Abstract
Soybean cyst nematode (SCN, Heterodera glycines) has become the major yield-limiting biological factor in soybean production. Common bean is also a good host of SCN, and its production is challenged by this emerging pest in many regions such as the upper Midwest USA. The use of host genetic resistance has been the most effective and environmentally friendly method to manage SCN. The objectives of this study were to evaluate the SCN resistance in the USDA common bean core collection and conduct a genome-wide association study (GWAS) of single nucleotide polymorphism (SNP) markers with SCN resistance. A total of 315 accessions of the USDA common bean core collection were evaluated for resistance to SCN HG Type 0 (race 6). The common bean core set was genotyped with the BARCBean6K_3 Infinium BeadChips, consisting of 4,654 SNPs. Results showed that 15 accessions were resistant to SCN with a Female Index (FI) at 4.8 to 9.4, and 62 accessions were moderately resistant (10 < FI < 30) to HG Type 0. The association study showed that 11 SNP markers, located on chromosomes Pv04, 07, 09, and 11, were strongly associated with resistance to HG Type 0. GWAS was also conducted for resistance to HG Type 2.5.7 and HG Type 1.2.3.5.6.7 based on the public dataset (N = 276), consisting of a diverse set of common bean accessions genotyped with the BARCBean6K_3 chip. Six SNPs associated with HG Type 2.5.7 resistance on Pv 01, 02, 03, and 07, and 12 SNPs with HG Type 1.2.3.5.6.7 resistance on Pv 01, 03, 06, 07, 09, 10, and 11 were detected. The accuracy of genomic prediction (GP) was 0.36 to 0.49 for resistance to the three SCN HG types, indicating that genomic selection (GS) of SCN resistance is feasible. This study provides basic information for developing SCN-resistant common bean cultivars, using the USDA core germ plasm accessions. The SNP markers can be used in molecular breeding in common beans through marker-assisted selection (MAS) and GS.
Highlights
Common bean (Phaseolus vulgaris L.) is the most important edible grain legume crop worldwide, with crop value equal to the combined value of all other food legumes such as peas and chickpeas (Jain et al, 2016)
All of the seven HG Type indicators were resistant with Female Index (FI) < 10, confirming that the soybean cyst nematode (SCN) used in this study was the HG Type 0 (Supplementary Table 2)
15 accessions of the USDA common bean core collection were observed for the resistance to SCN HG Type 0 with FI at 4.8 to 9.4; six single nucleotide polymorphism (SNP) markers, located on chromosomes Pv 04, 06, 07, 07, 09, and 11, respectively, were significantly associated with the resistance to this SCN HG Type 0
Summary
Common bean (Phaseolus vulgaris L.) is the most important edible grain legume crop worldwide, with crop value equal to the combined value of all other food legumes such as peas and chickpeas (Jain et al, 2016). About 2 million acres were planted, and approximately 1.3 million metric tons of common beans valued at US$2 billion were produced annually in the United States (US) (USDA NASS, 2020). The SCN is the most serious pathogen of soybean [Glycine max (L.) Merr.] in the US and suppresses a yield more than any other pathogen (Koenning and Wrather, 2010; Allen et al, 2017). The top four common bean-growing states, North Dakota, Michigan, Nebraska, and Minnesota, which produce approximately 70% of the common bean in the US, are in the North Central region. SCN infection can cause severe yield loss without any aboveground symptoms in common beans (Poromarto et al, 2010, 2012) and becomes a serious threat to common bean production
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