• 文献检索
  • 文档翻译
  • 深度研究
  • 学术资讯
  • Suppr Zotero 插件Zotero 插件
  • 邀请有礼
  • 套餐&价格
  • 历史记录
应用&插件
Suppr Zotero 插件Zotero 插件浏览器插件Mac 客户端Windows 客户端微信小程序
定价
高级版会员购买积分包购买API积分包
服务
文献检索文档翻译深度研究API 文档MCP 服务
关于我们
关于 Suppr公司介绍联系我们用户协议隐私条款
关注我们

Suppr 超能文献

核心技术专利：CN118964589B侵权必究
粤ICP备2023148730 号-1Suppr @ 2026

文献检索

告别复杂PubMed语法，用中文像聊天一样搜索，搜遍4000万医学文献。AI智能推荐，让科研检索更轻松。

立即免费搜索

文件翻译

保留排版，准确专业，支持PDF/Word/PPT等文件格式，支持 12+语言互译。

免费翻译文档

深度研究

AI帮你快速写综述，25分钟生成高质量综述，智能提取关键信息，辅助科研写作。

立即免费体验

利用新一代测序技术鉴定小麦中与多性状相关的标记

Using Next Generation Sequencing for Multiplexed Trait-Linked Markers in Wheat.

作者信息

Bernardo Amy, Wang Shan, St Amand Paul, Bai Guihua

机构信息

Department of Plant Pathology, Kansas State University, Manhattan, Kansas, United States of America.

Department of Agronomy, Kansas State University, Manhattan, Kansas, United States of America.

出版信息

PLoS One. 2015 Dec 1;10(12):e0143890. doi: 10.1371/journal.pone.0143890. eCollection 2015.

DOI:10.1371/journal.pone.0143890
PMID:26625271
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC4666610/
Abstract

With the advent of next generation sequencing (NGS) technologies, single nucleotide polymorphisms (SNPs) have become the major type of marker for genotyping in many crops. However, the availability of SNP markers for important traits of bread wheat (Triticum aestivum L.) that can be effectively used in marker-assisted selection (MAS) is still limited and SNP assays for MAS are usually uniplex. A shift from uniplex to multiplex assays will allow the simultaneous analysis of multiple markers and increase MAS efficiency. We designed 33 locus-specific markers from SNP or indel-based marker sequences that linked to 20 different quantitative trait loci (QTL) or genes of agronomic importance in wheat and analyzed the amplicon sequences using an Ion Torrent Proton Sequencer and a custom allele detection pipeline to determine the genotypes of 24 selected germplasm accessions. Among the 33 markers, 27 were successfully multiplexed and 23 had 100% SNP call rates. Results from analysis of "kompetitive allele-specific PCR" (KASP) and sequence tagged site (STS) markers developed from the same loci fully verified the genotype calls of 23 markers. The NGS-based multiplexed assay developed in this study is suitable for rapid and high-throughput screening of SNPs and some indel-based markers in wheat.

摘要

随着下一代测序（NGS）技术的出现，单核苷酸多态性（SNP）已成为许多作物基因分型的主要标记类型。然而，可有效用于标记辅助选择（MAS）的面包小麦（Triticum aestivum L.）重要性状的SNP标记仍然有限，且用于MAS的SNP检测通常是单重的。从单重检测转向多重检测将允许同时分析多个标记并提高MAS效率。我们从小麦中与20个不同的数量性状位点（QTL）或农艺重要性基因连锁的基于SNP或插入缺失的标记序列中设计了33个位点特异性标记，并使用Ion Torrent Proton测序仪和定制的等位基因检测流程分析扩增子序列，以确定24个选定种质资源的基因型。在这33个标记中，27个成功实现了多重检测，23个的SNP检出率为100%。对从相同位点开发的“竞争性等位基因特异性PCR”（KASP）和序列标签位点（STS）标记的分析结果充分验证了23个标记的基因型判定。本研究中开发的基于NGS的多重检测适用于小麦中SNP和一些基于插入缺失的标记的快速高通量筛选。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c7e5/4666610/9484de3a7214/pone.0143890.g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c7e5/4666610/005989b13a1c/pone.0143890.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c7e5/4666610/a1280e0a05a8/pone.0143890.g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c7e5/4666610/e0da5df8fbc0/pone.0143890.g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c7e5/4666610/8887465f8680/pone.0143890.g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c7e5/4666610/5cd619462440/pone.0143890.g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c7e5/4666610/a1f3acb01d0e/pone.0143890.g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c7e5/4666610/9484de3a7214/pone.0143890.g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c7e5/4666610/005989b13a1c/pone.0143890.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c7e5/4666610/a1280e0a05a8/pone.0143890.g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c7e5/4666610/e0da5df8fbc0/pone.0143890.g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c7e5/4666610/8887465f8680/pone.0143890.g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c7e5/4666610/5cd619462440/pone.0143890.g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c7e5/4666610/a1f3acb01d0e/pone.0143890.g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c7e5/4666610/9484de3a7214/pone.0143890.g007.jpg

