Genome-wide association analysis of anthracnose resistance in the Yellow Bean Collection of Common Bean

Beans play an important role in combating malnutrition due to their richness in protein, carbohydrates, and minerals, particularly iron and zinc. The crop has a rich diversity in traits such as seed color, seed size, and seed shape, which have been used to classify beans into different market classes. One of the market classes is the yellow bean, which is comprised of both Andean and Middle American genotypes. The yellow bean market class is commercially important in Latin America, the Caribbean, and Africa. In Africa, yellow beans are popular in Angola, Kenya, Tanzania, and Zambia. In Zambia, the Manteca yellow landrace known as Lusaka is preferred over other bean market classes and fetches higher market prices. In Tanzania, the Njano class is the most popular yellow seed type, and it is estimated that about 32% of total bean production there is for yellow beans, mainly the Njano type. Yellow beans have become increasingly important bean corridors of both East and Southern Africa. Consumers prefer yellow beans to other market classes due to their superiority in several end-use traits. Manteca yellow beans have shorter cooking time and higher iron bioavailability than other market classes. Despite the consumer preference and nutritional attributes of some yellow bean market classes, they have historically received less breeding efforts compared to other popular bean market classes. Average yields for yellow bean are often lower than other bean classes, and several abiotic and biotic stresses contribute to low yields. Diseases are a major contributing factor to the low yields of yellow beans. Anthracnose (ANTH), caused by Colletotrichum lindemuthianum, is a major disease that affects yellow beans. Depending on varietal susceptibility and weather conditions, ANTH can cause yield losses of up to 100%. ANTH is a seed-borne disease, and planting infected seed is a major mode of its transmission. This transmission mode of ANTH makes its control or management challenging because of the widespread use of on-farm saved seed in Africa and Latin America. To date, 19 dominant major-effect ANTH resistance genes have been identified in common bean. These genes are classified as either Andean or Middle American depending on whether they were identified in an Andean or Middle American genotype. Andean genes include Co-1, Co-12, Co-13, Co-14, Co-15, Co-x, Co-w, Co-y, and Co-z, while Middle American genes include Co-2, Co-3, Co-4, Co-5, Co-6, Co-11, Co-16, Co-17, Co-u, and Co-v. The genes Co-1, Co-3, Co-4, and Co-5 are multi-allelic. Some of these major genes are located in genomic regions that contain clusters of disease resistance genes that control resistance to multiple diseases. The Yellow Bean Collection (YBC) is a diversity panel that has been assembled in common bean. The YBC is comprised of landraces, varieties, and elite lines of yellow beans, which are variable for several traits, including anthracnose resistance. The YBC was genotyped with 72,866 SNPs, and genome-wide association analysis was conducted using Mixed Linear Model in TASSEL. Andean and Middle American genotypes with superior levels of resistance to the eight races of C. lindemuthianum were identified. YBC278 was the only one among 255 genotypes that was highly resistant to all eight races. Resistance to anthracnose in the YBC 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 overlapped 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.