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Genetic variation and genome-environment association of alfalfa (Medicago sativa L.) populations under long-term grazing




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Alfalfa (Medicago sativa. L) is the most valuable forage legume for the beef, dairy, and forage industries in Canada with approximately 4 million hectares of alfalfa and alfalfa-grass mixtures in Western Canada. Alfalfa forage production has been limited by low stand persistence due to the negative impacts of environmental factors and continuous grazing. The objectives of this study were: 1) to identify the phenotypic and genetic diversities of alfalfa populations collected from long-term grazing sites across four soil zones of Saskatchewan; 2) to compare genetic structure of the populations from long-term grazing sites to commercial alfalfa cultivars released between 1926 and 1980; 3) to identify the SNP markers linked to morphological traits and nutritive values; and 4) to detect SNP markers associated with environmental factors associated with plant persistence at long-term grazing sites. This study collected alfalfa populations across four soil zones of Saskatchewan representing 14 alfalfa stands with minimum 25 years of grazing history. The seven agro-morphological and three nutritive value traits of the 14 alfalfa populations from long-term grazing were evaluated in a replicated field trial using a nested randomized complete block design (RCBD). The genotyping-by-sequencing (GBS) reads were aligned to the Medicago sativa reference genome and 19,853 high-quality SNPs were generated. The STRUCTURE analysis identified that the alfalfa populations from long-term grazing sites were the hybrid cross from subspecies Medicago sativa subsp. sativa (hereafter M. sativa) and M. falcata. Plants from the Black soil zone produced the highest forage dry matter yield, plant height, and stem number, while the lowest values for these traits were recorded plants from the Brown soil zone. This was because the alfalfa populations from the Black soil zone had maintained more of the M. sativa genome over long-term grazing, while the alfalfa populations from the Brown soil zone maintained more of the M. falcata genome. The genotype-environment association (GEA) identified 70 SNPs for the alfalfa populations with grazing history including summer extreme temperature (22 SNPs), growing season precipitation (15 SNPs), soil nutrient (30 SNPs), and soil pH (3 SNPs). Fifty-three candidate genes were significantly associated with eight environmental factors, which were mainly involved in plant resistances to biotic and abiotic stresses, such as heat, drought, salt and diseases. The genome-wide-association-study (GWAS) analysis identified nine SNPs associated with stem number and nutritive value on the Medicago sativa reference genome. Once validated, these markers and candidate genes identified in the study would be useful for developing markers for marker-assisted selection to improve alfalfa cultivars with enhanced tolerance to long-term grazing and environmental stresses in Western Canada.



Genetic diversity and relationship, long-term grazing, alfalfa persistence in Western Canada, genotype-environment association, genome-wide association study



Doctor of Philosophy (Ph.D.)


Plant Sciences


Plant Sciences


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