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ARS Home » Pacific West Area » Pullman, Washington » Plant Germplasm Introduction and Testing Research » Research » Research Project #430090

Research Project: Developing Molecular Markers for Enhancing Resistance to Drought and High Salinity in Alfalfa

Location: Plant Germplasm Introduction and Testing Research

Project Number: 2090-21000-036-02-I
Project Type: Interagency Reimbursable Agreement

Start Date: Oct 1, 2015
End Date: Aug 31, 2019

Objective 1. Identify germplasm with drought and salt tolerance in the primary gene pool and develop alfalfa populations for mapping QTL and breeding for superior varieties with drought and salt resistance. Objective 2. Mapping QTL associated with drought and salt resistance using genome-wide association studies. Objective 3. Develop molecular markers for rapid selection of drought and salt tolerant alfalfa to accelerate breeding programs.

Quantitative traits such as biotic and abiotic stress resistance are likely under the control of multiple genes and influenced by environmental factors. Identification of resistance loci that contribute to variation in such complex traits, is a primary challenge in plant breeding and population genetics. In the proposed study we will use an integrated framework that merges a QTL mapping approach called ‘‘genome-wide association’’ with high-throughput genome sequencing methodologies called “genotyping by sequencing (GBS)” in order to map traits quickly, efficiently, and in a relatively inexpensive manner. This framework provides a statistical basis for analyzing marker-trait association using linkage disequilibrium. It will help to identify molecular markers associated with resistance to biotic and abiotic stresses in alfalfa. In general, segregation population or association panel will be used for mapping genes/QTL. Parents or progenies will be phenotyped for traits of interest. DNA will be extracted from each individual and will be digested using restriction enzymes. DNA libraries will be prepared for genotyping for sequencing. The sequencing data will be analyzed for single nucleotide polymorphism (SNP). The SNP markers can be used for constructing linkage map for mapping genes/QTL. The analysis of marker-trait association allows for identification of markers associated with the traits of interest. SNPs tightly linked to the specific trait can then be used for marker-assisted selection in breeding programs.