{"title":"开发具有成本效益的 SNP 标记,用于栽培梨(梨属)的遗传变异分析和品种鉴定","authors":"Jae-Hun Heo, Jeyun Yeon, Jin-Kee Jung, Il Sheob Shin, Sung-Chur Sim","doi":"10.3390/plants13182600","DOIUrl":null,"url":null,"abstract":"Pear (Pyrus 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 P. pyrifolia (53), P. ussuriensis (27), P. bretschneideri (19), P. communis (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 (P. pyrifolia, P. ussuriensis, and P. bretschneideri) and interspecific hybrids were genetically differentiated from the European species (P. communis). Furthermore, the P. pyrifolia 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.","PeriodicalId":20103,"journal":{"name":"Plants","volume":null,"pages":null},"PeriodicalIF":0.0000,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Development of Cost-Effective SNP Markers for Genetic Variation Analysis and Variety Identification in Cultivated Pears (Pyrus spp.)\",\"authors\":\"Jae-Hun Heo, Jeyun Yeon, Jin-Kee Jung, Il Sheob Shin, Sung-Chur Sim\",\"doi\":\"10.3390/plants13182600\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"Pear (Pyrus 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 P. pyrifolia (53), P. ussuriensis (27), P. bretschneideri (19), P. communis (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 (P. pyrifolia, P. ussuriensis, and P. bretschneideri) and interspecific hybrids were genetically differentiated from the European species (P. communis). Furthermore, the P. pyrifolia 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.\",\"PeriodicalId\":20103,\"journal\":{\"name\":\"Plants\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2024-09-18\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Plants\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.3390/plants13182600\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Plants","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.3390/plants13182600","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
引用次数: 0
摘要
梨(Pyrus spp.)是蔷薇科的一种主要水果作物,人们一直致力于培育优良品种。随着基因组测序技术的发展,单核苷酸多态性(SNPs)被普遍用作作物物种的 DNA 标记。本研究利用基因分型测序技术对 48 个梨栽培品种进行了大规模的 SNPs 发现。在 17 条染色体上共发现 256,538 个可信 SNP,并根据多态性信息含量、杂合率和基因组分布筛选出 288 个 SNP。这一 SNP 子集被用于对另外 144 个品种进行基因分型,包括 P. pyrifolia(53 个)、P. ussuriensis(27 个)、P. bretschneideri(19 个)、P. communis(26 个)、种间杂交种(14 个)和其他品种(5 个)。232 个 SNPs 具有可靠的多态性,揭示了 192 个梨品种之间和品种内部的遗传变异。亚洲种(P. pyrifolia、P. ussuriensis 和 P. bretschneideri)和种间杂交种与欧洲种(P. communis)存在遗传差异。此外,与其他种群相比,P. pyrifolia 种群表现出更高的遗传多样性。对 232 个 SNP 和四个子集(192、96、48 和 24 个 SNP)进行了品种鉴定评估。192 个 SNP 子集鉴定出 192 个登录品种中的 173 个(90.1%),与 232 个 SNP 中的 175 个(91.1%)相当。其他三个子集的鉴定率为 81.8%(24 个 SNPs)至 87.5%(96 个 SNPs)。所得到的 SNPs 将成为研究遗传变异和开发高效 DNA 条形码系统的有用资源,用于栽培梨的品种鉴定。
Development of Cost-Effective SNP Markers for Genetic Variation Analysis and Variety Identification in Cultivated Pears (Pyrus spp.)
Pear (Pyrus 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 P. pyrifolia (53), P. ussuriensis (27), P. bretschneideri (19), P. communis (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 (P. pyrifolia, P. ussuriensis, and P. bretschneideri) and interspecific hybrids were genetically differentiated from the European species (P. communis). Furthermore, the P. pyrifolia 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.