Skip to main content
ARS Home » Southeast Area » Mayaguez, Puerto Rico » Tropical Crops and Germplasm Research » Research » Research Project #434643

Research Project: Genetic Improvement of Stress Tolerance in Common Bean through Genetic Diversity and Accelerated Phenotyping

Location: Tropical Crops and Germplasm Research

2022 Annual Report

1. Develop genetic tools for breeding of heat, drought, and disease resistance in common bean, including novel quantitative trait loci (QTL), markers, and appropriate populations. 1a: Develop bulk breeding and recombinant inbred line (RIL) populations of common bean as a powerful approach for the pyramiding of complex traits for target production zones. 1b: Complete QTL analysis through the application of single nucleotide polymorphism (SNP) genotyping to common bean biparental populations and diversity panels and develop markers for key traits of interest. 2. Develop and release common bean germplasm with increased tolerance to high temperatures, drought, diseases, and insect pests and adapt high throughput phenotyping approaches for accelerating germplasm improvement. 2a: Develop and release germplasm for tolerance to high temperatures and drought, and for resistance to insect pests and diseases. 2b: Apply high-throughput phenotyping to common bean through the transfer of phenotyping cart technology for proximal analysis in the field. 3. Develop and release tepary bean (Phaseolus acutifolius) germplasm as an alternate pulse crop for marginal production zones, and use tepary as a source for introgression of abiotic stress tolerance into common bean.

Identification and mapping of important abiotic (heat and drought) and biotic traits will be completed using bi-parental and association mapping populations. Drought and heat tolerance traits, derived from common bean and tepary bean, will be evaluated using yield components and stress-response traits. Bulk breeding populations are also being developed in collaboration with ARS-Prosser and ARC-South Africa based on lines with superior performance from the ADP in trials conducted in multi-location trials in Sub-Saharan Africa, Puerto Rico and Washington State. Single plant selections will be completed from bulk breeding populations in target environment for traits previously indicated including abiotic (high temperature, drought, low soil fertility) and biotic (root rot, BCMV, BCMNV, common bacterial blight, angular leaf spot, rust) stress tolerance or disease resistance, respectively. Replicated phenotypic evaluations will be completed in appropriate field and greenhouse environments and this data used for the quantitative trait loci (QTL) and genome-wide association studies (GWAS) analyses. Genotypic analysis of the populations will begin with DNA extraction, followed by molecular analysis. The molecular analysis of the population will rely on PCR-based markers because of the robust nature of these markers, their requirement for small quantities of DNA, and cost-savings. The principal molecular markers for this analysis will be SNP markers. SNPs will be identified through genotyping-by-sequencing using the ApeKI enzyme. Putative QTL will be detected by employing the multiple interval mapping (MIM) function. LOD thresholds will be set at the appropriate levels based on permutation analysis. The GWAS statistical analysis will be used to analyze results from the diversity panels evaluated and will employ GAPIT software. Multiple models that correct for population structure and genotype relatedness will be tested. Principal component analysis will be used to determine population structure. Several areas of germplasm improvement will be pursued with the goal of releasing improved germplasm for key traits including drought and heat tolerance, and root rot and leaf hopper resistance. Pedigree and recurrent selection will continue to be used in addition to the bulk breeding method, as reviewed in above. Improved germplasm from TARS, other ARS programs and U.S. universities, the U. of Puerto Rico, Zamorano (Honduras), and CIAT, will provide the parental base for the generation of populations both for the breeding approaches for germplasm improvement. Similar plant breeding approaches will be used across sub-objectives, with the incorporation of additional key traits, such as common bacterial blight resistance, BGYMV, BCMV, and BCMNV resistance into the germplasm. High-throughput phenotypic data collection is being implemented to accelerate the selection of improved germplasm and for the identification of unique traits, while data processing steps will be improved and optimized. Hyperspectral measurements (leaf reflectance from 400 to 2,500 nm) have been implemented as well as canopy height and canopy temperature using a proximal sensing cart.

