Progress 10/01/23 to 09/30/24
Outputs
PROGRESS REPORT Objectives (from AD-416): 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 (from AD-416): 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. Progress was made on all objectives including Objective 1 focused on integrated genetic and genomic tools that use computational genomics and marker-assisted selection for improvement of Phaseolus species with an emphasis on gene introgression. For Objective 1a with the identification of genomic regions for agriculturally important disease resistance and simply inherited agronomic traits in common bean and tepary bean, a comprehensive diversity and GWAS study on the Tepary Diversity Panel (TDP) , focused on agriculturally important traits, was published in the journal Plant Genome. An additional panel of 192 lines (including checks) was assembled representing interspecific lines from crosses between common bean and tepary bean. This panel was genotyped using whole genome skim sequencing, and the panel was phenotyped in a replicated field trial in Isabela, Puerto Rico for agriculturally important traits. The TDP was evaluated for response to the powdery mildew disease and agronomic traits in field trials in Isabela, Puerto Rico in 2023 and repeated in 2024. In addition, the TDP was evaluated for response to the Bean common mosaic necrosis virus and to two strains of common bacterial blight in a screenhouse in Mayaguez, Puerto Rico. For Objective 1b, A manuscript was accepted for publication on the response to drought of the 384 Andean PIC breeding lines that were developed across Africa, the continental U.S., and Puerto Rico. Superior common bean parents were identified for breeding and quantitative trait loci were found for key agricultural traits through genome wide association analysis. This study found that bulk breeding in common bean is a powerful tool for efficient, collaborative breeding efforts on a global scale. Objective 2 is focused on developing and releasing novel common and tepary bean germplasm and cultivars with resistance or tolerance to biotic and abiotic stress. A pinto bean cultivar �Kikatiti� was approved for publication and released in Tanzania after broad on-station and on- farm testing that combines disease resistance and abiotic stress tolerance. Multiple virus and bruchid resistant Mesoamerican bean germplasm lines, PR1303-129 and PR1743-44, were released in an effort led by the University of Puerto Rico. These are the first releases in the region with this combination of traits. The fifth cycle of shuttle breeding with the University of Nebraska has resulted in pinto and great northern beans with good seed quality, broad adaptation, and drought tolerance. A tepary bean cultivar �USDA Fortuna� was released in the Journal of Plant Registrations. In addition, tepary bean lines developed through backcross breeding for resistance to Bean common mosaic necrosis virus are being tested for potential release. Crosses between wild and cultivated tepary beans are being advanced for powdery mildew resistance, bruchid resistance, and resistance to the leaf hopper and to the Asian bean flower thrip. Artificial Intelligence (AI)/Machine Learning (ML) Artificial Intelligence (AI) was employed through a collaboration with Mississippi State University, in a summer internship program, to evaluate a number of datasets that used agronomic, hand-held photosynthesis, a high-throughput proximal sensing cart, and drone methods to evaluate the response of common bean under drought stress. A research report was published in the Bean Improvement Cooperative Report indicating improved accuracy through combining the high-throughput proximal sensing cart and drone datasets. The goal is to understand associations and correlations between methods and to improve the efficiency of field data collection. ACCOMPLISHMENTS 01 �USDA Fortuna� tepary bean cultivar:. ARS researcher at Mayaguez, Puerto Rico collaborated in developing a tepary bean cultivar with good culinary traits, tolerance to Bean golden yellow mosaic virus and powdery mildew, resistance to common bacterial blight, and tolerance to heat and drought. This is the first known tepary bean cultivar released and was published in the Journal of Plant Registrations. USDA Fortuna is currently being tested in the US by a small seed company that sells direct to consumers. This effort should increase adoption rates of tepary bean.
Impacts
(N/A)
Publications
- Porch, T.G., Rosas, J.C., Cichy, K.A., Godoy Lutz, G., Rodriguez, I., Colbert, R.W., Demosthene, G., Hernandez, J.C., Beaver, J. 2023. Release of tepary bean cultivar �USDA Fortuna� with improved disease and insect resistance, seed size, and culinary quality. Journal of Plant Registrations. 18(1):42-51. https://doi.org/10.1002/plr2.20322.
- Beaver, J.S., Gonzalez, A., Mateo, B., Godoy De Lutz, G., Miranda, A., Rosas, J.C., Porch, T.G. 2023. Release of multiple virus and bruchid resistant Mesoamerican bean germplasm lines PR1303-129 and 1943-44. Journal of Plant Registrations. 18:149-156. https://doi.org/10.1002/plr2. 20344.
- Bornowski, N., Hart, J., Vargas Palacios, A., Ogg, B., Brick, M., Beaver, J., Hamilton, J., Buell, R., Porch, T.G. 2023. Genetic variation in a tepary bean (Phaseolus Acutifolius A. Gray) diversity panel reveals loci associated with biotic stress resistance. The Plant Genome. 16(3). Article e20363. https://doi.org/10.1002/tpg2.20363.
- Rosas-Sotomayor, J.C., Rodriguez, I.Y., Beaver, J.S., Porch, T.G. 2023. Comportamiento agron�mico de germoplasma de frijol com�n en condiciones de altas temperaturas en el Sur de Honduras. CEIBA: A Scientific and Technical Journal. 56(1):31-49.
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