Abstract
Rhizoctonia solani Kühn (teleomorph Thanatephorus cucumeris) is an important root rot pathogen of common bean (Phaseolus vulgaris L.). To uncover genetic factors associated with resistance to the pathogen, the Andean (ADP; n = 273) and Middle American (MDP; n = 279) diversity panels, which represent much of the genetic diversity known in cultivated common bean, were screened in the greenhouse using R. solani anastomosis group 2-2. Repeatability of the assay was confirmed by the response of five control genotypes. The phenotypic data for both panels were normally distributed. The resistance responses of ∼10% of the ADP (n = 28) and ∼6% of the MDP (n = 18) genotypes were similar or higher than that of the resistant control line VAX 3. A genome-wide association study (GWAS) was performed using ∼200k single nucleotide polymorphisms to discover genomic regions associated with resistance in each panel, For GWAS, the raw phenotypic score, and polynomial and binary transformation of the scores, were individually used as the input data. A major QTL peak was observed on Pv02 in the ADP, while a major QTL was observed on Pv01 with the MDP. These regions were associated with clusters of TIR-NB_ARC-LRR (TNL) gene models encoding proteins similar to known disease resistance genes. Other QTL, unique to each panel, were mapped within or adjacent to a gene model or cluster of related genes associated with disease resistance. This is a first case study that provides evidence for major as well as minor genes involved in resistance to R. solani in common bean. This information will be useful to integrate more durable root rot resistance in common bean breeding programs and to study the genetic mechanisms associated with root diseases in this important societal legume.
Highlights
Common bean (Phaseolus vulgaris L.) is one of the most important cultivated grain legumes for human consumption in the world (United States Dry Bean Council, 2017)
The objectives of this research were to: (1) demonstrate reproducibility of a greenhouse evaluation system for Rhizoctonia root rot in common bean; (2) characterize resistance to R. solani within the Andean Diversity Panel (ADP) and Middle American Diversity Panel (MDP); (3) discover genomic regions associated with resistance based on raw and transformed phenotypic data using genome-wide association study (GWAS); and (4) identify candidate genes underlying resistance to Rhizoctonia root rot in common beans
The wheat kernels were soaked for approximately 15 h at 22 ± 2◦C, water was drained from the trays, trays were covered with aluminum foil and autoclaved at 121◦C for 2 h, cooled for 24 h at room temperature, and autoclaved again for 2 h
Summary
Common bean (Phaseolus vulgaris L.) is one of the most important cultivated grain legumes for human consumption in the world (United States Dry Bean Council, 2017). The Andean genepool is divided into three races including Nueva Granada, Peru, and Chile (Singh et al, 1991). Middle American beans are primarily grown from North America, through Central America, and into northern South America. These include the pinto, navy, great northern, black, and small red beans market classes. From race Nueva Granada of the Andean gene pool, are prevalent in the US (United States Dry Bean Council, 2017) and Africa. Collections of 396 and 280 P. vulgaris accessions, referred as the Andean Diversity Panel (ADP; Cichy et al, 2015) and Middle American Diversity Panel (MDP; Moghaddam et al, 2016), were created to reflect the genetic diversity in the two major gene pools and facilitate gene pool specific genetic analyses
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