Based on SLAF-seq technology, 174 white clover accessions were analyzed using population structure and genetic evolution to develop SNP markers of all accessions. We obtained 2329.4 Mb reads of sequenced data, and the reads of the samples ranged from 4,701,984 to 31,540,232. The sequencing quality value (Q30) uniformly changed from 90.61% to 96.82%, with an average of 93.11%. The GC content of the samples changed from 38.96% to 43.98%, averaging 40.96%, with a control of 34.21%. A total of 320,417 SLAF tags were developed, with an average sequencing depth of 16.42×. There were 202,625 polymorphic SLAF tags, accounting for 63.24% of the total number of SLAF tags. Finally, 2,999,555 polymorphic SNPs were found, and 102,025 high-quality SNPs were selected for downstream analyses after filtering with minor allele frequency (MAF) > 0.05 and completeness > 0.5. Population structure analysis supported K = 2, indicating two major ancestral genetic backgrounds among the accessions. Phylogenetic analysis and principal component analysis further divided the accessions into three genetic subclusters, suggesting finer-scale genetic differentiation. In addition, one-way ANOVA and chi-squared tests revealed a significant association between genetic groups and geographic origin (χ2 = 25.78, df = 8, p = 0.0012; F = 3.489, p = 0.032), provided limited evidence for a possible association between genetic grouping and geographic origin. Compared with photosynthetic traits, agronomic traits showed a broader range of variations, with coefficient of variance values for agronomic traits ranging from 24.59% to 139.02% and for photosynthetic traits from 4.29% to 78.57%. This difference suggests that morphological traits were highly differentiated among the 174 accessions. The consistency between phenotypic clustering (based on agronomic traits) and molecular clustering (based on SNP data) suggests that our SNP dataset captures biologically meaningful genetic variation, providing a solid foundation for future genome-wide association studies (GWASs) and marker-assisted selection (MAS) in white clover.
Sang et al. (Thu,) studied this question.