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Genetic Analysis of Potato Breeding Collection Using Single-Nucleotide Polymorphism (SNP) Markers

文献类型： 外文期刊

作者： Xiao, Xi-ou 1 ; Zhang, Ning 1 ; Jin, Hui 3 ; Si, Huaijun 1 ;

作者机构： 1.Gansu Agr Univ, Coll Agron, Lanzhou 730070, Peoples R China

2.Gansu Agr Univ, State Key Lab Aridland Crop Sci, Lanzhou 730070, Peoples R China

3.Chinese Acad Trop Agr Sci, South Subtrop Crop Res Inst, Zhanjiang 524091, Peoples R China

4.Gansu Agr Univ, Coll Life Sci & Technol, Lanzhou 730070, Peoples R China

关键词： potato; genetic diversity; single-nucleotide polymorphism; SNP fingerprint

期刊名称：PLANTS-BASEL （ 影响因子：4.5； 五年影响因子：4.8 ）

ISSN：

年卷期： 2023 年 12 卷 9 期

页码：

收录情况： SCI

摘要： The autotetraploid potato (Solanum tuberosum L.) is an important crop in China, and it is widely cultivated from Northeast China to South China. Thousands of varieties are bred by breeding institutions or companies, and distinguishing the different varieties based on morphological characteristics is difficult. Using DNA fingerprints is an efficient method to identify varieties that plays an increasingly important role in germplasm identification and property rights protection. In this study, the genetic diversity and population structure of 135 autotetraploid potatoes were evaluated using specific-locus amplified fragment sequencing (SLAF-seq) methods. A total of 3,397,137 high-quality single-nucleotide polymorphisms (SNPs), which were distributed across 12 chromosomes, were obtained. Principal component analysis (PCA), neighbour-joining genetic trees, and model-based structure analysis showed that these autotetraploid potato subpopulations, classified by their SNPs, were not consistent with their geographical origins. On the basis of the obtained 3,397,137 SNPs, 160 perfect SNPs were selected, and 71 SNPs were successfully converted to penta-primer amplification refractory mutation (PARMS-SNP) markers. Additionally, 190 autotetraploid potato varieties were analysed using these 71 PARMS-SNP markers. The PCA results show that the accessions were not completely classified on the basis of their geographical origins. The SNP DNA fingerprints of the 190 autotetraploid potato varieties were also constructed. The SNP fingerprint results show that both synonyms and homonyms were present amongst the 190 autotetraploid potatoes. Above all, these novel SNP markers can lay a good foundation for the analysis of potato genetic diversity, DUS (distinctness, uniformity, and stability) testing, and plant variety protection.

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