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ARS Home » Pacific West Area » Pullman, Washington » Plant Germplasm Introduction and Testing Research » Research » Publications at this Location » Publication #329412

Title: Genomic Analysis of Verticillium Wilt Resistance and Drought Tolerance in Alfalfa

item Yu, Long-Xi
item LIU, XIANGPING - Heilongjiang Bayi Agricultural University (HLAU)
item Boge, William
item Rivera, Martha

Submitted to: North American Alfalfa Improvement Conference
Publication Type: Abstract Only
Publication Acceptance Date: 5/16/2016
Publication Date: N/A
Citation: N/A

Interpretive Summary: Quantitative traits such as biotic and abiotic stress resistance are most likely under the control of multiple genes and interact with 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 present study, we used an integrated framework that merges a QTL mapping approach called ‘‘genome-wide association (GWA)’’ with high-throughput genome sequencing methodology called “genotyping by sequencing (GBS)” to map resistance loci in autotetraploid alfalfa. This framework provides a statistical basis for analyzing marker-trait association using linkage disequilibrium. We have identified a group of molecular markers associated with resistance to Verticillium wilt and drought tolerance. A pairwise alignment (BLAST) using the flanking sequences of the resistance loci against the M. truncatula genome identified potential candidate genes with putative functions on disease and abiotic stress resistance. With further investigation, these markers may be implemented into breeding programs using marker-assisted selection, ultimately leading to increased resistance in alfalfa.

Technical Abstract: Alfalfa (Medicago sativa L.) is the fourth largest crop in the United States. Changing trends to multipurpose uses increases demand for alfalfa. However, the production of alfalfa is challenged by endemic and emerging diseases and adverse environmental factors. Identification of genes/loci controlling biotic and abiotic stress resistance will facilitate breeding for improving alfalfa production. In the present investigation, we applied an integrated framework of genome-wide association with high-throughput genotyping by sequencing for identifying genes/loci associated with Verticillium wilt (VW) and drought tolerance in alfalfa populations. An integrated pipeline for genotyping by sequencing was used for analyzing allelic variation in autotetraploid alfalfa. Marker-trait association by linkage disequilibrium identified a group of SNP markers significantly associated with VW resistance and drought tolerance, respectively. Alignment of their sequence tags to the reference genome revealed multiple chromosomal locations. Markers associated with VW resistance were located on chromosomes1, 5, 6, 7 and 8 (Fig.1). BLAST search using the flanking sequences of the resistance loci against M. truncatula genome identified candidate genes with disease resistance such as TIR-NBS-LRR protein and MDR-ABC transporter. Markers associated with drought tolerance were located in different chromosomal regions. Major loci identified in this work overlap with the reported QTLs in alfalfa. Our results have been published in peer-reviewed journals. 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 with improved resistance to the disease and abiotic stress.