Skip to main content
ARS Home » Pacific West Area » Salinas, California » Crop Improvement and Protection Research » Research » Research Project #444660

Research Project: Enhancement of Spinach & Leafy Vegetables for Disease Resistance & Nutritional Components using Genome-wide Association Study & Genomic Prediction

Location: Crop Improvement and Protection Research

Project Number: 2038-21530-003-016-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Sep 1, 2023
End Date: Aug 31, 2024

Objective:
The project objectives are: 1. To evaluate spinach and leafy vegetables for disease resistance and nutritional and health-promoting components; 2. To conduct genome-wide association study of disease resistance and nutritional and health-promoting components in spinach and leafy vegetables; and 3. To perform genomic prediction of disease resistance, nutritional and health-promoting components in spinach and leafy vegetables.

Approach:
Phenotyping: Spinach and leafy vegetable lines will be continuously evaluated for their resistance to several diseases such as downy mildew, white rust, leaf spot, and Pythium as well as nutritional traits in greenhouse and fields. The data will be analyzed for analysis of variance (ANOVA) using the general linear models (GLM) procedure of JMP Genomics 7. DNA extraction, GBS, SNP discovery and genotyping: Genomic DNA will be extracted from fresh leaves using the CTAB method. DNA sequencing will be conducted using genotyping by sequencing (GBS). The short-read sequences data (350bp) are analyzed using Tassel 5 and Stacks software for SNP discovery. Genetic diversity analysis: The genetic diversity will be analyzed using STRCTURE 2 and MAGA 7. Genome-wide association study (GWAS): GWAS will be performed using GAPIT3, where GLM, MLM, FarmCPU and BLINK will be used to identify associated SNP markers and candidate genes. Genomic selection: Genomic estimated breeding value (GEBV) will be estimated using rrBLUP, gBLUP, cBLUP, BayesA, BayesB, and Bayesian LASSO to conduct genomic prediction (GP) in the statistical analysis. Expected Outcomes: 1. Spinach lines with high disease resistance of downy mildew, white rust, leaf spot, and Pythium will be identified. 2. Nutritional and health-promoting components will be determined in genotypes of spinach and leafy vegetables. 3. GWAS and GP will be performed. SNP markers and genomic prediction models for disease resistance and nutritional and health-promoting components will be identified. 4. Six or more manuscripts will be written and published in refereed journals.