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ARS Home » Pacific West Area » Pullman, Washington » Plant Germplasm Introduction and Testing Research » Research » Publications at this Location » Publication #328884

Title: Genome-wide association study identifies loci for salt tolerance during germination in autotetraploid alfalfa (Medicago sativa L.) using genotyping-by-sequencing

item Yu, Long-Xi
item LIU, XINCHUN - Sichuan Agricultural University
item Boge, William
item LIU, XIANGPING - Washington State University

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/15/2016
Publication Date: 6/15/2016
Citation: Yu, L., Liu, X., Boge, W.L., Liu, X. 2016. Genome-wide association study identifies loci for salt tolerance during germination in autotetraploid alfalfa (Medicago sativa L.) using genotyping-by-sequencing. Frontiers in Plant Science. 7:956.

Interpretive Summary: The development of alfalfa cultivars with the ability to germinate under salt stress would be valuable in the reclamation of saline soils. However, it is difficult to develop a uniform, repeatable method for selecting alfalfa with the ability to germinate in the saline soil. Several techniques to screen alfalfa germplasm resistant to salt during germination have been developed. Among them, petri dishes containing saline solutions or growth media were commonly used for testing seed germination. In the present study, we used the standard protocol published in the NAAIC web page ( Using this protocol, we tested seed germination under 8 concentrations of salt treatments. However, only first four concentrations (0.0, 0.5, 0.75 and 1.0%) were statistically significant. Salt concentration more than 1.0% did not give any meaningful result as most of seeds were not germinated. We therefore only used the germination data from the first four treatments. Using these data, we successfully identified a group of genetic loci constantly associated with resistance to three salt stress treatments (0.5, 0.75 and 1.0%) during germination, while no significant locus was identified in the control. These markers can be used for marker-assisted selection in breeding program when validated.

Technical Abstract: : In this study, we used a diverse panel of alfalfa accessions to identify molecular markers associated with salt tolerance during germination by genome-wide association (GWA) mapping and genotyping-by-sequencing (GBS). Three levels of salt treatments were applied during seed germination. Phenotypic data of adjusted germination rates and SNP markers generated by GBS were used for GWA. Thirty six markers were significantly associated with salt tolerance in at least one salt treatment. Alignment of sequence tags to the Medicargo truncatula genome reveals genetic locations of the markers on all chromosomes except chromosome 3. Most significant markers were found on chromosomes 1, 2 and 4. BLAST search using the flanking sequences of significant markers reveals fourteen putative candidate genes linked to 22 significant markers. Most of them were repeatedly identified in two or three salt treatments. Several loci identified in the present study had similar genetic locations to the reported QTL associated with salt tolerance in M. truncatula. A locus identified on chromosome 6 by this study overlapped with that by drought by our previous study. Further investigation on these loci and their linked candidate genes would provide more inside to understand molecular mechanisms by which high salinity affects early growth of alfalfa and to develop molecular markers that can be used in MAS for accelerating breeding program to enhance salt and drought tolerance in alfalfa.