Anthracnose is a seed-borne disease of common bean (Phaseolus vulgaris L.) caused by the fungus Colletotrichum lindemuthianum, and the pathogen is cosmopolitan in distribution. The objectives of this study were to identify new sources of anthracnose resistance in a diverse panel of 230 Andean beans comprised of multiple seed types and market classes from the Americas, Africa, and Europe, and explore the genetic basis of this resistance using genome-wide association mapping analysis (GWAS). Twenty-eight of the 230 lines tested were resistant to six out of the eight races screened, but only one cultivar Uyole98 was resistant to all eight races (7, 39, 55, 65, 73, 109, 2047, and 3481) included in the study. Outputs from the GWAS indicated major quantitative trait loci (QTL) for resistance on chromosomes, Pv01, Pv02, and Pv04 and two minor QTL on Pv10 and Pv11. Candidate genes associated with the significant SNPs were detected on all five chromosomes. An independent QTL study was conducted to confirm the physical location of the Co-1 locus identified on Pv01 in an F4:6 recombinant inbred line (RIL) population. Resistance was determined to be conditioned by the single dominant gene Co-1 that mapped between 50.16 and 50.30 Mb on Pv01, and an InDel marker (NDSU_IND_1_50.2219) tightly linked to the gene was developed. The information reported will provide breeders with new and diverse sources of resistance and genomic regions to target in the development of anthracnose resistance in Andean beans.

Dry beans (Phaseolus vulgaris L.) of the Andean gene pool, including red mottled, kidney, cranberry, and yellow seed types are important in Africa and the Americas. Andean dry bean breeding gains have lagged behind those of Mesoamerican beans. This difference may result from a narrower genetic base in the Andean gene pool and reduced breeding efforts. The objective of this research was to establish, genotype, and phenotype a panel of bean germplasm to be used for Andean dry bean breeding. An Andean diversity panel (ADP) was assembled, consisting of 396 accessions and including important cultivars, breeding lines, and landraces that originate mostly from Africa, the Caribbean, and North and South America. The panel was genotyped using the Illumina BARCBean6K_3 SNP BeadChip. The population contained two subgroups: Andean and Mesoamerican bean germplasm. The ADP was comprised of 349 Andean, 21 Mesoamerican, and 26 Andean–Mesoamerican admixed accessions. Most admixed lines came from Africa (12 accessions) and the Caribbean (five accessions). Association mapping was conducted for determinacy. Significant single‐nucleotide polymorphism (SNP) trait associations were found on chromosome Pv01, with the most significant SNP marker being 3.1 kb from the Terminal Flower 1 PvTFL1y gene. The ADP was evaluated for numerous traits in field trials in the United States and Africa. Variability was found for resistance to rust, angular leaf spot and common bacterial blight diseases; tolerance to low soil fertility; cooking time; and other traits that can be used to improve Andean bean germplasm for Africa and the Americas.

A genome-wide association study (GWAS) using a global Andean diversity panel (ADP) of 237 genotypes of common bean (Phaseolus vulgaris L.) was conducted to gain insight into the genetic architecture of phenology, biomass, yield components, and seed yield traits. The panel was evaluated for 2 yr in field trials in Michigan and genotyped with 5398 single nucleotide polymorphism (SNP) markers. After correcting for population structure and cryptic relatedness, significant SNP markers associated with several agronomic traits were identified. Positional candidate genes, including Phvul.001G221100 on P. vulgaris (Pv) chromosome 01, associated with days to flowering and maturity were identified. Significant SNPs for seed yield were identified on Pv03 and Pv09 and colocalized with quantitative trait loci (QTL) for yield from previous studies conducted in several environments and contrasting genetic backgrounds. The majority of germplasm carrying the alleles with positive effects on seed yield was of African origin and largely underutilized in US breeding programs. The study provided insights into the genetic architecture of agronomic traits in Andean beans.

Significant SNPs and candidate genes for symbiotic nitrogen fixation (SNF) and related traits were identified on Pv03, Pv07 and Pv09 chromosomes of common bean. A genome-wide association study (GWAS) was conducted to explore the genetic basis of variation for symbiotic nitrogen fixation (SNF) and related traits in the Andean Diversity Panel (ADP) comprising 259 common bean (Phaseolus vulgaris) genotypes. The ADP was evaluated for SNF and related traits in both greenhouse and field experiments. After accounting for population structure and cryptic relatedness, significant SNPs were identified on chromosomes Pv03, Pv07 and Pv09 for nitrogen derived from atmosphere (Ndfa) in the shoot at flowering, and for Ndfa in seed. The SNPs for Ndfa in shoot and Ndfa in seed co-localized on Pv03 and Pv09. Two genes Phvul.007G050500 and Phvul.009G136200 that code for leucine-rich repeat receptor-like protein kinases (LRR-RLK) were identified as candidate genes for Ndfa. LRR-RLK genes play a key role in signal transduction required for nodule formation. Significant SNPs identified in this study could potentially be used in marker-assisted breeding to accelerate genetic improvement of common bean for SNF.

