Genome‐wide association analysis of resistance to Pythium ultimum in common bean (Phaseolus vulgaris)

Abstract

Common bean is the most important edible grain legume and dietary component in the world (Gepts et al., 2008). Bean contributes significantly to food and nutritional security of millions in sub-Saharan Africa and the developing world, providing a cheap protein source and micronutrients such as iron and zinc (Broughton et al., 2003; Graham et al., 2007), and income for smallholder farmers. However, productivity of common bean in many parts of Central and South America, and Africa is constrained by several diseases that includes root rots (RR) (Abawi and Corrales, 1990). Common bean RR caused by a complex of numerous soil-borne pathogenic fungi including Fusarium solani f. sp. phaseoli, Pythium spp., Rhizoctonia solani and Sclerotium rolfsii Sacc. are the primary cause of crop failures among subsistence farmers in the East African Region (Abawi and Corrales,

Genetic Analyses and Genomic Predictions of Root Rot Resistance in Common Bean Across Trials and Populations

“…The traits Pyth_COL (P. myriotylum response in the greenhouse) RRD_field (root rot damage in the field) and RRD_all (root rot damage combining both datasets) were evaluated in the RR panel in Colombia (COL). The traits Fus_UGA (F. cuneirostrum), Pyth_UGA (P. ultimum), Rhiz_USA (R. solani) and Fus_USA (F. solani) were evaluated in the ADP panel in Uganda (UGA) (Amongi et al, 2020;Onziga Dramadri et al, 2020) and the USA (Oladzad et al, 2019;Zitnick-Anderson et al, 2020). The ALS response was evaluated in the extBALSIT panel in Colombia (COL) and Uganda (UGA) (Nay et al, 2019).…”

“…We observed a similar trend in the RR and extBALSIT populations, but it was not the case for the ADP evaluations in Uganda (Figure 5), where the PA fell by around 40 points below the estimated heritability. This result can be attributable to the binary distribution with presence/absence scores that the original data display (Amongi et al, 2020;Onziga Dramadri et al, 2020), which confers high heritability estimates, and the RKHS model evaluated in this study, which performed the prediction of a trait with quantitative nature. Wen et al (2019) confirmed that traits with high heritability would have higher PAs.…”

“…The ADP represents the genetic diversity of cultivated germplasm of the Andean genepool, containing landraces, breeding lines and varieties from public and private breeding programs (Cichy et al, 2015a,b;Kamfwa et al, 2015a;Tock et al, 2017;Oladzad et al, 2019;Zitnick-Anderson et al, 2020). The ADP was evaluated for Pythium ultimum (Pyth_UGA) and Fusarium cuneirostrum (Fus_UGA) under greenhouse conditions at the CIAT-Kawanda research station (Uganda) as described by Amongi et al (2020) and Onziga Dramadri et al (2020). This panel was also evaluated under greenhouse conditions for resistance to Rhizoctonia solani (Rhiz_USA) and Fusarium solani (Fus_USA) at North Dakota State University (United States) as described by Oladzad et al (2019) and Zitnick-Anderson et al (2020).…”

“…To investigate a potential general quantitative tolerance to root diseases, we evaluated GP accuracies across previously published data sets on related traits. PAs across trials were investigated with data sets of Pythium, Fusarium (Fus), and Rhizoctonia (Rhiz) root rot evaluated in the Andean Diversity Panel (ADP) (Oladzad et al, 2019;Amongi et al, 2020;Onziga Dramadri et al, 2020;Zitnick-Anderson et al, 2020). Cross validation within this panel showed highest prediction accuracies for evaluations in Uganda (Pyth_Uga and Fus_Uga) ( Figure 6).…”

Genome‐wide association analysis of drought adaptive traits in common bean

“…The availability of high‐density, genome‐wide SNP markers has made genome‐wide association study (GWAS) a useful approach for identifying marker loci associated with causative variation in important traits in a diverse germplasm collection. In common bean, GWAS has been used for mapping genomic regions associated with a number of traits of economic importance, including phenology and yield component traits, cooking time, and disease resistance (Cichy et al., 2015; Dramadri et al., 2020; Hoyos‐Villegas et al., 2017; Kamfwa et al., 2015; Zuiderveen et al., 2016). The development of bean cultivars with enhanced tolerance to DS can be improved through the identification of genomic regions and associated key agronomic and PS traits and a better understanding of the genetic control and physiological mechanisms associated with the key traits regulating drought tolerance.…”