Heo Jae-Hun, Yeon Jeyun, Jung Jin-Kee, Shin Il Sheob, Sim Sung-Chur
Department of Bioindustry and Bioresource Engineering, Sejong University, Seoul 05006, Republic of Korea.
Seed Testing and Research Center, Korea Seed & Variety Service, Gimcheon 39660, Republic of Korea.
Plants (Basel). 2024 Sep 18;13(18):2600. doi: 10.3390/plants13182600.
Pear ( spp.) is a major fruit crop in the Rosaceae family, and extensive efforts have been undertaken to develop elite varieties. With advances in genome sequencing technologies, single-nucleotide polymorphisms (SNPs) are commonly used as DNA markers in crop species. In this study, a large-scale discovery of SNPs was conducted using genotyping by sequencing in a collection of 48 cultivated pear accessions. A total of 256,538 confident SNPs were found on 17 chromosomes, and 288 SNPs were filtered based on polymorphic information content, heterozygosity rate, and genome distribution. This subset of SNPs was used to genotype an additional 144 accessions, consisting of (53), (27), (19), (26), interspecific hybrids (14), and others (5). The 232 SNPs with reliable polymorphisms revealed genetic variations between and within species in the 192 pear accessions. The Asian species (, , and ) and interspecific hybrids were genetically differentiated from the European species (). Furthermore, the population showed higher genetic diversity relative to the other populations. The 232 SNPs and four subsets (192, 96, 48, and 24 SNPs) were assessed for variety identification. The 192 SNP subset identified 173 (90.1%) of 192 accessions, which was comparable to 175 (91.1%) from the 232 SNPs. The other three subsets showed 81.8% (24 SNPs) to 87.5% (96 SNPs) identification rates. The resulting SNPs will be a useful resource to investigate genetic variations and develop an efficient DNA barcoding system for variety identification in cultivated pears.
梨（蔷薇科梨属）是蔷薇科的一种主要水果作物，人们已付出巨大努力来培育优良品种。随着基因组测序技术的进步，单核苷酸多态性（SNPs）在作物品种中普遍用作DNA标记。在本研究中，通过对48个栽培梨品种进行简化基因组测序来大规模发现SNPs。在17条染色体上共发现了256,538个可靠的SNPs，并基于多态信息含量、杂合率和基因组分布筛选出288个SNPs。该SNPs子集用于对另外144个品种进行基因分型，这144个品种包括秋子梨（53个）、白梨（27个）、沙梨（19个）、西洋梨（26个）、种间杂种（14个）和其他品种（5个）。232个具有可靠多态性的SNPs揭示了192个梨品种种间和种内的遗传变异。亚洲梨品种（秋子梨、白梨和沙梨）和种间杂种在遗传上与欧洲梨品种（西洋梨）有所区别。此外，秋子梨种群相对于其他种群表现出更高的遗传多样性。对232个SNPs和四个子集（192、96、48和24个SNPs）进行了品种鉴定评估。192个SNPs子集鉴定出了192个品种中的173个（90.1%），与232个SNPs鉴定出的175个（91.1%）相当。其他三个子集的鉴定率在81.8%（24个SNPs）到87.5%（96个SNPs）之间。所得的SNPs将成为研究遗传变异以及开发用于栽培梨品种鉴定的高效DNA条形码系统的有用资源。