Progress Report
Substantial results were realized over the fourth year of this project. Progress was made on all objectives including Objective 1 focused on developing genetic tools for breeding abiotic and biotic traits. A novel common bean panel, the Phaseolus vulgaris Yellow Bean Collection, is being used as an important resource for genetic diversity and characterization for cooking time. Genomic prediction was used by ARS scientists at Mayaguez, Puerto Rico, in the evaluation of data from the Andean Diversity Panel in Africa and applied to climbing beans and published in Frontiers in Plant Science. Advances in breeding for resistance and integrated management of web blight in common bean was published in Crop Science and a review of the role of common bean in agricultural sustainability was published in Legume Science. Under Objective 2, the shuttle breeding program between the University of Nebraska and ARS has released two novel drought tolerant germplasms, SB-DT2 (pinto) and SB-DT3 (small red) with adaptation to major U.S. production environments in the Journal of Plant Registrations. These new germplasm lines were featured in CSA News and are important sources of genetic diversity for drought tolerance. A Pinto bean is in the final review stages for formal release in Tanzania for release, while an Andean breeding line from the Phaseolus Improvement Cooperative (PIC) bulk populations is being prepared for release in Tanzania. Objective 3 focuses on the introgression of useful genes from tepary bean into common bean and on the development of tepary bean as a new crop. ARS scientists in Mayaguez, Puerto Rico, and collaborators have developed and released TARS-Tep 23 with broad adaptation to drought and heat, and with high levels of resistance to rust and common bacterial blight in the Journal of Plant Registrations. An additional tepary bean breeding line with improved seed quality, faster cooking time, Bean Golden Yellow Mosaic Virus tolerance, and leaf hopper resistance is being considered for release. In a collaborative effort, bridging genotypes have been identified that allow for the hybridization of tepary bean and common bean, promising dramatic improvement of both crops for abiotic and biotic resistance.

1. Preparation for release of tepary bean germplasm TARS-Tep 23. A tepary bean germplasm with broad adaptation, rust immunity, common bacterial blight resistance and heat and drought tolerance, TARS-Tep 23, has been prepared by ARS scientists at Mayaguez, Puerto Rico, for release. Tepary is currently grown on a small scale, but TARS-Tep 23 is being tested and used in the U.S. and internationally by breeders and for potential distribution to farmers. Tepary could impact legume production environments marginalized by high temperatures and drought by providing an alternative crop for farmers and by increasing resilience through diversification of the production system.

Review Publications
Sadohara, R., Izquierdo, P., Alves, F.C., Porch, T.G., Beaver, J., Urrea, C., Cichy, K.A. 2022. The Phaseolus vulgaris Yellow Bean Collection: Genetic diversity and characterization for cooking time. Genetic Resources and Crop Evolution. 69:1627-1648.
Beaver, J.S., Martinez Figueroa, H., Godoy De Lutz, G., Estevez De Jensen, C., Porch, T.G., Rosas, J.C. 2021. Breeding for resistance and integrated management of web blight in common beans (Phaseolus vulgaris L.). Crop Science. 62:20-35.
Beaver, J., Gonzalez, A., Lorenzo Vazquez, G., Macchiavelli, R., Porch, T.G., Estevez De Jensen, C. 2021. Performance of Mesoamerican bean (Phaseolus vulgaris L.) lines in an unfertilized oxisol. Agronomia Mesoamericana (Mesoamerican Journal of Agronomy-Agriculture and Livestock) (ISSN:2215-3608). 32(3).
Uebersax, M., Cichy, K.A., Gomez, F., Porch, T.G., Heitholt, J., Osorno, J., Kamfwa, K., Snapp, S., Bales, S. 2022. Dry beans (Phaseolus vulgaris L.) as a vital component of sustainable agriculture and food security – A review. Legume Science. Article e155.
Keller, B., Ariza-Suarez, D., Portilla-Benavides, A., Buendia, H., Aparicio, J., Amongi, W., Mbiu, J., Nchimbi-Msolla, S., Miklas, P.N., Porch, T.G., Burridge, J., Mukankusi, C., Studer, B., Raatz, B. 2022. Genomic predictions in climbing beans and their genetic associations with bush bean populations. Frontiers in Plant Science. 13. Article 830896.