Genome-wide association analysis of anthracnose resistance in the yellow bean collection of common bean

Authors: KUWABO, KUWABO - University Of Zambia; HAMABWE, SWIVIA - University Of Zambia; KACHAPULULA, PAUL - University Of Zambia; Cichy, Karen; PARKER, TRAVIS - University Of California, Davis; MUKUMA, CHIKOTI - Zambia Agricultural Research Institute; KAMFWA, KELVIN - University Of Zambia

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/8/2023
Publication Date: 11/10/2023
Citation: Kuwabo, K., Hamabwe, S., Kachapulula, P., Cichy, K.A., Parker, T., Mukuma, C., Kamfwa, K. 2023. Genome-wide association analysis of anthracnose resistance in the yellow bean collection of common bean. PLOS ONE. 18(11). Article e0293291. https://doi.org/10.1371/journal.pone.0293291.
DOI: https://doi.org/10.1371/journal.pone.0293291

Interpretive Summary: Dry bean is a source of food and nutritional security for millions of households worldwide with the highest consumption in Africa. Yellow beans have become increasingly important bean corridors of both East and Southern Africa where they are valued for their flavor and faster cooking times. In spite of their favorable culinary qualities, yellow beans are susceptible to many diseases, thereby reducing their seed yields and making them more challenging for farmers to grow. Anthracnose is a seed borne bacterial disease that under environmental conditions that favor the pathogen and in combination with a susceptible variety, can devastate yellow bean production. Genetic resistance is a very effective means to reduce the negative consequences of anthracnose on bean production. The goal of this research was to evaluate a diverse set of 255 yellow bean genotypes for resistance to the eight races of anthracnose known to infect dry beans and identify regions in the bean genome conferring resistance. Three bean genotypes were identified with resistance to seven of eight races and one was identified with resistance to all eight races. These genotypes will be useful in breeding improved yellow bean cultivars. Identification of genomics regions associated with the resistance will be useful to improve the breeding process to effectively incorporate anthracnose resistance genes.

Technical Abstract: Anthracnose caused by Colletotrichum lindemuthianum is a major disease of common bean (Phaseolus vulgaris) worldwide. Yellow beans are a major market class of common bean especially in eastern and southern Africa. The objectives of this study were i) evaluate the yellow bean collection for resistance to eight races of C. lindemuthianum, and ii) conduct genome-wide association analysis to identify genomic regions and candidate genes associated with resistance to ten races of C. lindemuthianum. The Yellow Bean Collection comprised of 255 diverse yellow bean genotypes was evaluated for resistance to races 5, 19, 39, 51, 81, 183, 1050 and 1105 of C. lindemuthianum. The Yellow Bean Collection was genotyped with 72,866 SNPs using Genotyping by Sequencing and genome-wide association analysis was conducted using Mixed Linear Model in TASSEL. Several genotypes with superior levels of resistance to the eight races used in the current study were identified. The genotype YBC278 was the only one among 255 genotypes that was highly resistant to all eight races. Resistance in the Yellow Bean Collection to the eight races used in the current study was controlled by major-effect loci on chromosomes Pv01, Pv03, Pv04, Pv05 and Pv07. The genomic region on Pv01, which overlapped with the Andean locus Co-1 provided resistance to races 81, 1050 and 1105. Significant SNPs for resistance to race 39 were identified on Pv02. The genomic region on Pv04, which overlaps with known major-effect loci Co-3, Co-15, Co-16, Co-y and Co-z, provided resistance to races 5, 19, 51 and 183. Novel genomic regions for resistance to race 39 were identified on Pv05 and Pv07. Plant resistance genes (R genes) with NB-ARC and LRR domains, which occurred in clusters, were identified as positional candidate genes for genomic regions on Pv02 and Pv04.