Sources of Resistance to Fusarium solani and Associated Genomic Regions in Common Bean Diversity Panels

Abstract

Common bean (Phaseolus vulgaris L.) production worldwide is hampered by Fusarium root rot (FRR), which is caused by Fusarium solani. Screening for FRR resistance on a large scale is notoriously difficult and often yields inconsistent results due to variability within the environment and pathogen biology. A greenhouse screening assay was developed incorporating multiple isolates of F. solani to improve assay reproducibility. The Andean (ADP; n = 270) and Middle American (MDP; n = 280) Diversity Panels were screened in the greenhouse to identify genetic factors associated with FRR resistance. Forty-seven MDP and 34 ADP lines from multiple market classes were identified as resistant to FRR. Greenhouse phenotyping repeatability was confirmed via five control lines. Genome-wide association mapping using ∼200k SNPs was performed on standard phenotyping score 1-9, as well as binary and polynomial transformation of score data. Sixteen and seven significant genomic regions were identified for ADP and MDP, respectively, using all three classes of phenotypic data. Most candidate genes were associated with plant immune/defense mechanisms. For the ADP population, ortholog of glucan synthase-like enzyme, senescence-associated genes, and NAC domain protein, associated with peak genomic region Pv08:0.04-0.18 Mbp, were the most significant candidate genes. For the MDP population, the peak SNPs Pv07:15.29 Mbp and Pv01:51 Mbp mapped within gene models associated with ethylene response factor 1 and MAC/Perforin domain-containing gene respectively. The research provides a basis for bean improvement through the use of resistant genotypes and genomic regions for more durable root rot resistance.

Using Breeding Populations With a Dual Purpose: Cultivar Development and Gene Mapping—A Case Study Using Resistance to Common Bacterial Blight in Dry Bean (Phaseolus vulgaris L.)

“…Oladzad et al (2019b) identified resistance to Rhizoctonia solani in both gene pools, with no similar resistance regions identified. Similarly, Zitnick-Anderson et al (2020) found no similarity in significant regions associated with resistance to Fusarium solani between the two gene pools. In contrast, the similarity of the associated locations of CBB resistance in this study suggests that a similar genetic factor or mechanism produces the phenotype in both the Andean and Middle American populations.…”

“…The combination of the sequencing and assembly of the P. vulgaris genome (Schmutz et al, 2014) and the availability of massively parallel sequencing enabled the use of genomewide association studies (GWAS) in dry bean using GBSgenerated SNP data (Cichy et al, 2015;Kamfwa et al, 2015;Moghaddam et al, 2016;Zuiderveen et al, 2016;Soltani et al, 2017;Oladzad et al, 2019a,b;Zitnick-Anderson et al, 2020). In dry bean, the Middle American and Andean diversity panels were established by individually selecting primarily cultivated genotypes from the two gene pools (Cichy et al, 2015;Moghaddam et al, 2016).…”

“…In dry bean, the Middle American and Andean diversity panels were established by individually selecting primarily cultivated genotypes from the two gene pools (Cichy et al, 2015;Moghaddam et al, 2016). Both panels have been used to map various agronomic, food quality, and disease resistance traits (Cichy et al, 2015;Kamfwa et al, 2015;Moghaddam et al, 2016;Zuiderveen et al, 2016;Soltani et al, 2017;Oladzad et al, 2019b;Zitnick-Anderson et al, 2020) with GWAS. These diversity panels are a great tool for mapping genes and finding new sources of genetic variability to incorporate into breeding material.…”

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

“…Different data sets previously reported for other common bean root rot-related pathogens in the Andean Diversity Panel ADP were also used in this study. 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).…”

“…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). In addition, we used the Angular Leaf Spot (ALS) datasets reported by Nay et al (2019).…”