Genome-wide association mapping for component traits of drought tolerance in dry beans (Phaseolus vulgaris L.).

Understanding the genetic basis of traits of economic importance under drought stressed and well-watered conditions is important in enhancing genetic gains in dry beans (Phaseolus vulgaris L.). This research aims to: (i) identify markers associated with agronomic and physiological traits for drought tolerance and (ii) identify drought-related putative candidate genes within the mapped genomic regions. An andean and middle-american diversity panel (AMDP) comprising of 185 genotypes was screened in the field under drought stressed and well-watered conditions for two successive seasons. Agronomic and physiological traits, viz., days to 50% flowering (DFW), plant height (PH), days to physiological maturity (DPM), grain yield (GYD), 100-seed weight (SW), leaf temperature (LT), leaf chlorophyll content (LCC) and stomatal conductance (SC) were phenotyped. Principal component and association analysis were conducted using the filtered 9370 Diversity Arrays Technology sequencing (DArTseq) markers. The mean PH, GYD, SW, DPM, LCC and SC of the panel was reduced by 12.1, 29.6, 10.3, 12.6, 28.5 and 62.0%, respectively under drought stressed conditions. Population structure analysis revealed two sub-populations, which corresponded to the andean and middle-american gene pools. Markers explained 0.08-0.10, 0.22-0.23, 0.29-0.32, 0.43-0.44, 0.65-0.66 and 0.69-0.70 of the total phenotypic variability (R2) for SC, LT, PH, GYD, SW and DFW, respectively under drought stressed conditions. For well-watered conditions, R2 varied from 0.08 (LT) to 0.70 (DPM). Overall, 68 significant (p < 10-03) marker-trait associations (MTAs) and 22 putative candidate genes were identified across drought stressed and well-watered conditions. Most of the identified genes had known biological functions related to regulating the response to drought stress. The findings provide new insights into the genetic architecture of drought stress tolerance in common bean. The findings also provide potential candidate SNPs and putative genes that can be utilized in gene discovery and marker-assisted breeding for drought tolerance after validation.

Farmers' perceptions of navy bean (Phaseolus vulgaris L.) production constraints, preferred traits and farming systems and their implications on bean breeding: a case study from South East Lowveld region of Zimbabwe.

BACKGROUND: Navy bean is an important legume crop in Zimbabwe. Although its production in Zimbabwe is limited by multiple constraints including biotic, abiotic and socio-economic, there is no documented evidence. Thus, this study aimed at identifying farmers' production constraints, preferred traits and cultivars of navy bean, and strategies used to mitigate some of these constraints. METHODS: A Participatory Rural Appraisal approach involving transect walks, focus group discussions (FGDs), and formal surveys with semi-structured questionnaires was conducted in four villages of the Lowveld region of Zimbabwe. In each of the four villages, two FGDs (one for men and one for women) were conducted. A total of 176 (75 males and 101 females) navy bean-growing households were interviewed. Data from household interviews and FGDs was analysed using the Statistical Package for Social Scientists computer package. RESULTS: The most important constraints to navy bean production were drought stress (Females-86%, Males-73%), heat stress (Females-58%, Males-55%), power outages (Females-46%, Males-54%), poor soil fertility (Females-32%; Males-33%) and susceptibility to pod shattering (Females-32%, Males-43%). Mitigation strategies included mulching (18%), ridges (12%), reduced acreage (11%), and cultivating to retain more soil moisture (11%) for drought stress, while irrigating at night (32%), and adjusting planting dates (29%) were used to manage heat stress. Farmer-preferred traits included tolerance to drought and heat, early maturing varieties and disease resistance. Marketing constraints included non-payment for produce in hard currency, lack of diversity in terms of off-takers, high inflation, low grain producer price, delayed payment and breach of contract by contractors. CONCLUSION: There will be increased adoption of improved navy bean cultivars if breeding programs address the aforementioned constraints and consider farmer-preferred traits when developing new cultivars. Breeders should work closely with extension officers to ensure that cultivars released are cultivated with appropriate agronomic packages for increased productivity and high adoption.

Analyses of African common bean (Phaseolus vulgaris L.) germplasm using a SNP fingerprinting platform: diversity, quality control and molecular breeding.

Common bean (Phaseolus vulgaris L.) is an important staple crop for smallholder farmers, particularly in Eastern and Southern Africa. To support common bean breeding and seed dissemination, a high throughput SNP genotyping platform with 1500 established SNP assays has been developed at a genotyping service provider which allows breeders without their own genotyping infrastructure to outsource such service. A set of 708 genotypes mainly composed of germplasm from African breeders and CIAT breeding program were assembled and genotyped with over 800 SNPs. Diversity analysis revealed that both Mesoamerican and Andean gene pools are in use, with an emphasis on large seeded Andean genotypes, which represents the known regional preferences. The analysis of genetic similarities among germplasm entries revealed duplicated lines with different names as well as distinct SNP patterns in identically named samples. Overall, a worrying number of inconsistencies was identified in this data set of very diverse origins. This exemplifies the necessity to develop and use a cost-effective fingerprinting platform to ensure germplasm purity for research, sharing and seed dissemination. The genetic data also allows to visualize introgressions, to identify heterozygous regions to evaluate hybridization success and to employ marker-assisted selection. This study presents a new resource for the common bean community, a SNP genotyping platform, a large SNP data set and a number of applications on how to utilize this information to improve the efficiency and quality of seed handling activities, breeding, and seed dissemination through molecular tools.