Bean (Phaseolus vulgaris) anthracnose caused by the hemi-biotrophic pathogen Colletotrichum lindemuthianum is a major factor limiting production worldwide. Although sources of resistance have been identified and characterized, the early molecular events in the host-pathogen interface have not been investigated. In the current study, we conducted a comprehensive transcriptome analysis using Illumina sequencing of two near isogenic lines (NILs) differing for the presence of the Co-1 gene on chromosome Pv01 during a time course following infection with race 73 of C. lindemuthianum. From this, we identified 3,250 significantly differentially expressed genes (DEGs) within and between the NILs over the time course of infection. During the biotrophic phase the majority of DEGs were up regulated in the susceptible NIL, whereas more DEGs were up-regulated in the resistant NIL during the necrotrophic phase. Various defense related genes, such as those encoding PR proteins, peroxidases, lipoxygenases were up regulated in the resistant NIL. Conversely, genes encoding sugar transporters were up-regulated in the susceptible NIL during the later stages of infection. Additionally, numerous transcription factors (TFs) and candidate genes within the vicinity of the Co-1 locus were differentially expressed, suggesting a global reprogramming of gene expression in and around the Co-1 locus. Through this analysis, we reduced the previous number of candidate genes reported at the Co-1 locus from eight to three. These results suggest the dynamic nature of P. vulgaris–C. lindemuthianum interaction at the transcriptomic level and reflect the role of both pathogen and effector triggered immunity on changes in plant gene expression.

Key message Cooked bean flavor and texture vary within and across 20 Andean seed types; SNPs are significantly associated with total flavor, beany, earthy, starchy, bitter, seed-coat perception, and cotyledon texture. Abstract Common dry beans are a nutritious food recognized as a staple globally, but their consumption is low in the USA. Improving bean flavor and texture through breeding has the potential to improve consumer acceptance and suitability for new end-use products. Little is known about genetic variability and inheritance of bean sensory characteristics. A total of 430 genotypes of the Andean Diversity Panel representing twenty seed types were grown in three locations, and cooked seeds were evaluated by a trained sensory panel for flavor and texture attribute intensities, including total flavor, beany, vegetative, earthy, starchy, sweet, bitter, seed-coat perception, and cotyledon texture. Extensive variation in sensory attributes was found across and within seed types. A set of genotypes was identified that exhibit extreme attribute intensities generally stable across all three environments. seed-coat perception and total flavor intensity had the highest broad-sense heritability (0.39 and 0.38, respectively), while earthy and vegetative intensities exhibited the lowest (0.14 and 0.15, respectively). Starchy and sweet flavors were positively correlated and highest in white bean genotypes according to principal component analysis. SNPs associated with total flavor intensity (six SNPs across three chromosomes), beany (five SNPs across four chromosomes), earthy (three SNPs across two chromosomes), starchy (one SNP), bitter (one SNP), seed-coat perception (three SNPs across two chromosomes), and cotyledon texture (two SNPs across two chromosomes) were detected. These findings lay a foundation for incorporating flavor and texture in breeding programs for the development of new varieties that entice growers, consumers, and product developers alike.

The common bean weevil (Acanthoscelides obtectus [Say]) is an important postharvest pest of common bean (Phaseolus vulgaris L.) seed. To expand the current knowledge of resistance to A. obtectus, a quantitative trait loci (QTL) analysis was conducted using a common bean population of 210 F4:5 recombinant inbred lines derived from a cross of Solwezi, a susceptible bean landrace from Zambia, with breeding line AO‐1012‐29‐3‐3A that possesses resistance to A. obtectus. This population was genotyped with 5398 single nucleotide polymorphism (SNP) markers, and evaluated for resistance to A. obtectus and seed weight. Three QTL for resistance to A. obtectus were identified on chromosomes Pv04 and on Pv06. One of the QTL on Pv04, named as AO4.1SA, was previously reported as the arcelin, phytohemagglutinin and α‐amylase, (APA) resistance locus. The other two QTL for resistance to A. obtectus are new. In addition, four QTL for seed weight were identified on Pv04 (SW4.1SA), Pv07 (SW7.1SA), Pv08 (SW8.1AN,SA), and Pv09 (SW9.4SA). The AO4.1SA and SW4.1SA QTL for A. obtectus resistance and seed weight, respectively, co‐localized on Pv04. Once markers linked to the identified QTL for resistance are validated, they could potentially be used in marker‐assisted breeding to accelerate development of common bean cultivars with resistance to A. obtectus.

Aluminum toxicity in acidic soils is a major constraint to common bean (Phaseolus vulgaris L.) production. The objective of this study was to identify quantitative trait loci (QTL) for Al resistance in a population of 150 F 4:8 recombinant inbred lines (RILs) derived from parents Solwezi and AO-1012-29-3-3A, which contrasted in resistance to Al. The RILs and their parents were evaluated for Al resistance in a hydroponic system that had two nutrient solutions with either 0 μM (control solution) or 15 μM Al concentration (Al stress solution). Primary traits including root length (RL), root dry weight (RDW), and shoot dry weight (SDW) were measured. Percentage reductions in RL, RDW, and SDW were calculated from their respective primary traits. The RILs were genotyped with 5,398 single nucleotide polymorphisms and QTL identified using composite interval mapping. A total of eight QTL for Al resistance were identified on chromosomes Pv02, Pv04, Pv06, Pv07, Pv09, and Pv10. Variation in Al resistance explained by individual QTL ranged from 7.6 to 14.7%. Aluminum resistance QTL RL10.1 on Pv10 explained 10% of the genetic variation in RL. The QTL RL10.1 overlapped with QTL RDW10.1 identified for RDW in Al stress solution. Another Al resistance QTL RL6.1, which explained 10% of Al resistance variation, was identified on Pv06. The QTL on Pv02 and Pv07 appear to overlap with previously reported QTL for Al resistance. A candidate gene Phvul.007G025900 encoding an Al-activated malate transporter was identified within the QTL RL7.1 The genetic architecture of Al resistance in the Solwezi and AO-1012-29-3-3A population is polygenic with additive action.Abbreviations: LOD, logarithm of odds; QTL, quantitative trait locus/loci; RDW, root dry weight; RIL, recombinant inbred line; RL, root length; SDW, shoot dry weight; SNP, single nucleotide polymorphism.