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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

2020 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 second year of this project. Progress was made by ARS researchers at Mayaguez, Puerto Rico, on all objectives including Objective 1 focused on developing genetic tools for breeding abiotic and biotic traits. A phylogenic analysis on angular leaf spot, caused by Pseudocercospora griseola, using isolates from Puerto Rico, Central America and Tanzania confirmed the existence of the Afro-Andean clade. Sources of resistance to angular leaf spot were also identified in common bean through greenhouse screening. ARS-Washington led the publication of a genotype plus genotype-by-environment (GGE) biplot analysis for evaluation of yield stability of the Andean Diversity Panel (ADP) grown in Tanzania, leading to the identification of superior performing ADP lines. A novel single nucleotide polymorphism (SNP) genotyping service was used by ARS researchers at Mayaguez, Puerto Rico, to evaluate SNPs closely linked to disease resistance alleles in over 1,500 common bean breeding lines and cultivars. High-throughput phenotyping is yielding valuable information for genetic analyses. Objective 2, develop and release common bean germplasm with higher levels of abiotic stress tolerance and with multiple resistance, ARS scientists in Mayaguez, Puerto Rico, released a leafhopper resistant pinto bean germplasm, TARS-LH1, with resistance to both the Empoasca kraemeri and E. fabae species. Two superior ADP lines with biotic and abiotic stress tolerance were identified for release by Sokoine University (Tanzania), ARS scientists in Mayaguez, Puerto Rico, the Agriculture Research Council (South Africa), and the Tanzanian Agricultural Research Institute in Tanzania. The University of Puerto Rico, in collaboration with ARS scientists in Mayaguez, Puerto Rico, released ‘Hermosa’, a black bean cultivar with Bean golden and Bean common mosaic virus resistance, and tolerance to low fertility soils. Superior lines from Andean and Middle American bean bulk breeding populations are in advanced yield trials. Three Middle American advanced black bean lines that performed well in regional trials in Central America over several years are being tested for adaptation in the U.S. A set of 10 Andean Phaseolus Improvement Cooperative (PIC) lines are in final on-station and on-farm testing in Tanzania, while about 15 of these PIC lines have been incorporated in breeding programs in the U.S. and are under drought evaluation in the Nebraska/Puerto Rico shuttle breeding program. High-throughput phenotypic data from drought trials is being shared with Regional Project W-3150 collaborators. Objective 3, focuses on introgression of useful genes from tepary bean into common bean and on the development of tepary bean as a new crop, ARS researchers at Mayaguez, Puerto Rico have developed several tepary bean lines with improved seed quality, tolerance to Bean golden yellow mosaic virus, drought, and heat, and with resistance to the leaf hopper pest, that are being prepared for release. The introgression of Bean common mosaic virus from wild tepary into cultivated tepary bean is being advanced. A multi-institutional effort has completed the sequencing and annotation of the tepary genome using the G40001 accession.

1. Release of leafhopper resistant pinto germplasm. A pinto germplasm with leafhopper resistance, TARS-LH1, was released by ARS researchers at Mayaguez, Puerto Rico, in the Journal of Plant Registrations and was highlighted on Crop Science Society of America (CSSA) Science News at and in other media news outlets. TARS-LH1, has resistance to both the tropical, Empoasca kraemeri, and the temperate, E. fabae, species of leafhopper. This pinto bean germplasm could help to increase conventional and organic common bean production and reduce pesticide usage, through incorporation of this resistance in cultivars used by farmers.

Review Publications
Porch, T.G., Brisco-Mccann, E.I., Demosthene, G., Colbert, R.W., Beaver, J.S., Kelly, J.D. 2020. Release of TARS-LH1 a pinto bean germplasm with resistance to the leafhopper pest. Journal of Plant Registrations.
Mndolwa, Msolla, S.N., Porch, T.G., Miklas, P.N. 2019. CGE biplot analysis of yield stability for andean dry bean accessions grown under different abiotic stress regimes in Tanzania. African Crop Science Journal. 27:413-425.
8eaver, J., Estevez De Jensen, C., Ruiz-Quiles, L., Vasquez, G., Gonzalez, A., Martinez, H., Porch, T.G. 2018. Release of ‘Hermosa’ Black Bean Cultivar. Journal of Agriculture of the University of Puerto Rico. 102:123-128.
De Ron, A.M., Kalavacharla, V., Alvarez-Garcia, S., Beaver, J.S., Bedmar-Villanueva, A., Carro-Huelga, H., Casquero, P.A., De La Rosa, L., Dworkin, M., Galvan, M.Z., Goncalves-Vidigal, M.C., Gutierrez, S., Lorenzana, A., Mayo-Prieto, S., Porch, T.G., Rodiño, A., Rodriguez-Gonzalez, A., Sofkova-Bobcheva, S., Suarez-Villanueva, V. 2019. Common bean genetics, breeding, and genomics for adaptation to changing to new agri-environmental conditions. In: Kole, C., editor. Designing of climate-smart pulse crops. Switzerland: Springer Nature Switzerland. p. 1-106.
Cichy, K.A., Wiesinger, J.A., Berry, M., Nchimbi-Msolla, S., Fourie, D., Porch, T.G., Ambechew, D., Miklas, P.N. 2019. The role of genotype and production environment in determining the cooking time of dry beans (Phaseolus vulgaris L.). Legume Science. 1(1):e13.
Serrato-Diaz, L.M., Navarro-Monserrat, E.D., Rosas, J.C., Chilagane, L.A., Bayman-Gupta, P., Porch, T.G. 2020. Phylogeny of Pseudocercospora griseola from Puerto Rico, Central America and Tanzania confirms the existence of an Afro-Andean clade. European Journal of Plant Pathology. 157:533-547.
Rodriguez, D., Beaver, J., Estevez De Jensen, C., Porch, T.G. 2019. Identification of resistance sources of common bean (Phaseolus vulgaris L.) to angular leaf spot (Pseudocercospora griseola)”. Revista Facultad Nacional de Agronomia Medellin. 72(2):8785-8791.