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ARS Home » Southeast Area » Griffin, Georgia » Plant Genetic Resources Conservation Unit » Research » Research Project #436920

Research Project: Evaluation and Association of Drought Tolerance in USDA Cowpea Germplasm

Location: Plant Genetic Resources Conservation Unit

Project Number: 6046-21000-012-013-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Jul 1, 2019
End Date: Aug 31, 2022

(1) Evaluate drought tolerance in world-wide cowpea germplasm. (2) Conduct genome-wide association study (GWAS) of drought tolerance in cowpea. DETAILS FOR AMENDMENT TO ADD SALT TOLERANCE WORK WITH FY 20 FUNDS FROM ONP CAN BE FOUND ATTACHED IN E-GREEN.

Plant Materials and Evaluation of drought tolerance in world-wide cowpea germplasm: A panel of 300 cowpea accessions have been chosen for drought tolerance evaluation, genome-wide association study (GWAS), and Genomic Selection (GS) analysis. Among these, 260 accessions were from United States Department of Agriculture (USDA) and other 40 accessions were developed from the cowpea breeding programs in University of Arkansas. Cowpea seeds were increased during the summer 2017-18. The greenhouse experiments are carried out in the greenhouses of the Rosen Center of the University of Arkansas (UofA), Fayetteville, Arkansas, using the same ‘Wooden Box’ screening methodology established by Singh et al. (1999) and Verbee et al. (2015). Phenotypic data analysis: The cowpea drought tolerant data will be performed for analysis of variance (ANOVA) using the general linear models (GLM) procedure of JMP Genomics 7. The 300 cowpea genotypes will also be used for genome-wide association study and genomic selection of drought tolerance. Genomic DNA will be extracted from freeze dry leaves of cowpea plants using the Cetyl trimethylammonium bromide (CTAB) method (Kisha et al., 1997). DNA sequencing by whole genome resequencing (WGR) will be conducted in Novogene or BGI companies. The short-read sequences data (350bp) are analyzed using the short oligonucleotide alignment program (SOAP) family software (Li, 2011; Li et al., 2009; Li et al., 2010) for Single Nucleotide Polymorphism (SNP) discovery and genotyping. Further, the phenotpic data of dorught tolerance will be subjected to association analysis with the SNPs. Association tests are performed with the mixed linear model method as described in TASSEL 5 (Bradbury et al., 2007) and the analysis will be also performed with compressed mixed linear model (Zhang et al., 2010) implemented in the GAPIT R package (Lipka et al., 2012) and in FarmCPU and BLINK (Liu et al., 2016; Zhang & Zhou, 2018). DETAILS FOR AMENDMENT TO ADD SALT TOLERANCE WORK WITH FY 20 FUNDS FROM ONP CAN BE FOUND ATTACHED IN E-GREEN.