Yang Feiyang, Lang Tao, Wu Jingyu, Zhang Cong, Qu Huijuan, Pu Zhigang, Yang Fan, Yu Ma, Feng Junyan
Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610011, China.
School of life science and engineering, Southwest University of Science and Technology, Mianyang, Sichuan, 621010, China.
BMC Genomics. 2024 Dec 24;25(1):1245. doi: 10.1186/s12864-024-11139-8.
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 and application of KASP markers in sweetpotato. However, due to sweetpotato's polyploidy, heterozygosity and the complex genome, the KASP marker conversion rate in this study was relatively low. To improve the KASP marker conversion rate, and accuracies in SNP discovery and marker validation, further studies including more accessions from underrepresented regions are needed in sweetpotato.
甘薯（Ipomoea batatas L.）是世界上一种重要的粮食和经济作物，具有高度杂合的六倍体基因组，这使得单核苷酸多态性（SNP）标记的开发具有挑战性。鉴定SNP位点并开发实用的SNP标记对于甘薯的基因组和遗传研究至关重要。本研究对60份甘薯种质进行了限制性位点相关DNA测序分析，获得了约797万个SNP。值得注意的是，从21681个高质量SNP中获得了954个候选SNP。基于其稳定性和多态性，随后开发了274个竞争性等位基因特异性PCR（KASP）标记，并将其均匀分布在染色体上。利用这274个KASP标记对93份甘薯种质进行基因分型，以评估其在种质评价、遗传多样性分析和群体结构分析中的应用价值。这些标记的次要等位基因频率、杂合度、基因多样性和多态信息含量（PIC）的平均值分别为0.24、0.34、0.31和0.25。它们的遗传谱系导致所有种质被分为三个主要类群，这些类群既相互关联又相互独立。最后，选择了74个PIC值大于0.35的KASP标记作为核心标记。这些标记用于构建93份甘薯种质的DNA指纹图谱，能够区分所有种质。据我们所知，这是首次在甘薯中开发和应用KASP标记。然而，由于甘薯的多倍性、杂合性和复杂的基因组，本研究中KASP标记的转化率相对较低。为了提高KASP标记的转化率以及SNP发现和标记验证的准确性，在甘薯中需要进一步开展包括来自代表性不足地区的更多种质的研究。
