Abstract
Soybean cyst nematode (SCN), Heterodera glycines Ichinohe, is one of the most devastating pathogens affecting soybean production in the U.S. and worldwide. The use of SCN-resistant soybean cultivars is one of the most affordable strategies to cope with SCN infestation. Because of the limited sources of SCN resistance and changes in SCN virulence phenotypes, host resistance in current cultivars has increasingly been overcome by the pathogen. Host tolerance has been recognized as an additional tool to manage the SCN. The objectives of this study were to conduct a genome-wide association study (GWAS), to identify single nucleotide polymorphism (SNP) markers, and to perform a genomic selection (GS) study for SCN tolerance in soybean based on reduction in biomass. A total of 234 soybean genotypes (lines) were evaluated for their tolerance to SCN in greenhouse using four replicates. The tolerance index (TI = 100 × Biomass of a line in SCN infested / Biomass of the line without SCN) was used as phenotypic data of SCN tolerance. GWAS was conducted using a total of 3,782 high quality SNPs. GS was performed based upon the whole set of SNPs and the GWAS-derived SNPs, respectively. Results showed that (1) a large variation in soybean TI to SCN infection among the soybean genotypes was identified; (2) a total of 35, 21, and 6 SNPs were found to be associated with SCN tolerance using the models SMR, GLM (PCA), and MLM (PCA+K) with 6 SNPs overlapping between models; (3) GS accuracy was SNP set-, model-, and training population size-dependent; and (4) genes around Glyma.06G134900, Glyma.15G097500.1, Glyma.15G100900.3, Glyma.15G105400, Glyma.15G107200, and Glyma.19G121200.1 (Table 4). Glyma.06G134900, Glyma.15G097500.1, Glyma.15G100900.3, Glyma.15G105400, and Glyma.19G121200.1 are best candidates. To the best of our knowledge, this is the first report highlighting SNP markers associated with tolerance index based on biomass reduction under SCN infestation in soybean. This research opens a new approach to use SCN tolerance in soybean breeding and the SNP markers will provide a tool for breeders to select for SCN tolerance.
Highlights
Soybean [Glycine max (L.) Merr.] is a widely grown legume with high oil and protein contents
Chromosome 18 harbored a total 4 significant single nucleotide polymorphism (SNP) markers mapped on a 7-Mb genomic region. These SNPs consisted of Gm18_51128392_G_A (LOD = 3.37, MAF = 6.86%), Gm18_51659540_A_G (LOD = 3.44, MAF = 6.86%), Gm18_51867289_C_T (LOD = 3.27, MAF = 6.53%), and Gm18_58588820_A_C (LOD = 3.35, MAF = 6.86%) (Table 3) (Fig 2A). These results indicated that the 7-Mb region of chromosome 18 harboring the aforementioned SNPs had a strong likelihood of loci affecting tolerance index based on biomass reduction under Soybean cyst nematode (SCN) infestation in soybean
This study reported the variation in tolerance index based on biomass reduction of a total of 234 soybean genotypes
Summary
Soybean [Glycine max (L.) Merr.] is a widely grown legume with high oil and protein contents. Soybean is one of the most economically important cultivated legumes worldwide. The value of biofuel made from soybean was reported to exceed $35 billion in the United States Increase in need for soybean production has been significant [2]. This requires the use of high-yielding soybean cultivars and the expansion of croplands for soybean cultivation. Soybean production has been constrained by various factors. Heterodera glycines Ichinohe, has been one of the most devastating biotic stresses affecting soybean production worldwide. Costs associated with soybean production loss due to SCN have exceeded $1.5 billion in the U.S alone [3]
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