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

2021 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 third year of this project. Progress was made on all objectives by ARS scientists at Mayaguez, Puerto Rico including Objective 1 focused on developing genetic tools for breeding abiotic and biotic traits. A novel single nucleotide polymorphism (SNP) genotyping service developed from SNP markers developed at multiple collaborative institutions is being implemented for high throughput marker-assisted selection. High-throughput phenotypic data using a proximal sensing cart from drought trials is being shared with Regional Project W-3150 collaborators. Studies were published on the genetics and physiology of seed dormancy, a crucial trait in common bean domestication, and on genetic factors associated with nodulation and nitrogen derived from the atmosphere in a common bean panel under low soil fertility. Objective 2, Develop and release common bean germplasm with higher levels of abiotic stress tolerance and with multiple resistance. Multi-year on-farm and on-station trials in Tanzania resulted in the description of Baetao-Manteiga 41 and ‘Yunguilla’ as superior Andean common beans for Tanzanian production environments. Scientists at the University of Puerto Rico, with ARS Mayaguez, Puerto Rico as one of the collaborators, registered PR1572-19 and PR1572-26 pinto bean germplasm lines with broad disease resistance to bean rust, Bean golden yellow mosaic virus, Bean common mosaic virus, and Bean common mosaic necrosis virus. The shuttle breeding program between the University of Nebraska/ARS Mayaguez, Puerto Rico has submitted two drought tolerant lines for release. Superior lines from Andean and Middle American common bean bulk breeding populations are in advanced yield trials for heat tolerance, drought tolerance, and broad adaptation. Several Andean Phaseolus Improvement Cooperative (PIC) lines are in final on-station and on-farm testing in Tanzania for release. 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. Additional tepary lines with traits including faster cooking time, Bean golden yellow mosaic virus tolerance, and leaf hopper resistance are being prepared for release. In a collaborative effort, bridging genotypes have been identified by ARS scientists at Mayaguez, Puerto Rico that allow for the hybridization of tepary bean and common bean, promising dramatic improvement of both crops for abiotic and biotic resistance. Resistance to Bean common mosaic virus from wild tepary has been introduced into cultivated tepary bean and these lines are being advanced and tested. A multi-institutional effort has released the first wild and cultivated tepary genome sequences.

1. Tepary Bean Genome: The tepary bean is a climate resilient traditional crop of the Native Indian peoples of the Southwestern U.S., Mexico and Central America. Both wild and cultivated genome sequences were published by ARS scientists at Mayaguez, Puerto Rico in Nature Communications by a consortium of researchers using cutting-edge sequencing and bioinformatics methods. These genomes show high levels of similarity to each other and to common bean, showing the potential for tepary bean to improve drought and heat tolerance of common bean. These genomes will give researchers access to the unique climate resilient traits of tepary bean, facilitate introgression of these traits into common bean, and will eventually result in enhanced heat and drought tolerant pulse crops for farmers and consumers.

Review Publications
Oladzad, A., Gonzalez, A., Macchiavelli, R., Estevez De Jensen, C., Beaver, J., Porch, T.G., Mcclean, P. 2020. Genetic factors associated with nodulation and nitrogen derived from atmosphere in a middle american common bean panel under low soil fertility. Frontiers in Plant Science.
Soltani, A., Walter, K.A., Wiersma, A., Santiago, J.P., Quiqley, M., Chitwood, D., Sharkey, T.D., Porch, T.G., Miklas, P.N., McClean, P.E., Osorno, J.M., Lowry, D.B. 2021. Loss of physical seed dormancy, a major domestication trait in common bean, is likely caused by a single loss-of-function mutation. Biomed Central (BMC) Plant Biology. 21, Article 58.
Nchimbi, S., Miklas, P.N., Fourie, D., Kilango, M., Porch, T.G. 2020. Release of ‘Sakila 20’ and ‘SUA Kalima’ Superior Andean Common Bean Cultivars for Tanzanian Production Environments. Journal of Plant Registrations. 14:234-241.
Beaver, J.S., Gonzalez, A., Godoy De Luz, G., Rosas, J.C., Hurtado-Gonzales, O.P., Pastor Corrales, M.A., Porch, T.G. 2020. Registration of PR1572-19 and PR1572-26 Pinto Bean Germplasm Lines with broad resistance to rust, BGYMV, BCMV, and BCMNV. Journal of Plant Registrations.
Beaver, J., Estevez, C., Miklas, P.N., Porch, T.G. 2020. Contributions in Puerto Rico to Phaseolus spp. research. Journal of Agriculture of the University of Puerto Rico. 104(1):43-111.
Mafimoghaddam, S., Oladzad, A., Koh, C., Ramsay, L., Hart, J.P., Mamidi, S., Hoopes, G., Sreedasyam, A., Wiersma, A., Grimwood, J., Hamilton, J.P., Jenkins, J., Vaillancourt, B., Wood, J., Rokhsar, D., Schmutz, J., Kagale, S., Porch, T.G., Bett, K.E., Buell, R., Mcclean, P.E. 2021. Genome sequences of wild and landrace tepary bean provide insight into evolution and domestication under heat stress. Nature Genetics. 12:2638.