SLAF-seq efficiently identifies SNP markers for wheat (Triticum aestivum L.) improvement

Molecular markers are indispensable tools for identifying genetic variation among plant individuals and enhancing breeding efficiency. In this study, we developed SNP markers, conducted genetic diversity assessment, and established fingerprint maps for 306 wheat germplasm accessions from China using SLAF-seq technology. We obtained 4978.16 Mb of clean reads after quality control of individual sample sequencing data. The number of SNP markers detected per sample ranged from 7.03 to 35.92 million. A total of 554,315 SLAF tags were identified, including 356,643 polymorphic tags. After population-level SNP filtering, 52,228 highly consistent and effective SNP markers were retained. Genetic diversity analysis revealed relatively close genetic relationships among the wheat varieties, with an average observed heterozygosity of 0.090 and a mean polymorphism information content (PIC) of 0.251. Population structure analysis (K = 4) indicated that most accessions shared close ancestral relationships, with evidence of admixture. Cluster analysis grouped the 306 wheat germplasm resources into four distinct clusters. Further filtering identified 114 core SNP markers, enabling the successful construction of a fingerprint database encompassing all 306 accessions. This study demonstrates that SLAF-seq is a cost-effective and efficient method for high-throughput SNP marker development and a powerful tool for wheat germplasm genetic analysis. The SNP markers identified here can facilitate germplasm identification, varietal improvement, protection, utilization, and QTL mapping of important traits with yield and quality, significantly advancing molecular breeding efforts in wheat.