• 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

多亲本杂交低覆盖度测序基因分型数据中缺失标记的高效填充

Efficient imputation of missing markers in low-coverage genotyping-by-sequencing data from multiparental crosses.

作者信息

Huang B Emma, Raghavan Chitra, Mauleon Ramil, Broman Karl W, Leung Hei

机构信息

Computational Informatics and Food Futures Flagship, Commonwealth Scientific and Industrial Research Organization, Dutton Park, Queensland, Australia 4102.

出版信息

Genetics. 2014 May;197(1):401-4. doi: 10.1534/genetics.113.158014. Epub 2014 Feb 28.

DOI:10.1534/genetics.113.158014
PMID:24583583
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC4012496/
Abstract

We consider genomic imputation for low-coverage genotyping-by-sequencing data with high levels of missing data. We compensate for this loss of information by utilizing family relationships in multiparental experimental crosses. This nearly quadruples the number of usable markers when applied to a large rice Multiparent Advanced Generation InterCross (MAGIC) study.

摘要

我们考虑对具有高缺失数据水平的低覆盖度测序基因分型数据进行基因组填充。我们通过利用多亲本实验杂交中的家系关系来弥补这种信息损失。当应用于一项大型水稻多亲本高级世代互交（MAGIC）研究时，这几乎使可用标记的数量增加了四倍。

相似文献

1
Efficient imputation of missing markers in low-coverage genotyping-by-sequencing data from multiparental crosses.多亲本杂交低覆盖度测序基因分型数据中缺失标记的高效填充
Genetics. 2014 May;197(1):401-4. doi: 10.1534/genetics.113.158014. Epub 2014 Feb 28.
2
Accurate Genotype Imputation in Multiparental Populations from Low-Coverage Sequence.多亲本群体低覆盖度序列下的精确基因型推断。
Genetics. 2018 Sep;210(1):71-82. doi: 10.1534/genetics.118.300885. Epub 2018 Jul 25.
3
Approaches in Characterizing Genetic Structure and Mapping in a Rice Multiparental Population.水稻多亲本群体中遗传结构表征与图谱构建的方法
G3 (Bethesda). 2017 Jun 7;7(6):1721-1730. doi: 10.1534/g3.117.042101.
4
Construction of Genetic Linkage Maps in Multiparental Populations.构建多亲本群体的遗传连锁图谱。
Genetics. 2019 Aug;212(4):1031-1044. doi: 10.1534/genetics.119.302229. Epub 2019 Jun 10.
5
Saturated linkage map construction in Rubus idaeus using genotyping by sequencing and genome-independent imputation.利用测序基因型和与基因组无关的推断构建树莓饱和连锁图谱。
BMC Genomics. 2013 Jan 16;14:2. doi: 10.1186/1471-2164-14-2.
6
Genomic preselection with genotyping-by-sequencing increases performance of commercial oil palm hybrid crosses.基因组预选择与测序基因分型提高了商业油棕杂交种的性能。
BMC Genomics. 2017 Nov 2;18(1):839. doi: 10.1186/s12864-017-4179-3.
7
Low-depth genotyping-by-sequencing (GBS) in a bovine population: strategies to maximize the selection of high quality genotypes and the accuracy of imputation.牛群中的低深度测序基因分型（GBS）：最大化高质量基因型选择和归因准确性的策略。
BMC Genet. 2017 Apr 5;18(1):32. doi: 10.1186/s12863-017-0501-y.
8
Bridging the genotyping gap: using genotyping by sequencing (GBS) to add high-density SNP markers and new value to traditional bi-parental mapping and breeding populations.弥合基因分型差距：利用测序基因分型 (GBS) 为传统的双亲作图和育种群体添加高密度 SNP 标记和新价值。
Theor Appl Genet. 2013 Nov;126(11):2699-716. doi: 10.1007/s00122-013-2166-x. Epub 2013 Aug 6.
9
Whole-genome characterization in pedigreed non-human primates using genotyping-by-sequencing (GBS) and imputation.利用简化基因组测序（GBS）和填充技术对圈养非人灵长类动物进行全基因组特征分析。
BMC Genomics. 2016 Aug 24;17(1):676. doi: 10.1186/s12864-016-2966-x.
10
Flexible and scalable genotyping-by-sequencing strategies for population studies.用于群体研究的灵活且可扩展的测序基因分型策略。
BMC Genomics. 2014 Nov 18;15(1):979. doi: 10.1186/1471-2164-15-979.

