potentials of the QTLallele matrix in optimal cross design and population genetic and genomic studies, which may have provided a solution to match the breeding by design strategy at both QTL and gene levels in breeding programs.
GWAS study of Sclerotinia stem rot (SSR) in soybean, conducted on 466 accessions, genotyped with the SoySNP50K BeadChip.
Genotyping Platform:
SoySNP50K
Genotypes:
466 accessions from the USDA Soybean Core Germplasm Collection
Description:
GWAS and GWES studies along with expression studies in soybean were leveraged to dissect the genetics of Sclerotinia stem rot (SSR), a significant fungal disease causing yield and quality losses. A large association panel of 466 diverse plant introduction accessions were phenotyped in multiple field and controlled environments to: (1) discover sources of resistance, (2) identify SNPs associated with resistance, and (3) determine putative candidate genes to elucidate the mode of resistance.
GWAS study of eight traits in soybean, conducted on 139 accessions, genotyped using GBS-derived markers.
Genotyping Platform:
Sonah_ODonoughue_2015
Genotypes:
139 soya bean lines
Description:
Soya bean is a major source of edible oil and protein for human consumption as well as animal feed. Understanding the genetic basis of different traits in soya bean will provide important insights for improving breeding strategies for this crop. A genome-wide association study (GWAS) was conducted to accelerate molecular breeding for the improvement of agronomic traits in soya bean. A genotyping-by-sequencing (GBS) approach was used to provide dense genome-wide marker coverage (>47 000 SNPs) for a panel of 304 short-season soya bean lines. A subset of 139 lines, representative of the diversity among these, was characterized phenotypically for eight traits under six environments (3 sites × 2 years). Marker coverage proved sufficient to ensure highly significant associations between the genes known to control simple traits (flower, hilum and pubescence colour) and flanking SNPs. Between one and eight genomic loci associated with more complex traits (maturity, plant height, seed weight, seed oil and protein) were also identified. Importantly, most of these GWAS loci were located within genomic regions identified by previously reported quantitative trait locus (QTL) for these traits. In some cases, the reported QTLs were also successfully validated by additional QTL mapping in a biparental population. This study demonstrates that integrating GBS and GWAS can be used as a powerful complementary approach to classical biparental mapping for dissecting complex traits in soya bean.
GWAS of Soybean Cyst Nematode (SCN) (Heterodera glycines) resistance for Soybean, relative to the Williams 82 assembly 2.0.
Genotyping Platform:
Tran_Steketee_2019
Genotypes:
448 accessions (MG 0 to VIII) from the United States Department of Agriculture (USDA) Soybean Germplasm Collection and the University of Georgia (UGA) soybean breeding program.
Description:
The most damaging pest in the production of Soybean (Glycine max) is the soybean cyst nematode (SCN) (Heterodera glycines). This study assessed the genome-wide marker–trait associations of SCN resistance in soybean. 462 genotypes were analyzed using Illumina's SoySNP50K iSelect Beadchips and three functional SCN KASP SNP markers GSM 381, GSM 383, and GSM 191 developed at the Rhg1 and Rhg4 loci. SCN resistance was measured using the FI index, which was defined as a ratio between the number of cysts on a given line and on Lee 74 (susceptible control line). The genome-wide association study (GWAS) identified 12 single-nucleotide polymorphisms (SNPs) on four chromosomes that had a significant (P < 0.05) association with the FI index. Significance was defined as a FI index below 30% and therefore sub-catagorized as resistant (R) (FI > 10%) or moderately resistant (MR) (10% < FI < 30%) to soybean cyst nematodes. 26 other SCN associated SNPs were identified on other chromosomes of soybean, but none of them were above the p-value cutoff point of 0.05.
