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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 Yellow Bean Collection (YBC), which is comprised of 255 genotypes, and has not been used previously in genetic studies on anthracnose, is an excellent genetic resource for understanding the extent of anthracnose resistance and its genetic architecture in the yellow bean market class. The objectives of this study were i) evaluate the YBC for resistance to races 5, 19, 39, 51, 81, 183, 1050 and 1105 of C. lindemuthianum. and ii) conduct genome-wide association analysis to identify genomic regions and candidate genes associated with resistance to C. lindemuthianum. 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 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.

The low genetic diversity in Andean common bean (Phaseolus vulgaris) presents opportunities to improve stress tolerance and increase productivity. Thus, this study aimed to develop Andean bean breeding populations and evaluate them in suboptimal environments. Phaseolus Improvement Cooperative (PIC) populations were developed by crossing 53 Andean and five Middle American bean parents using bulk breeding. Selection and evaluation in Puerto Rico, South Africa, Tanzania, and Washington State resulted in 384 superior PIC lines used in subsequent studies. The PIC lines and the parents were genotyped using the common bean 12K single nucleotide polymorphism (SNP) chip, which yielded an initial set of 10,457 polymorphic SNPs. Population structure analyses using 2334 high‐quality SNPs indicated the strongest separation between heat tolerant landrace Indeterminate Jamacia Red (ADP‐0683)‐derived PIC lines and a group of lines derived from North American parents. The PIC lines and parents were grown under water stress in Puerto Rico in 2019 (n = 288) and 2020 (n = 176) to assess agronomic traits including seed yield. The best linear unbiased predictions for seed yield ranged from 31 to 388 kg ha−1 in 2019 and from 169 to 1762 kg ha−1 in 2020. Almost all the PIC lines matched or outperformed the parents in 2019, showing the utility of crossing lines from various origins. Genome‐wide association analysis identified SNPs associated with yield under drought stress at 44.2 Mb on Pv10, which could inform genetic studies for yield and drought tolerance. Overall, the PIC populations were useful for improving the genetic diversity and agronomic performance of Andean beans in suboptimal environments. Core Ideas: Phaseolus Improvement Cooperative (PIC) populations were developed from Andean bean bulk breeding populations.PIC populations were selected in Tanzania, South Africa, Puerto Rico, and Washington to reflect local preferences.Several Andean Diversity Panel accessions were frequently represented as parents in pedigrees of superior lines.Bulk breeding populations serve as an efficient resource for improvement of stress tolerance and productivity. [ABSTRACT FROM AUTHOR]

Wild crop germplasm and landrace varieties have long been considered as a source of novel genetic variation for improving domesticated crops. Due to genetic bottlenecks that occurred during domestication, dissemination, and subsequent crop improvement, many beneficial genes are absent from commercial varieties and elite breeding germplasm, yet are still present in wild populations. To catalog potential novel disease resistance genes useful for breeding more resilient dry beans, we screened wild and landrace Phaseolus vulgaris L. accessions archived in the USDA GRIN seed bank for untapped resistance to anthracnose (Colletotrichum lindemuthianum) and bean common mosaic necrosis virus (BCMNV). A population of 194 wild and 55 landrace accessions were screened for resistance to two highly virulent races of anthracnose (race 2047 and race 3481) and for resistance to the BCMNV strain NL‐3. Thirteen accessions, all wild, were resistant to both anthracnose races, with MX‐QT‐3 and PI 661812 displaying complete resistance with no disease symptoms across all replications. Surprisingly, no natural resistance to BCMNV strain NL‐3 was detected in the wild germplasm. PI 442541, PI 661891, and W6 10164 were the only three accessions that expressed the I‐gene phenotype and all three have some history of cultivation. This study provides a resource for introgression of genetic diversity for anthracnose resistance into cultivated beans and reveals that innate resistance to BCMNV may not exist in wild populations of P. vulgaris. Core Ideas: Wild Phaseolus vulgaris germplasm has genetic and phenotypic diversity not present in cultivated varieties.Resistance to two races of anthracnose exists in wild bean germplasm.Resistance to BCMNV NL‐3 was not found in wild bean germplasm, but in three landraces. [ABSTRACT FROM AUTHOR]

Kidney beans (Phaseolus vulgaris L.) have strict market specifications for seed and end‐use quality. One major quality concern is the appearance of cracks, also termed checks in the seed coat caused by mechanical damage occurring during harvest and postharvest handling. Genetic variability for seed coat checks (SCCs) has not been well characterized in kidney beans. The objectives of this study were (1) to test an existing screening method for easy assessment of seed coat mechanical damage, (2) to explore the genetic variability for mechanically induced seed coat damage in kidney bean and its relationship to seed coat thickness, (3) to characterize the relationship of SCC to end‐use quality, and (4) to identify potential germplasm resources for genetic improvement. A collection of dark red, light red, and white kidney beans were grown over 2 years and harvested with two threshing methods to mimic mild and severe treatments of mechanical damage. Belt threshing produced mild damage, and combine threshing produced severe damage. Seed coat thickness was not correlated with SCC of the combine‐threshed beans but was negatively correlated with the belt‐threshed beans at r = –0.33. Seed moisture content played an important role in SCC. Higher SCC severity scores resulted in lower canning quality appearance scores (r = –0.51). The SCC severity score of combine‐threshed seeds can be used as a selection factor in variety improvement for resilience to mechanical damage. Genotypes with low SCC severity score were identified for breeding initiatives. Core Ideas: Seed coat damage and cracking induced during mechanical harvest is known as seed coat check (SCC) in dry beans.Kidney bean germplasm exhibits variation for SCC.Seed coat thickness is not a good indicator for kidney bean germplasm susceptibility to SCC.SCC severity score of combine‐threshed seeds can be used for selecting resilient germplasm.Higher SCC severity scores resulted in lower canning quality appearance scores. [ABSTRACT FROM AUTHOR]

Tepary bean (Phaseolus acutifolius A. Gray) is a viable and nutritious alternative to common bean (P. vulgaris L.) in areas with excessively high temperatures and/or chronic drought. Tepary bean is a traditional crop of the Tohono O'odham Indians of the Sonoran Desert in the Southwest United States and Mexico, as well as other Indigenous peoples of the United States, Mexico, and Central America. Despite its potential for broad applications for reduced water‐input agriculture or for hot, semi‐arid, marginal production zones, tepary bean remains an orphan crop. 'USDA Fortuna' (Reg. no. CV‐352, PI 698459) is an improved tepary bean cultivar with enhanced seed size, seed quality, tolerance to Bean golden yellow mosaic virus, and resistance to local strains of rust in Puerto Rico. It has leafhopper pest resistance, common bacterial blight resistance, and moderate resistance to powdery mildew. USDA Fortuna is a high‐yielding tepary bean with an attractive black speckled seed color and a quick cooking time. This cultivar was developed cooperatively by the USDA‐ARS, the University of Puerto Rico, Zamorano University, the Instituto Dominicano de Investigaciones Agropecuarias y Forestales (IDIAF) of the Dominican Republic, Quisqueya University of Haiti, the National Seed Service of Haiti, Instituto Nacional de Innovación y Transferencia en Tecnología Agropecuaria (INTA) of Costa Rica, and Iowa State University. Core Ideas: Tepary bean has promise as a nutritious plant protein source in marginal environmentsUSDA Fortuna tepary bean has improved seed size and quality, and fast cooking timeUSDA Fortuna shows high common bacterial blight and moderate powdery mildew resistance, as well as leafhopper resistance [ABSTRACT FROM AUTHOR]