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ARS Home » Pacific West Area » Pullman, Washington » Plant Germplasm Introduction and Testing Research » Research » Publications at this Location » Publication #342953

Title: Identification of loci Associated with Resistance to Root-Rot Diseases in Autotetraploid Alfalfa using Genome-Wide Sequencing and Association Mapping

item Yu, Long-Xi
item HAWKINS, CHARLES - Washington State University
item Samac, Deborah - Debby

Submitted to: Plant Biology Annual Meeting
Publication Type: Abstract Only
Publication Acceptance Date: 6/9/2017
Publication Date: N/A
Citation: N/A

Interpretive Summary: Root rot diseases are fungal diseases that causes severe yield loss in alfalfa. The most effective method to control the diseases is through the development and use of resistant varieties. Identification of gene loci linked to VW resistance will facilitate breeding for disease-resistant alfalfa. In the present investigation, we applied an integrated framework of genome-wide association with high-throughput genotyping by sequencing to identify resistance loci in 3 panels of alfalfa populations developed for mapping the disease resistance. Phenotyping was done by manual inoculation of the pathogens to replicated cloned plants of each individual and scored for disease resistance using the standard protocol. Groups of DNA markers for the disease resistance and the associated genes were identifed using the flanking sequences of the resistance loci against the M. truncatula genome. These genes play roles in the disease resistance. With further investigation, they can be used for marker-assisted selection for breeding root rot resistant alfalfa.

Technical Abstract: Alfalfa (Medicago sativa L.) is the world-wide forage crop. Changing trends to multipurpose uses increases demand for alfalfa. However, the production of alfalfa is challenged by endemic and emerging diseases. Identification of genes/loci controlling disease resistance will facilitate breeding for improving alfalfa production. In the present investigation, we used an integrated framework of genome-wide association study (GWAS) with high-throughput genotyping by sequencing (GBS) to identify loci associated with resistance to root rot diseases including Verticillium wilt (VW) and Aphanomyces root rot (ARR) in various alfalfa populations. Genotyping was done by GBS, followed by genotype calling using the haplotype-based FreeBayes pipeline. SNP markers with allele dosage generated from the GBS pipeline were used for marker-trait association. Marker loci significantly associated with VW resistance were identified and they were located on multiple chromosomal locations. Most significant markers were found on chromosomes 6 and 8 in the S &W and Forage Genetics populations, respectively. Loci associated with resistance to ARR races 1 and 2 were located on chromosomes 1 and 2, respectively. BLAST search using the flanking sequences of VW resistance loci against M. truncatula genome identified candidate genes with disease resistance such as TIR-NBS-LRR protein and MDR-ABC transporter. Whereas a group of candidates involved in the hypersensitive response were found for ARR resistance. Validation of resistance loci in a broad range of alfalfa populations has been conducting using high throughput strategies. Functional markers closely linked to the resistance loci or derived from functional genes will be developed and used for genomics-assisted breeding for alfalfa cultivars with improved resistance to the root-rot diseases.