Location: Tropical Crops and Germplasm Research
Project Number: 6090-21000-063-000-D
Project Type: In-House Appropriated
Start Date: May 9, 2023
End Date: May 8, 2028
Objective:
1: Conduct research to develop integrated genetic and genomic tools that use computational genomics and marker-assisted selection for improvement of Phaseolus species with emphasis on gene introgression.
1.A: Identify genomic regions for agriculturally important disease resistance and simply inherited agronomic traits in common bean and tepary bean using synteny and QTL analyses for KASP marker development.
1.B: Identify genomic regions for novel agriculturally important drought and high ambient temperature response traits in common bean and tepary bean through genetic analysis of RIL populations and diversity panels.
2: Conduct research to develop and release novel common bean germplasm and cultivars with resistance or tolerance to biotic and abiotic stress.
2.A: Develop and release novel common bean germplasm and cultivars.
2.B: Develop and release novel tepary bean germplasm and cultivars.
Approach:
Development of novel genetic and genomic tools for accelerated transfer of traits between Phaseolus vulgaris (common bean) and other Phaseolus species, such as P. acutifolius (tepary bean), will be used to facilitate the deployment of heat, drought, disease, and insect resistance into improved germplasm and cultivars. Exploiting the close evolutionary relationship between these two species, heat and drought tolerance will be introgressed into common bean and disease resistance into tepary bean using KASP markers developed from synteny studies.
Disease and pest evaluations will include common bacterial blight, Bean golden yellow mosaic virus, Bean common mosaic virus, Bean common mosaic necrosis virus, rust, powdery mildew, and leafhopper and bruchid insects, utilizing natural infection or collections of these pathogens maintained at the ARS and the U. of Puerto Rico. For abiotic stress response, phenotypic data will be generated from field trials under drought stress and non-stress conditions in the semi-arid climate at the UPR Ag. Substation in Juana Diaz, PR using yield components and stress-response traits. These evaluations will be completed in tepary bean and common bean, on the RIL populations and GWAS panels, for cross-species enabled KASP marker development.
The genetic structure of these traits will thus also be elucidated using quantitative trait loci (QTL) and genome wide association studies (GWAS). Genotypic analysis of the populations will begin with DNA extraction, followed by molecular analysis. The principal molecular markers for these analyses will be k-mer, SNP, and KASP markers. Putative QTL will be detected and GWAS statistical analysis will be used to analyze results from recombinant inbred line populations and diversity panels. Principal component analysis will be used to determine population structure and multiple models that correct for population structure will be tested.
Pedigree, recurrent selection, and the bulk breeding methods will continue to be used. Using bridging parents recently identified at TARS, and interspecific crosses developed between common bean and tepary bean, traits will also be introgressed across species. Mesoamerican, Durango and Andean market classes will be targeted for improvement of tolerance to high temperature stress and drought. For tepary bean, the development of adapted tepary bean breeding lines with common bean-introgressed BCMV, BCMNV, and BGYMV virus resistance, powdery mildew fungal resistance, and with improved seed size, growth habit, and non-shattering pods will be pursued.
The project will result in novel traits transferred into common bean and tepary bean and new or improved methods will be discovered to recombine genomes and result in rapid introgression of alleles and novel diversity. These new methods will produce sustainable, higher yielding crop plants with stable performance across a wide range of environments, including biotic and abiotic stresses, and resilience to climate and environmental extremes that will serve both breeders and farmers.
