Identification of Loci Associated with Drought Resistance Traits in Heterozygous Autotetraploid Alfalfa (Medicago sativa L.) Using Genome-Wide Association Studies with Genotyping by Sequencing

Tiejun Zhang; Long-Xi Yu; Ping Zheng; Yajun Li; Martha Rivera; Dorrie Main; Stephanie L Greene

doi:10.1371/journal.pone.0138931

Identification of Loci Associated with Drought Resistance Traits in Heterozygous Autotetraploid Alfalfa (Medicago sativa L.) Using Genome-Wide Association Studies with Genotyping by Sequencing

PLoS One. 2015 Sep 25;10(9):e0138931. doi: 10.1371/journal.pone.0138931. eCollection 2015.

Authors

Tiejun Zhang¹, Long-Xi Yu¹, Ping Zheng², Yajun Li¹, Martha Rivera¹, Dorrie Main², Stephanie L Greene³

Affiliations

¹ Plant and Germplasm Introduction and Testing Research, United States Department of Agriculture-Agricultural Research Service, Prosser, Washington, United States of America.
² Department of Horticulture, Washington State University, Pullman, Washington, United States of America.
³ National Center for Genetic Resource Preservation, United States Department of Agriculture-Agricultural Research Service, Fort Collins, Colorado, United States of America.

Abstract

Drought resistance is an important breeding target for enhancing alfalfa productivity in arid and semi-arid regions. Identification of genes involved in drought tolerance will facilitate breeding for improving drought resistance and water use efficiency in alfalfa. Our objective was to use a diversity panel of alfalfa accessions comprised of 198 cultivars and landraces to identify genes involved in drought tolerance. The panel was selected from the USDA-ARS National Plant Germplasm System alfalfa collection and genotyped using genotyping by sequencing. A greenhouse procedure was used for phenotyping two important traits associated with drought tolerance: drought resistance index (DRI) and relative leaf water content (RWC). Marker-trait association identified nineteen and fifteen loci associated with DRI and RWC, respectively. Alignments of target sequences flanking to the resistance loci against the reference genome of M. truncatula revealed multiple chromosomal locations. Markers associated with DRI are located on all chromosomes while markers associated with RWC are located on chromosomes 1, 2, 3, 4, 5, 6 and 7. Co-localizations of significant markers between DRI and RWC were found on chromosomes 3, 5 and 7. Most loci associated with DRI in this work overlap with the reported QTLs associated with biomass under drought in alfalfa. Additional significant markers were targeted to several contigs with unknown chromosomal locations. BLAST search using their flanking sequences revealed homology to several annotated genes with functions in stress tolerance. With further validation, these markers may be used for marker-assisted breeding new alfalfa varieties with drought resistance and enhanced water use efficiency.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Chromosome Mapping
Droughts
Gene Expression Regulation, Plant
Genome-Wide Association Study / methods*
Genotyping Techniques / methods*
Medicago sativa / chemistry
Medicago sativa / classification
Medicago sativa / genetics*
Medicago sativa / physiology
Phylogeny
Plant Leaves / chemistry
Plant Leaves / genetics
Plant Proteins / genetics*
Quantitative Trait Loci*
Sequence Analysis, DNA
Water / analysis

Substances

Plant Proteins
Water

Grants and funding

This work was supported by USDA-ARS National Program Project No. 5354-21000-015-00D and by a partial grant from the National Alfalfa and Forage Alliance to L-X Yu. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.