相似文献

1
Using Next Generation Sequencing for Multiplexed Trait-Linked Markers in Wheat.利用新一代测序技术鉴定小麦中与多性状相关的标记
PLoS One. 2015 Dec 1;10(12):e0143890. doi: 10.1371/journal.pone.0143890. eCollection 2015.
2
Rapid identification of an adult plant stripe rust resistance gene in hexaploid wheat by high-throughput SNP array genotyping of pooled extremes.通过对极端混合样本进行高通量SNP阵列基因分型快速鉴定六倍体小麦中的一个成株期抗条锈病基因
Theor Appl Genet. 2018 Jan;131(1):43-58. doi: 10.1007/s00122-017-2984-3. Epub 2017 Sep 30.
3
Overcoming polyploidy pitfalls: a user guide for effective SNP conversion into KASP markers in wheat.克服多倍体陷阱：小麦中有效 SNP 转化为 KASP 标记的用户指南。
Theor Appl Genet. 2020 Aug;133(8):2413-2430. doi: 10.1007/s00122-020-03608-x. Epub 2020 Jun 4.
4
Development of a high-density linkage map and mapping of the three-pistil gene (Pis1) in wheat using GBS markers.利用GBS标记构建小麦高密度连锁图谱并定位三雌蕊基因（Pis1）
BMC Genomics. 2017 Jul 31;18(1):567. doi: 10.1186/s12864-017-3960-7.
5
A SNP-based genetic dissection of versatile traits in bread wheat (Triticum aestivum L.).基于单核苷酸多态性的普通小麦（Triticum aestivum L.）多种性状的遗传解析。
Plant J. 2021 Nov;108(4):960-976. doi: 10.1111/tpj.15407. Epub 2021 Nov 9.
6
Simultaneous selection of major and minor genes: use of QTL to increase selection efficiency of coleoptile length of wheat (Triticum aestivum L.).主效基因和微效基因的同时选择：利用数量性状基因座提高小麦（普通小麦）胚芽鞘长度的选择效率。
Theor Appl Genet. 2009 Jun;119(1):65-74. doi: 10.1007/s00122-009-1017-2. Epub 2009 Apr 10.
7
Identification of candidate genes, regions and markers for pre-harvest sprouting resistance in wheat (Triticum aestivum L.).小麦（普通小麦）收获前穗发芽抗性候选基因、区域及标记的鉴定。
BMC Plant Biol. 2014 Nov 29;14:340. doi: 10.1186/s12870-014-0340-1.
8
GBS-based single dosage markers for linkage and QTL mapping allow gene mining for yield-related traits in sugarcane.基于GBS的单剂量标记用于连锁和QTL定位，有助于甘蔗产量相关性状的基因挖掘。
BMC Genomics. 2017 Jan 11;18(1):72. doi: 10.1186/s12864-016-3383-x.
9
Genome-wide linkage mapping of yield-related traits in three Chinese bread wheat populations using high-density SNP markers.利用高密度 SNP 标记对三个中国面包小麦群体的产量相关性状进行全基因组连锁作图。
Theor Appl Genet. 2018 Sep;131(9):1903-1924. doi: 10.1007/s00122-018-3122-6. Epub 2018 Jun 1.
10
Construction of a high-density genetic map by specific locus amplified fragment sequencing (SLAF-seq) and its application to Quantitative Trait Loci (QTL) analysis for boll weight in upland cotton (Gossypium hirsutum.).利用特异性位点扩增片段测序（SLAF-seq）构建高密度遗传图谱及其在陆地棉（Gossypium hirsutum.）铃重数量性状位点（QTL）分析中的应用
BMC Plant Biol. 2016 Apr 11;16:79. doi: 10.1186/s12870-016-0741-4.

引用本文的文献

1
Cost-Effective Detection of SNPs and Structural Variations in Full-Length Genes of Wheat and Sunflower Using Multiplex PCR and Rapid Nanopore Kit.使用多重PCR和快速纳米孔试剂盒对小麦和向日葵全长基因中的单核苷酸多态性和结构变异进行经济高效的检测
Biology (Basel). 2025 Jan 29;14(2):138. doi: 10.3390/biology14020138.
2
Genetic architecture of adult-plant resistance to stripe rust in bread wheat ( L.) association panel.面包小麦（L.）关联群体中成年植株对条锈病抗性的遗传结构
Front Plant Sci. 2023 Dec 7;14:1256770. doi: 10.3389/fpls.2023.1256770. eCollection 2023.
3
Whole-exome sequencing of selected bread wheat recombinant inbred lines as a useful resource for allele mining and bulked segregant analysis.

