Diversity Analysis of Global White Clover (Trifolium repens L.) Germplasm Based on Agronomic and Photosynthetic Traits and SLAF-Seq Technology
Abstract
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…
Read the paper
Related studies
- Understanding the factors influencing fall armyworm (Spodoptera frugiperda J.E. Smith) damage in African smallholder maize fields and quantifying its impact on yield. A case study in Eastern Zimbabwe
- Alarming situation of emerging H5 and H7 avian influenza and effective control strategies
- Livestock and food security: vulnerability to population growth and climate change
- Atmosphere–ocean oxygen and productivity dynamics during early animal radiations
- Characterization of the global distribution and diversified plasmid reservoirs of the colistin resistance gene mcr-9
- The global seroprevalence of Toxoplasma gondii in pigs: A systematic review and meta-analysis
Go deeper in Evidence Hub
Evidence Hub adds a study data sheet (design, sample size, evidence level, key numbers), an AI summary and a chat grounded in the paper's text.