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ARS Home » Pacific West Area » Pullman, Washington » Plant Germplasm Introduction and Testing Research » Research » Publications at this Location » Publication #352646
Title: Genetic loci associated with salt tolerance in advanced breeding populations of tetraploid alfalfa using genome-wide association studies

Author
item LIU, XIANG-PING - Heilongjiang Bayi Agricultural University (HLAU)
item HAWKINS, CHARLES - Washington State University
item Peel, Michael
item Yu, Long-Xi

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/19/2018
Publication Date: 2/1/2019
Citation: Liu, X., Hawkins, C., Peel, M., Yu, L. 2019. Genetic loci associated with salt tolerance in advanced breeding populations of tetraploid alfalfa using genome-wide association studies. The Plant Genome. 12:180026. https://doi.org/10.3835/plantgenome2018.05.0026.
DOI: https://doi.org/10.3835/plantgenome2018.05.0026

Interpretive Summary: The production of alfalfa is challenged by adverse environmental stress factors such as drought and high salinity. Developing resistant alfalfa varieties is an important breeding objective for enhancing alfalfa productivity in arid and semi-arid regions. To understand the genetic bases of salt resistance in alfalfa, we studied genetic regions associated with salt tolerance in 198 alfalfa accessions in greenhouse conditions. Biomass yield under salt treatment was measured and compared with control. Marker-trait assciaition identified a number of marker loci associated with biomass yield physiological traits under salt stress. With further investigation, these markers can be used for marker-assisited selection in breeding programs for developing alfalfa cultivars with enhanced resistance to high salinity and other abiotic stresses.

Technical Abstract: Alfalfa is an important forage crop worldwide. Most of alfalfa cultivars lack tolerance to high saline soils. Developing salt tolerant varieties is imperative for sustainable alfalfa production with increasing soil salinity. To better understand genetic architecture of salt resistance in alfalfa, in the present study, we conducted genome-wide association studies (GWAS) in advanced breeding populations for salt related traits. Plants were grown in a greenhouse under both salt and control conditions. Five traits related to salt tolerance including biomass dry (DW) and fresh weight (FW), plant height (PH), leaf relative water content (RWC) and stomatal conductance (SC) were phenotyped using salt susceptible index (SSI). The plants were genotyped using genotyping-by-sequencing (GBS). Seven thousand and four hundreds meaningful SNPs were obtained and used for marker-trait association analysis. A total of 53 significant SNPs associated with salt tolerance were identified and they were located at 49 loci on all chromosomes. Among those, 26 significant SNPs were detected in both SSI-DW and SSI-FW. BLAST search revealed 46 functional genes linked to 51 significant SNP markers. Some of them linked genes involved in response to abiotic stress. With further validation, these markers may be useful for marker-assisted selection (MAS) in breeding salt-tolerant alfalfa.