本文引用的文献

1
Spiked GBS: a unified, open platform for single marker genotyping and whole-genome profiling.Spiked GBS：用于单标记基因分型和全基因组分析的统一开放平台。
BMC Genomics. 2015 Mar 28;16(1):248. doi: 10.1186/s12864-015-1404-9.
2
Genotyping-by-sequencing (GBS) identified SNP tightly linked to QTL for pre-harvest sprouting resistance.通过测序进行基因分型（GBS）鉴定出与抗穗发芽QTL紧密连锁的单核苷酸多态性（SNP）。
Theor Appl Genet. 2015 Jul;128(7):1385-95. doi: 10.1007/s00122-015-2513-1. Epub 2015 Apr 8.
3
PolyMarker: A fast polyploid primer design pipeline.
对选定的面包小麦重组自交系进行全外显子组测序，作为等位基因挖掘和混合分组分析法的有用资源。
Front Genet. 2022 Nov 22;13:1058471. doi: 10.3389/fgene.2022.1058471. eCollection 2022.
4
Identification of Secreted Protein Gene-Based SNP Markers Associated with Virulence Phenotypes of f. sp. , the Wheat Stripe Rust Pathogen.鉴定与小麦条锈病菌致病型相关的分泌蛋白基因 SNP 标记。
Int J Mol Sci. 2022 Apr 8;23(8):4114. doi: 10.3390/ijms23084114.
5
Molecular Fingerprinting and Hybridity Authentication in Cowpea Using Single Nucleotide Polymorphism Based Kompetitive Allele-Specific PCR Assay.利用基于单核苷酸多态性的竞争性等位基因特异性PCR检测法进行豇豆的分子指纹识别和杂种鉴定
Front Plant Sci. 2021 Oct 5;12:734117. doi: 10.3389/fpls.2021.734117. eCollection 2021.
6
Genotyping by multiplexed sequencing (GMS): A customizable platform for genomic selection.多重测序基因分型（GMS）：基因组选择的定制化平台。
PLoS One. 2020 May 1;15(5):e0229207. doi: 10.1371/journal.pone.0229207. eCollection 2020.
7
Multifamily QTL analysis and comprehensive design of genotypes for high-quality soft wheat.多户 QTL 分析及优质软小麦基因型的综合设计。
PLoS One. 2020 Mar 11;15(3):e0230326. doi: 10.1371/journal.pone.0230326. eCollection 2020.
8
Multiplex restriction amplicon sequencing: a novel next-generation sequencing-based marker platform for high-throughput genotyping.多重限制扩增子测序：一种高通量基因分型的新型下一代测序标记平台。
Plant Biotechnol J. 2020 Jan;18(1):254-265. doi: 10.1111/pbi.13192. Epub 2019 Jul 23.
9
Imputation accuracy of wheat genotyping-by-sequencing (GBS) data using barley and wheat genome references.利用大麦和小麦基因组参考序列提高小麦基因分型测序（GBS）数据的插补准确性。
PLoS One. 2019 Jan 7;14(1):e0208614. doi: 10.1371/journal.pone.0208614. eCollection 2019.
10
Development and validation of diagnostic markers for Fhb1 region, a major QTL for Fusarium head blight resistance in wheat.开发和验证 Fhb1 区域的诊断标记物，该区域是小麦抗赤霉病的主要 QTL。
Theor Appl Genet. 2018 Nov;131(11):2371-2380. doi: 10.1007/s00122-018-3159-6. Epub 2018 Aug 22.
PolyMarker：一个快速的多倍体引物设计管道。
Bioinformatics. 2015 Jun 15;31(12):2038-9. doi: 10.1093/bioinformatics/btv069. Epub 2015 Feb 2.
4
Identification of candidate genes, regions and markers for pre-harvest sprouting resistance in wheat (Triticum aestivum L.).小麦（普通小麦）收获前穗发芽抗性候选基因、区域及标记的鉴定。
BMC Plant Biol. 2014 Nov 29;14:340. doi: 10.1186/s12870-014-0340-1.
5
RNA-Seq bulked segregant analysis enables the identification of high-resolution genetic markers for breeding in hexaploid wheat.RNA-Seq bulked segregant 分析可用于鉴定六倍体小麦中用于育种的高分辨率遗传标记。
Plant Biotechnol J. 2015 Jun;13(5):613-24. doi: 10.1111/pbi.12281. Epub 2014 Nov 8.
6
A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome.六倍体普通小麦（Triticum aestivum）基于染色体的草图序列。
Science. 2014 Jul 18;345(6194):1251788. doi: 10.1126/science.1251788.
7
FLEXBAR-Flexible Barcode and Adapter Processing for Next-Generation Sequencing Platforms.FLEXBAR—用于下一代测序平台的灵活条码和接头处理
Biology (Basel). 2012 Dec 14;1(3):895-905. doi: 10.3390/biology1030895.
8
SNP genotyping: the KASP assay.单核苷酸多态性基因分型：竞争性等位基因特异性PCR法
Methods Mol Biol. 2014;1145:75-86. doi: 10.1007/978-1-4939-0446-4_7.
9
From genes to markers: exploiting gene sequence information to develop tools for plant breeding.从基因到标记：利用基因序列信息开发植物育种工具。
Methods Mol Biol. 2014;1145:21-36. doi: 10.1007/978-1-4939-0446-4_2.
10
Characterization of polyploid wheat genomic diversity using a high-density 90,000 single nucleotide polymorphism array.利用高密度90,000单核苷酸多态性阵列对多倍体小麦基因组多样性进行表征。
Plant Biotechnol J. 2014 Aug;12(6):787-96. doi: 10.1111/pbi.12183. Epub 2014 Mar 20.