引用本文的文献

1
Using genotype imputation to integrate Canola populations for genome-wide association and genomic prediction of blackleg resistance.利用基因型填充整合油菜群体以进行全基因组关联分析和黑胫病抗性的基因组预测。
BMC Genomics. 2025 Mar 4;26(1):215. doi: 10.1186/s12864-025-11250-4.
2
Genotyping Platforms for Genome-Wide Association Studies: Options and Practical Considerations.全基因组关联研究的基因分型平台：选择和实际考虑因素。
Methods Mol Biol. 2022;2481:29-42. doi: 10.1007/978-1-0716-2237-7_3.
3
Multi-parent populations in crops: a toolbox integrating genomics and genetic mapping with breeding.作物多亲种群：整合基因组学和遗传图谱与育种的工具包。
Heredity (Edinb). 2020 Dec;125(6):396-416. doi: 10.1038/s41437-020-0336-6. Epub 2020 Jul 3.
4
Construction, characteristics and high throughput molecular screening methodologies in some special breeding populations: a horticultural perspective.一些特殊育种群体的构建、特征及高通量分子筛选方法：园艺学视角
J Genet. 2019 Sep;98.
5
Genotyping by low-coverage whole-genome sequencing in intercross pedigrees from outbred founders: a cost-efficient approach.低覆盖度全基因组测序在杂交系中进行基因分型：一种具有成本效益的方法。
Genet Sel Evol. 2019 Aug 14;51(1):44. doi: 10.1186/s12711-019-0487-1.
6
Generating High Density, Low Cost Genotype Data in Soybean [ (L.) Merr.].在大豆 [（L.）Merr.] 中生成高密度、低成本的基因型数据。
G3 (Bethesda). 2019 Jul 9;9(7):2153-2160. doi: 10.1534/g3.119.400093.
7
GBS-derived SNP catalogue unveiled wide genetic variability and geographical relationships of Italian olive cultivars.GBS 衍生 SNP 目录揭示了意大利橄榄品种的广泛遗传多样性和地理关系。
Sci Rep. 2018 Oct 26;8(1):15877. doi: 10.1038/s41598-018-34207-y.
8
Accurate Genotype Imputation in Multiparental Populations from Low-Coverage Sequence.多亲本群体低覆盖度序列下的精确基因型推断。
Genetics. 2018 Sep;210(1):71-82. doi: 10.1534/genetics.118.300885. Epub 2018 Jul 25.
9
Accounting for Errors in Low Coverage High-Throughput Sequencing Data When Constructing Genetic Maps Using Biparental Outcrossed Populations.利用双交群体构建遗传图谱时，考虑低覆盖率高通量测序数据中的错误。
Genetics. 2018 May;209(1):65-76. doi: 10.1534/genetics.117.300627. Epub 2018 Feb 27.
10
Efficient genome-wide genotyping strategies and data integration in crop plants.作物中高效的全基因组基因分型策略与数据整合
Theor Appl Genet. 2018 Mar;131(3):499-511. doi: 10.1007/s00122-018-3056-z. Epub 2018 Jan 19.

本文引用的文献

1
Multi-parent advanced generation inter-cross (MAGIC) populations in rice: progress and potential for genetics research and breeding.水稻多亲本聚合杂交（MAGIC）群体：遗传学研究与育种的进展和潜力。
Rice (N Y). 2013 May 6;6(1):11. doi: 10.1186/1939-8433-6-11.
2
Imputation of unordered markers and the impact on genomic selection accuracy.无序标记的推断及其对基因组选择准确性的影响。
G3 (Bethesda). 2013 Mar;3(3):427-39. doi: 10.1534/g3.112.005363. Epub 2013 Mar 1.
3
Saturated linkage map construction in Rubus idaeus using genotyping by sequencing and genome-independent imputation.利用测序基因型和与基因组无关的推断构建树莓饱和连锁图谱。
BMC Genomics. 2013 Jan 16;14:2. doi: 10.1186/1471-2164-14-2.
4
Imputing missing genotypes with weighted k nearest neighbors.使用加权最近邻法推断缺失基因型。
J Toxicol Environ Health A. 2012;75(8-10):438-46. doi: 10.1080/15287394.2012.674910.
5
Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes.对 50 份栽培稻和野生稻进行重测序，得到了可用于鉴定农艺重要基因的标记。
Nat Biotechnol. 2011 Dec 11;30(1):105-11. doi: 10.1038/nbt.2050.
6
A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species.一种用于高多样性物种的稳健、简单的测序分型（GBS）方法。
PLoS One. 2011 May 4;6(5):e19379. doi: 10.1371/journal.pone.0019379.
7
Discovery of genome-wide DNA polymorphisms in a landrace cultivar of Japonica rice by whole-genome sequencing.通过全基因组测序发现粳稻地方品种的全基因组 DNA 多态性。
Plant Cell Physiol. 2011 Feb;52(2):274-82. doi: 10.1093/pcp/pcr003. Epub 2011 Jan 21.
8
R/mpMap: a computational platform for the genetic analysis of multiparent recombinant inbred lines.R/mpMap：一个用于多亲本重组自交系遗传分析的计算平台。
Bioinformatics. 2011 Mar 1;27(5):727-9. doi: 10.1093/bioinformatics/btq719. Epub 2011 Jan 8.
9
MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes.MaCH：利用序列和基因型数据来估计单倍型和未观测基因型。
Genet Epidemiol. 2010 Dec;34(8):816-34. doi: 10.1002/gepi.20533.
10
Genetic properties of the maize nested association mapping population.玉米巢式关联作图群体的遗传特性
Science. 2009 Aug 7;325(5941):737-40. doi: 10.1126/science.1174320.