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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

2019 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
This is the report for the project 6090-21000-059-00D which began in May 2018 and is a continuation of the previous project. Substantial results were realized over the first year of this new project. Progress was made on all objectives including Objective 1 focused on developing genetic tools for breeding abiotic and biotic traits. With the goal of broadening genetic diversity and mining novel alleles for traits of interest approximately 200 Andean, 10 Tepary and 10 Middle American bean bulk breeding populations were developed over several years through collaboration, and single plant selections were completed in Puerto Rico, Washington, Honduras, Guatemala, Malawi, Tanzania, and South Africa on subsets of these populations. Superior lines from these selections are being assembled in the U.S. for phenotypic and genotypic analysis and for testing as potential releases in the U.S. and abroad. In a collaborative effort, a genome-wide association analysis (GWAS) was published of a Middle American common bean abiotic stress panel (BASE 120) that identified genetic factors associated with heat and drought stress environments in Honduras and Puerto Rico. A common bean recombinant inbred line (RIL) population was evaluated over multiple years for response to high temperature and drought stress response in Puerto Rico and Colombia, and QTL (Quantitative Trait Loci) were identified for yield response under heat and drought stress, and for phenology under these conditions that can potentially be used for the development of markers for marker assisted selection. Under Objective 2, develop and release common bean germplasm with higher levels of abiotic stress tolerance and with multiple resistance, an ARS scientist in Mayaguez, Puerto Rico, is preparing to release a pinto bean germplasm with resistance to both the tropical and temperate leaf hopper pest after testing in Michigan, Puerto Rico and Haiti over multiple years. Leaf hoppers are a major constraint for the production of conventional and organic common beans. A pinto bean with drought tolerance and broad adaptation and developed from the shuttle breeding program between ARS-Puerto Rico and Nebraska is being released. Superior black bean breeding lines, selected from the Middle American bulk breeding populations mentioned in Objective 1, with Bean golden yellow mosaic virus resistance, Bean common mosaic virus resistance, and abiotic stress tolerance are being tested in regional trials in multiple countries of Central America for a second year. High-throughput phenotyping was implemented in the breeding program and data from these efforts were shared with participants in the Dry Bean Drought Nursery (DBDN) for a second year in a row. Under Objective 3, that was focused on introgression of useful genes from tepary bean into common bean and on the development of tepary bean as a new crop, ARS has developed a new tepary bean nursery of 10 advanced breeding lines that are being tested in the U.S. and Central America. Several of these lines with improved seed quality, tolerance to Bean golden yellow mosaic virus, drought, and heat, and with resistance to the leaf hopper pest are being considered for release. The introgression of Bean common mosaic virus from wild tepary into cultivated tepary bean is being pursued. ARS is participating in a multi-institutional effort that is completing the sequencing and annotation of the tepary genome using the G40001 genotype.

1. Development of Phaseolus Improvement Cooperative (PIC) bulk breeding lines. PIC bulk breeding populations were developed by and ARS scientist in Mayaguez, Puerto Rico, to address the lack of genetic diversity and breeding progress in Andean common beans and to facilitate worldwide Andean bean improvement through collaborative breeding. Over 200 bulk breeding populations were developed from superior accessions from collaborators in Washington and South Africa that combine abiotic and biotic stress tolerance. Bulk populations in the F5 generation were distributed to interested breeding programs in Africa, the U.S. and the Caribbean for targeted selection. Advanced lines were selected from each location after replicated and multi-location trials. Stakeholders in the U.S. and Canada have tested and shown interest in advanced lines that show drought tolerance and superior yield potential in key U.S. production zones such as Michigan and Nebraska, and can be incorporated in their breeding programs. In addition, the bulk breeding method in beans was shown to improve the efficiency, broad collaboration and impact of breeding efforts.

Review Publications
Cominelli, E., Confalioneri, M., Carlessi, M., Cortinovis, G., Daminati, M.G., Porch, T.G., Losa, A., Sparvoli, F. 2018. Phytic acid transport in Phaseolus vulgaris: a new low phytic acid mutant in the PvMRP1 gene and study of the PvMRPs promoters in two different plant systems. Plant Science. 270:1-15.
Katuuramu, D.N., Hart, J.P., Porch, T.G., Grusak, M.A., Cichy, K.A. 2018. Genome-wide association study for nutritional composition traits in cooked common bean seeds. Molecular Breeding. 38:44.
Strock, C., Burridge, J., Massas, A., Beaver, J., Camilo, S., Fourie, D., Jochua, C., Miguel, M., Miklas, P.N., Mndolwa, E., Nchimbi-Msolla, S., Porch, T.G., Rosas, J., Trapp, J., Beebe, S., Lynch, J. 2019. Seedling root architecture and its relationship with seed yield across diverse environments in Phaseolus vulgaris. Field Crops Research. 237:53-64.
Traub, J., Porch, T.G., Naeem, M., Urrea, C., Austic, G., Kelly, J., Loescher, W. 2018. Screening for heat tolerance in Phaseolus spp. using multiple methods. Crop Science.
Oladzad, A., Porch, T.G., Rosas, J.C., Moghaddam, S., Beaver, J., Beebe, S.E., Burridge, J., Jochua, C.N., Magalhaes, A.M., Miklas, P.N., Ratz, B., White, J.W., Lynch, J., McClean, P.E. 2019. Single and multi-trait GWAS identify genetic factors associated with production traits in common bean under abiotic stress environments. G3, Genes/Genomes/Genetics. 9(6):1881-1892.