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 Tropical Crops and Germplasm Research: Mayaguez, PR
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ARS Home Southeast Area Mayaguez, Puerto Rico Tropical Crops and Germplasm Research Research





- Porch, Timothy - Tim
- 2023
- 2022
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- 2018
- Publications
- Plant Genetic Resources, Genomics and Genetic Improvement (301)

Research Project: **Location:
                            Tropical Crops and Germplasm Research** Project Number: 6090-21000-059-000-D
                        
                        Project Type: In-House Appropriated Start Date: May 9, 2018
                        
                        End Date: May 8, 2023 **Objective:**
                        
                        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.


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