Genetic diversity and local adaption of alfalfa populations (Medicago sativa L.) under long-term grazing

Abstract

Genomic information on alfalfa adaptation to long-term grazing is useful for alfalfa genetic improvement. In this study, 14 alfalfa populations were collected from long-term grazing sites (> 25 years) across four soil zones in western Canada. Alfalfa cultivars released between 1926 and 1980 were used to compare degree of genetic variation of the 14 populations. Six agro-morphological and three nutritive value traits were evaluated from 2018 to 2020. The genotyping-by-sequencing (GBS) data of the alfalfa populations and environmental data were used for genotype-environment association (GEA). Both STRUCTURE and UPGMA based on 19,853 SNPs showed that the 14 alfalfa populations from long-term grazing sites had varying levels of parentages from alfalfa sub-species Medicago sativa and M. falcata. The linear regression of STRUCTURE membership probability on phenotypic data indicated genetic variations of forage dry matter yield, spring vigor and plant height were low, but genetic variations of regrowth, fall plant height, days to flower and crude protein were still high for the 14 alfalfa populations from long-term grazing sites. The GEA identified 31 SNPs associated with 13 candidate genes that were mainly associated with six environmental factors of. Candidate genes underlying environmental factors were associated with a variety of proteins, which were involved in plant responses to abiotic stresses, i.e., drought, cold and salinity-alkali stresses.

Effects of SNP marker density and training population size on prediction accuracy in alfalfa (Medicago sativa L.) genomic selection

“…Our previous study found that the 141 genotypes representing 14 alfalfa populations from long‐term grazing were hybrid between the subspecies of M. sativa and M. falcata with a similar population structure (Wang et al., 2023). In this study, we also found that the genomic relationship among these 141 genotypes was close as indicated by GRM values ranging from −0.1 to 0.6, further confirming a similar genetic structure found in our previous study (Wang et al., 2023). This might contribute to a relatively higher prediction accuracy when using training populations over 1000 repeats in our study, as closely related populations usually had higher GS prediction accuracy compared to unrelated or distantly related populations (Habier et al., 2010).…”

“…The details on plant materials, experimental design, phenotypic data collection, DNA extraction, and sequencing are described in Wang et al. (2023). In brief, 14 alfalfa populations were collected from 14 grazing sites with a minimum of 25 years of use.…”

“…The accuracy of estimated SNP effects was affected by heterogeneous marker effects (Rio et al, 2020) due to differences in population structure (De Roos et al, 2009;Guo et al, 2014;Isidro et al, 2015;Windhausen et al, 2012) and genomic relationship between the TRN and TST populations (Albrecht et al, 2011;Clark et al, 2011Clark et al, , 2012Pszczola et al, 2012). Our previous study found that the 141 genotypes representing 14 alfalfa populations from long-term grazing were hybrid between the subspecies of M. sativa and M. falcata with a similar population structure (Wang et al, 2023). In this study, we also found that the genomic relationship among these 141 genotypes was close as indicated by GRM values ranging from −0.1 to 0.6, further confirming a similar genetic structure found in our previous study (Wang et al, 2023).…”

Multi-Trait Selection of Quinoa Ideotypes at Different Levels of Cutting and Spacing

“…On the other hand, NDF is the most common measure of fiber used for animal feed analysis but does not represent a unique class of chemical compounds. NDF measures most of the structural components of plant cells such as cellulose, hemicellulose, and lignin but not pectin [71]. In general, both ADF and NDF values increased as the forage matured.…”