Location: Tropical Crops and Germplasm Research
2023 Annual Report
Objectives
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.
Approach
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 final report for the project 6090-21000-059-000D which terminated in May 2023.Substantial results were realized over the life of this project. Progress was made on all objectives including Objective 1 focused on developing genetic tools for breeding abiotic and biotic traits. Recently, Kompetitive allele specific polymerase chain reaction (KASP) markers were widely employed in the breeding program for early generation selection of lines with pyramided disease resistance. High-throughput phenotypic data using a proximal sensing cart from drought trials is being shared with collaborators. Studies were published on non-nodulating mutants altered in Rhizobial infection that elucidate our understanding of symbiotic nitrogen fixation. 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. Other 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.
Under Objective 2, Develop and release common bean germplasm with higher levels of abiotic stress tolerance and with multiple resistance. The shuttle breeding program between the University of Nebraska/ARS (Mayaguez, Puerto Rico) has released SB-DT2, a pinto bean, and SB-DT3, a red bean with drought tolerance and broad adaptation. Scientists at the University of Puerto Rico, with ARS (Mayaguez, Puerto Rico), registered ‘Rosalinda’, the first pink bean release in Puerto Rico with broad disease resistance to Bean golden yellow mosaic virus, Bean common mosaic virus, and Bean common mosaic necrosis virus. A pinto bean cultivar with broad adaption, and Bean common mosaic virus, and Bean common mosaic necrosis virus resistance is in the final stages of testing for release in Tanzania. Previously, a pinto bean germplasm (TARS-LH1) was released with resistance to both the tropical and temperate leaf hopper pest after testing in Michigan, Puerto Rico and Haiti over multiple years. 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, PR) 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.
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 released TARS-Tep 23 with broad adaptation to drought and heat, and with high levels of resistance to rust and common bacterial blight. The first tepary bean cultivar ‘USDA Fortuna’ with faster cooking time, Bean golden yellow mosaic virus tolerance, and leaf hopper resistance has been submitted for release. Interspecific lines, between tepary bean and common bean, have been developed and are being tested for unique abiotic and biotic resistance. The tepary diversity panel has been used to evaluate the population structure of tepary bean and to identify key biotic and agronomic traits of agricultural importance using genome-wide association studies. Previously, both the wild and cultivated genome sequences were published 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.
Accomplishments
1. Development of tepary bean diversity panel. ARS researchers at Mayaguez, Puerto Rico collaborated in developing the tepary bean diversity panel, that is composed of all available tepary bean accessions, for the study of the population structure and genetics of this orphan crop. Little information is known about the genetics of key agricultural traits in tepary bean, thus the panel was used to identify loci associated with disease and insect resistance and several agronomic traits. The diversity panel of 422 cultivated, weedy, and wild tepary bean accessions revealed eight subpopulations and the differentiation of botanical varieties within P. acutifolius. Genome-wide association studies revealed loci and candidate genes underlying biotic stress resistance including quantitative trait loci for resistance to weevils, common bacterial blight, Fusarium wilt, and bean common mosaic necrosis virus. These agriculturally important traits can be harnessed for tepary bean improvement and for common bean improvement, thus potentially improving the productivity of both crops for the farmer and consumer.
Review Publications
Parker, T.A., Gallegos, J.A., Beaver, J., Brick, M., Brown, J.K., Cichy, K.A., Debouck, D., Delgado-Salinas, A., Dohle, S., Ernest, E., Estevez de Jensen, C., Gomez, F., Hellier, B.C., Karasev, A.V., Kelly, J.D., McClean, P., Miklas, P.N., Myers, J.R., Osorno, J., Pasche, J.S., Pastor-Corrales, M.A., Porch, T.G., Steadman, J.R., Urrea, C., Wallace, L.T., Diepenbrock, C.H., Gepts, P. 2022. Genetic resources and breeding priorities in Phaseolus beans: Vulnerability, resilience, and future challenges. Plant Breeding Reviews. Volume 46. Somerset, New Jersey: John Wiley & Sons, Inc. p. 289-420. https://doi.org/10.1002/9781119874157.ch6.
Urrea, C.A., Smith, J.R., Porch, T.G. 2022. Registration of drought tolerant pinto SB-DT2 and small red SB-DT3 common bean germplasm from a shuttle breeding program between Nebraska and Puerto Rico. Journal of Plant Registrations. 16:400-409. https://doi.org/10.1002/plr2.20196.
Porch, T.G., Barrera, S., Berny Mier Y Teran, J.C., Diaz-Ramirez, J., Pastor Corrales, M.A., Gepts, P., Urrea, C.A., Rosas, J.C. 2022. Release of tepary bean TARS-Tep 23 germplasm with broad abiotic stress tolerance and rust and common bacterial blight resistance. Journal of Plant Registrations. 16:109-119. https://doi.org/10.1002/plr2.20180.
Reyero-Saavedra, M., Fuentes, S.I., Leija-Salas, A., Jimenez-Nopala, G., Pelaez, P., Ramirez, M., Girard, L., Porch, T.G., Hernandez, G. 2023. Identification and characterization of common bean (Phaseolus vulgaris) non-nodulating mutants altered in rhizobial infection. Plants. 12(6): 1310. https://doi.org/10.3390/plants12061310.
Beaver, J.S., Estevez De Jensen, C., Gonzalez, A., Porch, T.G. 2023. Release of 'Rosalinda' pink bean cultivar. Journal of Agriculture of the University of Puerto Rico. 106(2):301-307.
