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ARS Home » Pacific West Area » Pullman, Washington » Plant Germplasm Introduction and Testing Research » Research » Research Project #432580

Research Project: Marker Assisted Breeding In Elite Alfalfa Germplasm To Enhance Biomass Productivity During Drought

Location: Plant Germplasm Introduction and Testing Research

Project Number: 2090-21000-036-005-R
Project Type: Reimbursable Cooperative Agreement

Start Date: Jan 1, 2017
End Date: Jun 30, 2022

Objective 1: Construct an elite alfalfa germplasm suitable for association mapping and genomic selection, and phenotype this population for yield, quality, and fall dormancy traits during drought stress. Objective 2: Develop a high-density DNA marker platform in elite alfalfa germplasm. Objective 3: Implement association mapping using phenotypic data and a GBS marker platform to identify biomass, forage quality, and fall dormancy genes/QTL at high mapping resolution in drought-stressed alfalfa. Objective 4: Implement genomic selection using phenotypic data and a GBS marker platform to identify individuals with superior breeding values for improving alfalfa drought resilience, forage quality, and fall dormancy.

Maternal half-sib families from each C0 plant will be seeded in a randomized complete block design with three replicates at both Las Cruces, NM and Prosser, WA. Half-sib family plots will be planted adjacent to control plots of the drought resilient cultivar NuMex Bill Melton (fall dormancy class 7). During 2017-19 all plots will be grown under limited irrigation management (one irrigation per forage regrowth cycle) and forage yield will be harvested seven and four times annually at Las Cruces and Prosser, respectively. Forage samples will be collected from two or three replicates of each half-sib family during the second forage regrowth cycle at the Las Cruces site in 2018 and 2019. These samples will be oven dried and sequentially ground using a Wiley Mill and a Udy-Mill, and subsequently shipped to Alforex Seeds for analysis of forage quality parameters. Note: Sampling forage from two or three replicates will generate 400 and 600 samples respectively in each year. Genotyping and mapping: DNA will be isolated and quantified from each of the 200 C0 plants at Las Cruces, NM. Samples will be shipped to the LCG genomics for genotyping by sequencing (GBS) analysis in 2018. Sequence data, including single nucleotide polymorphisms (SNPs), will be downloaded and used for tetraploid allele calling and locating the position of each SNP in the Medicago genome. The technology roadmap of the proposed research will use multiple genomics tools including genome-wide association mapping, second generation sequencing and comparative genomics to identify genes/QTLs associated with drought resistance, forage quality, and fall dormancy. We will also identify high throughput diagnostic markers tightly linked to the loci influencing these traits, and use them in future MAS efforts to develop alfalfa varieties with improved drought resilience, nutritive value, and appropriate fall dormancy.