Abstract
A genome-wide association study (GWAS) was applied to detect single nucleotide polymorphisms (SNPs) significantly associated with resistance to Heterodera glycines (HG) also known as the soybean cyst nematode (SCN) in the core collection of common bean, Phaseolus vulgaris. There were 84,416 SNPs identified in 363 common bean accessions. GWAS identified SNPs on chromosome (Chr) 1 that were significantly associated with resistance to HG type 2.5.7. These SNPs were in linkage disequilibrium with a gene cluster orthologous to the three genes at the Rhg1 locus in soybean. A novel signal on Chr 7 was detected and associated with resistance to HG type 1.2.3.5.6.7. Genomic predictions (GPs) for resistance to these two SCN HG types in common bean achieved prediction accuracy of 0.52 and 0.41, respectively. Our study generated a high-quality SNP panel for 363 common bean accessions and demonstrated that both GWAS and GP were effective strategies to understand the genetic architecture of SCN resistance in common bean.
Highlights
Common bean (Phaseolus vulgaris L.) is one of the most important grain legumes in the human diet and a major source of protein for many people in developing countries[1]
Greenhouse evaluations of the common bean core collection for resistance to soybean cyst nematode (SCN) Heterodera glycines (HG) type 2.5.7 resulted in a normal distribution with a range of best linear unbiased prediction (BLUP) from 8 to 395 (FI from 0.5 to 198.9) (Fig. 1a)
The identification of single nucleotide polymorphisms (SNPs) associated with SCN resistance can help in the understanding of genetic architecture in common bean, and facilitates the genetic improvement of cultivars and the identification of resistance
Summary
Common bean (Phaseolus vulgaris L.) is one of the most important grain legumes in the human diet and a major source of protein for many people in developing countries[1]. Common bean has two geographical and genetic pools, one of which is the Mesoamerican gene-pool domesticated in Mexico and another is the Andean genepool domesticated in Central and South America[2,3]. Common bean and soybean (Glycine max (L.) Merr.) belong to the family Fabaceae, and encounter many of the same pathogens including soybean cyst nematode (SCN), Heterodera glycines (HG) Ichinohe[4]. The top 10-producing states for soybean include North Dakota, Minnesota, and Michigan, and these states when combined make up 60% of the common bean production Much of the area planted to common bean overlaps with soybean production areas and they are planted in late spring or early summer, which coincides with the period when SCN eggs hatch to become infectious juveniles
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