GWAS of Soybean Cyst Nematode (SCN) (Heterodera glycines) resistance for Soybean, relative to the Wm82.gnm2 assembly (originally reported with respect to Wm82.gnm1)
Genotyping Platform:
Vuong_Sonah_2015
Genotypes:
553 soybean plant introductions (PIs) from MG III to V
Description:
A diverse panel of 553 soybean germplasm accessions, which were undergone multivariate selection procedures and best represents the diversity of the total collection, was evaluated for response to SCN HG Type 0. Over 50,000 SNP markers of the soybean genome generated in the SoySNP50K iSelect BeadChip were accessed from www.soybase.org. A total of 35,270 SNPs were selected for GWAS after excluding SNPs with more than 20 % missing data and a minor allele frequency less than 5 %. GWAS was performed using generalized linear model (GLM) identified 223 SNPs distributed over 19 different chromosomes and associated with resistance to SCN HG Type 0. The MLM identified 41 SNPs distributed over 16 loci on 14 different chromosomes that were significantly associated with resistance to SCN HG Type 0 (Table 2, Fig. 7). The known loci rhg1 on Chr. 18 and Rhg4 on Chr. 8, were also identified in this study. Highly significant SNPs on Chr. 8 between 7.5 to 8.6 Mb and on Chr. 18 between 1.2 to 6.6 Mb were associated with SCN resistance. These loci did not show a high level of significance even though these loci harbor a very high level of resistance.
GWAS study of seed weight in soybean, conducted on 166 from the USDA soybean collection, genotyped using the SoySNP50K BeadChip.
Genotyping Platform:
SoySNP50K
Genotypes:
166 lines from the USDA soybean collection with large or small seed weight
Description:
We selected 166 accessions from the USDA Soybean Germplasm Collection with either large or small seed weight and could typically grow in the same location. The accessions were evaluated for seed weight in the field for two years and genotyped with the SoySNP50K BeadChip containing >42,000 SNPs. Of the 17 SNPs on six chromosomes that were significantly associated with seed weight in two years based on a GWAS of the selective population, eight on chromosome 4 or chromosome 17 had significant Fst values between the large and small seed weight sub-populations. The seed weight difference of the two alleles of these eight significant SNPs varied from 8.1 g to 11.7 g/100 seeds in two years. We also identified haplotypes in three haplotype blocks with significant effects on seed weight. These findings were validated in a panel with 3753 accessions from the USDA Soybean Germplasm Collection.
GWAS study of architecture and yield-related traits in soybean, conducted on 219 accessions, genotyped using the 1536-SNP USLP1 array.
Genotyping Platform:
1536_USLP1
Genotypes:
219 accessions: 9 unknown origin, 7 USA, 1 Japan, 1 Brazil, and remainder from China
Description:
In this study, we performed genetic association analysis to dissect the relationships between plant architecture and yield component traits. Two hundred and nineteen accessions were employed, and eight agronomic traits were evaluated in six environments. Our results revealed strong positive correlations of plant architecture traits with yield components and the significant association of 4 SNPs with plant architecture traits and of 7 SNPs with yield component traits in two or more environments. Eight SNPs were co-associated with two traits.
GWAS study of flowering time, maturity dates and plant height in soybean, conducted on 309 soybean accessions, genotyped using the SoySNP50K BeadChip.
Genotyping Platform:
SoySNP50K
Genotypes:
309 accessions from the USDA Soybean Germplasm Collection
Description:
The linkage disequilibrium (LD) decayed slowly in soybean, and a substantial difference in LD pattern was observed between euchromatic and heterochromatic regions. A total of 27, 6, 18 and 27 loci for DTF, DTM, DFTM and PH were detected via GWAS, respectively. The Dt1 gene was identified in the locus strongly associated with both DTM and PH. Ten candidate genes homologous to Arabidopsis flowering genes were identified near the peak single nucleotide polymorphisms (SNPs) associated with DTF. Four of them encode MADS-domain containing proteins. Additionally, a pectin lyase-like gene was also identified in a major-effect locus for PH where LD decayed rapidly.
GWAS study of seed weight in soybean, conducted on 309 soybean accessions, genotyped using the SoySNP50K BeadChip.
Genotyping Platform:
SoySNP50K
Genotypes:
309 plant introductions (PIs) from the USDA Soybean Germplasm Collection
Description:
Genome-wide association study in a population of 309 soybean germplasm accessions using 31,045 single nucleotide polymorphisms (SNPs), estimating the prediction accuracy of genomic selection (GS) and marker-assisted selection (MAS) for seed weight (SW). Twenty-two loci of minor effect associated with SW were identified, including hotspots on Gm04 and Gm19. The mixed model containing these loci explained 83.4 % of phenotypic variation.
The aim of the present study was to investigate the genome-wide genetic architecture of resistance to SCN HG Type 2.5.7 (race 1) in landrace and elite cultivated soybeans.
