SNP loci identification and KASP marker development system for genetic diversity, population structure, and fingerprinting in sweetpotato (Ipomoea batatas L.)

作者：Feiyang Yang, Tao Lang, Jingyu Wu, Cong Zhang, Huijuan Qu, Zhigang Pu, Fan Yang, Ma Yu, Junyan Feng · 发表于：BMC Genomics · 年份：2024 · DOI：10.1186/s12864-024-11139-8 · 被引用次数：16 · 研究领域：Plant Virus Research Studies、Plant Pathogenic Bacteria Studies、Plant Disease Resistance and Genetics

Sweetpotato (Ipomoea batatas L.), an important food and industrial crop in the world, has a highly heterozygous hexaploid genome, making the development of single nucleotide polymorphism (SNP) markers challenging. Identifying SNP loci and developing practical SNP markers are crucial for genomic and genetic research on sweetpotato. A restriction site-associated DNA sequencing analysis of 60 sweetpotato accessions in this study yielded about 7.97 million SNPs. Notably, 954 candidate SNPs were obtained from 21,681 high-quality SNPs. Based on their stability and polymorphism, 274 kompetitive allele specific PCR (KASP) markers were then developed and uniformly distributed on chromosomes. The 274 KASP markers were used to genotype 93 sweetpotato accessions to evaluate their utility for assessing germplasm and analyzing genetic diversity and population structures. These markers had respective mean values of 0.24, 0.34, 0.31, and 0.25 for minor allele frequency, heterozygosity, gene diversity, and polymorphic information content (PIC). Their genetic pedigree led to the division of all accessions into three primary clusters, which were found to be both interrelated and independent. Finally, 74 KASP markers with PIC values greater than 0.35 were selected as core markers. These markers were used to construct the DNA fingerprints of 93 sweetpotato accessions and were able to differentiate between all accessions. To the best of our knowledge, this is the first attempt at the development a...