{"title":"Wheat improvement through advances in single nucleotide polymorphism (SNP) detection and genotyping with a special emphasis on rust resistance","authors":"Subramaniam Geethanjali, Palchamy Kadirvel, Sambasivam Periyannan","doi":"10.1007/s00122-024-04730-w","DOIUrl":null,"url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">Key message</h3><p>Single nucleotide polymorphism (SNP) markers in wheat and their prospects in breeding with special reference to rust resistance.</p><h3 data-test=\"abstract-sub-heading\">Abstract</h3><p>Single nucleotide polymorphism (SNP)-based markers are increasingly gaining momentum for screening and utilizing vital agronomic traits in wheat. To date, more than 260 million SNPs have been detected in modern cultivars and landraces of wheat. This rapid SNP discovery was made possible through the release of near-complete reference and pan-genome assemblies of wheat and its wild relatives, coupled with whole genome sequencing (WGS) of thousands of wheat accessions. Further, genotyping customized SNP sites were facilitated by a series of arrays (9 to 820Ks), a cost effective substitute WGS. Lately, germplasm-specific SNP arrays have been introduced to characterize novel traits and detect closely linked SNPs for marker-assisted breeding. Subsequently, the kompetitive allele-specific PCR (KASP) assay was introduced for rapid and large-scale screening of specific SNP markers. Moreover, with the advances and reduction in sequencing costs, ample opportunities arise for generating SNPs artificially through mutations and in combination with next-generation sequencing and comparative genomic analyses. In this review, we provide historical developments and prospects of SNP markers in wheat breeding with special reference to rust resistance where over 50 genetic loci have been characterized through SNP markers. Rust resistance is one of the most essential traits for wheat breeding as new strains of the <i>Puccinia</i> fungus, responsible for rust diseases, evolve frequently and globally.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"8 1","pages":""},"PeriodicalIF":4.4000,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Theoretical and Applied Genetics","FirstCategoryId":"97","ListUrlMain":"https://doi.org/10.1007/s00122-024-04730-w","RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"AGRONOMY","Score":null,"Total":0}
引用次数: 0
Key message
Single nucleotide polymorphism (SNP) markers in wheat and their prospects in breeding with special reference to rust resistance.
Abstract
Single nucleotide polymorphism (SNP)-based markers are increasingly gaining momentum for screening and utilizing vital agronomic traits in wheat. To date, more than 260 million SNPs have been detected in modern cultivars and landraces of wheat. This rapid SNP discovery was made possible through the release of near-complete reference and pan-genome assemblies of wheat and its wild relatives, coupled with whole genome sequencing (WGS) of thousands of wheat accessions. Further, genotyping customized SNP sites were facilitated by a series of arrays (9 to 820Ks), a cost effective substitute WGS. Lately, germplasm-specific SNP arrays have been introduced to characterize novel traits and detect closely linked SNPs for marker-assisted breeding. Subsequently, the kompetitive allele-specific PCR (KASP) assay was introduced for rapid and large-scale screening of specific SNP markers. Moreover, with the advances and reduction in sequencing costs, ample opportunities arise for generating SNPs artificially through mutations and in combination with next-generation sequencing and comparative genomic analyses. In this review, we provide historical developments and prospects of SNP markers in wheat breeding with special reference to rust resistance where over 50 genetic loci have been characterized through SNP markers. Rust resistance is one of the most essential traits for wheat breeding as new strains of the Puccinia fungus, responsible for rust diseases, evolve frequently and globally.
摘要以单核苷酸多态性（SNP）为基础的标记在筛选和利用小麦重要农艺性状方面的势头日益强劲。迄今为止，已在现代小麦栽培品种和陆地品系中检测到超过 2.6 亿个 SNP。小麦及其野生近缘种近乎完整的参考基因组和泛基因组组装的发布，加上对数千个小麦品种的全基因组测序（WGS），使得这种快速的 SNP 发现成为可能。此外，一系列阵列（9 至 820Ks）为定制 SNP 位点的基因分型提供了便利，这是一种具有成本效益的 WGS 替代品。最近，又引入了种质特异性 SNP 阵列，以表征新性状和检测密切相关的 SNP，用于标记辅助育种。随后，又引入了竞争性等位基因特异性 PCR（KASP）测定法，用于快速、大规模筛选特异性 SNP 标记。此外，随着测序技术的进步和测序成本的降低，通过突变以及结合新一代测序和比较基因组分析人工产生 SNP 的机会也越来越多。在本综述中，我们将介绍 SNP 标记在小麦育种中的历史发展和前景，特别是在抗锈病方面，已有 50 多个遗传位点通过 SNP 标记得到了表征。抗锈病性是小麦育种最基本的性状之一，因为导致锈病的普氏真菌的新菌株在全球范围内频繁进化。
期刊介绍：
Theoretical and Applied Genetics publishes original research and review articles in all key areas of modern plant genetics, plant genomics and plant biotechnology. All work needs to have a clear genetic component and significant impact on plant breeding. Theoretical considerations are only accepted in combination with new experimental data and/or if they indicate a relevant application in plant genetics or breeding. Emphasizing the practical, the journal focuses on research into leading crop plants and articles presenting innovative approaches.
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