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ARS Home » Pacific West Area » Pullman, Washington » Plant Germplasm Introduction and Testing Research » Research » Research Project #445776

Research Project: Genetic Improvement of Alfalfa for Enhanced Productivity under Abiotic Stress

Location: Plant Germplasm Introduction and Testing Research

Project Number: 2090-21500-001-000-D
Project Type: In-House Appropriated

Start Date: Feb 26, 2024
End Date: Feb 25, 2029

Objective 1: Develop molecular strategies to genetically increase drought and salt tolerance in alfalfa. Sub-objective 1A: Identify genetic loci associated with drought resistance using genome-wide association studies and develop statistical models for selection of drought tolerant alfalfa. Sub-objective 1B: Identify DNA markers and germplasm associated with salt tolerance to clearly define the genetic basis of resistance to salt and accelerate breeding programs in alfalfa. Objective 2: Develop genetic strategies for rapid selection of alfalfa to enhance productivity while maintaining high quality.

To develop and deploy genomic tools for breeding synthetic alfalfa varieties with enhanced drought and salt tolerance, 32 previously selected drought-tolerant plants will be crossed with plants of the elite cultivar ‘Guardsman II’ that has high yield and quality attributes but is susceptible to drought. F1 progenies will be backcrossed (BC) with the susceptible Guardsman II parents to develop BC1 populations. The BC1 populations will be screened for drought tolerance in the field for two years. All plots will be drought stressed. Yield and other data from the half-sib families and their respective covariate check will be collected in each replication and subjected to analysis of variance and best linear unbiased estimates to adjust soil variation in the field trials. The same population used for phenotyping will be genotyped using a targeted genotyping platform (DArTag) by Breeding Insight at Cornell University. Markers with the correct allele dosage as determined in the present study will enable GWAS with the GWASpoly software, which was originally designed for association mapping in the autotetraploid potato species. Genome-wide association studies will be performed using the R package GWASpoly using a Q+K linear mixed model. Genomic selection will use both phenotypic and genotypic data from a large reference population (also called the training population) for training models to predict a genomic estimate of breeding value (GEBV). This test data set will then be used to estimate model parameters such the highest possible genetic variation for a trait is explained by the markers analyzed. The GEBV will be used for selection of the target trait (drought tolerance) of each individual. To develop genetic strategies for rapid selection of alfalfa with enhanced productivity while maintaining high quality, high-yield and high-quality alfalfa plants were selected previously as parents for developing polycross populations. These plants are being grown in pots in USDA greenhouses and will be caged before flowering for pollination using leaf cutter bees. Seeds from each maternal plant will be collected and planted in the field and phenotypic data for yield and major quality traits will be collected for combining ability tests and selection. The estimates of general combining ability and specific combining ability of parents and progeny will be obtained. Biomass and plant height will be measured as described above. Forage quality traits will be measured using NIRS. Phenotypic data of biomass yield and important quality factors such as crude protein, lignin, neutral detergent fiber content, neutral detergent fiber digestibility and relative forage quality will be used for the selection of individuals. The polycross population containing 600 individuals will be genotyped using DArTag as described above. Genome-wide association studies will be conducted between markers and phenotypic traits including biomass and forage quality traits. Markers associated with the traits will be identified using GWASPoly as described above.