Abstract
Salinity is one of major abiotic stresses limiting alfalfa (Medicago sativa L.) production in the arid and semi-arid regions in US and other counties. In this study, we used a diverse panel of alfalfa accessions previously described by Zhang et al. (2015) to identify molecular markers associated with salt tolerance during germination using genome-wide association study (GWAS) and genotyping-by-sequencing (GBS). Phenotyping was done by germinating alfalfa seeds under different levels of salt stress. Phenotypic data of adjusted germination rates and SNP markers generated by GBS were used for marker-trait association. Thirty six markers were significantly associated with salt tolerance in at least one level of salt treatments. Alignment of sequence tags to the Medicago truncatula genome revealed 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 identified 14 putative candidate genes linked to 23 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 in our previous study. To our knowledge, this is the first report on mapping loci associated with salt tolerance during germination in autotetraploid alfalfa. Further investigation on these loci and their linked genes would provide insight into understanding molecular mechanisms by which salt and drought stresses affect alfalfa growth. Functional markers closely linked to the resistance loci would be useful for MAS to improve alfalfa cultivars with enhanced resistance to drought and salt stresses.
Highlights
Many agricultural lands in The United States and other counties are composed of soil with high salinity
The genotypic coefficient√variation (GCV) was calculated using the formula GVC(%) = VG X × 100, where X is average of germination rates of the whole association panel
The average germination rates of salt treatments decreased as salt concentration increased
Summary
Many agricultural lands in The United States and other counties are composed of soil with high salinity. High salinity levels are detrimental to sensitive crop survival and production, especially under limited water conditions. Soil salinity is a long term problem and should be addressed through development of crops tolerant. GWAS on Salt Tolerance in Alfalfa to high soil salinity. Alfalfa (Medicago sativa L.) is an important forage crop in the Western United States and lacks tolerance to many of these high saline soils (Miller et al, 2014). Developing salt tolerant alfalfa varieties is imperative for sustainable alfalfa production in the west
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