Genotyping Platform:
Zhao_Teng_2017
Genotypes:
200 diverse soybean accessions
Description:
A total of 200 diverse soybean accessions were screened for resistance to SCN HG Type 2.5.7 and genotyped through sequencing using the Specific Locus Amplified Fragment Sequencing (SLAF-seq) approach with a 6.14-fold average sequencing depth. A total of 33,194 SNPs were identified with minor allele frequencies (MAF) over 4%, covering 97% of all the genotypes. Genome-wide association mapping (GWAS) revealed thirteen SNPs associated with resistance to SCN HG Type 2.5.7. These SNPs were distributed on five chromosomes (Chr), including Chr7, 8, 14, 15 and 18. Four SNPs were novel resistance loci and nine SNPs were located near known QTL. A total of 30 genes were identified as candidate genes underlying SCN resistance. Conclusions: A total of sixteen novel soybean accessions were identified with significant resistance to HG Type 2.5.7. The beneficial alleles and candidate genes identified by GWAS might be valuable for improving marker-assisted breeding efficiency and exploring the molecular mechanisms underlying SCN resistance.
GWAS of soybean yield-related traits, conducted on 113 wild soybean accessions, genotyped with 85 simple sequence repeat (SSR) markers.
Genotyping Platform:
Hu_Zhang_2014
Genotypes:
113 wild soybean accessions
Description:
To identify yield-enhancing quantitative trait locus (QTL) or gene from wild soybean, 113 wild soybeans accessions were phenotyped for five yield-related traits and genotyped with 85 simple sequence repeat (SSR) markers to conduct association mapping. A total of 892 alleles were detected for the 85 SSR markers, with an average 10.49 alleles; the corresponding PIC values ranged from 0.07 to 0.92, with an average 0.73. The genetic diversity of each SSR marker ranged from 0.07 to 0.93, with an average 0.75. A total of 18 SSR markers were identified for the five traits. Two SSR markers, sct_010 and satt316, which are associated with the yield per plant were stably expressed over two years at two experimental locations.
GWAS of Soybean Cyst Nematode (SCN) resistance in 1032 accessions of Glycine soja, using the SoySNP50K marker set relative to the Wm82.gnm1 assembly
Genotyping Platform:
SoySNP50K
Genotypes:
1032 accessions of Glycine soja, representing 88.3% of the USDA wild soybean germplasm collection.
Description:
The soybean cyst nematode (SCN) is one of the most destructive pathogens of soybean plants worldwide. Host-plant resistance is an environmentally friendly method to mitigate SCN damage. To date, the resistant soybean cultivars harbor limited genetic variation, and some are losing resistance. Thus, a better understanding of the genetic mechanisms of the SCN resistance, as well as developing diverse resistant soybean cultivars, is urgently needed. In this study, a genome-wide association study (GWAS) was conducted using 1032 wild soybean (Glycine soja) accessions with over 42,000 single-nucleotide polymorphisms (SNPs) to understand the genetic architecture of G. soja resistance to SCN race 1. Ten SNPs were significantly associated with the response to race 1. Three SNPs on chromosome 18 were localized within the previously identified quantitative trait loci (QTLs), and two of which were localized within a strong linkage disequilibrium block encompassing a nucleotide-binding (NB)-ARC disease resistance gene (Glyma.18G102600). Genes encoding methyltransferases, the calcium-dependent signaling protein, the leucine-rich repeat kinase family protein, and the NB-ARC disease resistance protein, were identified as promising candidate genes. The identified SNPs and candidate genes can not only shed light on the molecular mechanisms underlying SCN resistance, but also can facilitate soybean improvement employing wild genetic resources.
GWAS study of domestication-related traits in soybean, conducted on 105 wild and 262 cultivated soybeans, genotyped using the NJAU 355K SoySNP array.
Genotyping Platform:
NJAU355K
Genotypes:
105 wild and 262 cultivated soybean accessions
Description:
We developed a high-throughput NJAU 355K SoySNP array and used this array to study the genetic variation patterns in 367 soybean accessions, including 105 wild soybeans and 262 cultivated soybeans. The population genetic analysis suggests that cultivated soybeans have tended to originate from northern and central China, from where they spread to other regions, accompanied with a gradual increase in seed weight.
