• 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

在全基因组关联研究中有效利用遗传数据可提高水稻数量性状位点检测的可信度。

Effective use of legacy data in a genome-wide association studies improves the credibility of quantitative trait loci detection in rice.

机构信息

Faculty of Food and Agricultural Sciences, Institute of Fermentation Sciences, Fukushima University, Fukushima 960-1296, Japan.

Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan.

出版信息

Plant Physiol. 2023 Mar 17;191(3):1561-1573. doi: 10.1093/plphys/kiad018.

DOI:10.1093/plphys/kiad018
PMID:36652387
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10022637/
Abstract

Genome-wide association studies (GWASs) are used to detect quantitative trait loci (QTL) using genomic and phenotypic data as inputs. While genomic data are obtained with high throughput and low cost, obtaining phenotypic data requires a large amount of effort and time. In past breeding programs, researchers and breeders have conducted a large number of phenotypic surveys and accumulated results as legacy data. In this study, we conducted a GWAS using phenotypic data of temperate japonica rice (Oryza sativa) varieties from a public database. The GWAS using the legacy data detected several known agriculturally important genes, indicating reliability of the legacy data for GWAS. By comparing the GWAS using legacy data (L-GWAS) and a GWAS using phenotypic data that we measured (M-GWAS), we detected reliable QTL for agronomically important traits. These results suggest that an L-GWAS is a strong alternative to replicate tests to confirm the reproducibility of QTL detected by an M-GWAS. In addition, because legacy data have often been accumulated for many traits, it is possible to evaluate the pleiotropic effect of the QTL identified for the specific trait that we focused on with respect to various other traits. This study demonstrates the effectiveness of using legacy data for GWASs and proposes the use of legacy data to accelerate genomic breeding.

摘要

全基因组关联研究（GWAS）用于使用基因组和表型数据作为输入来检测数量性状基因座（QTL）。虽然可以高通量、低成本地获取基因组数据，但获取表型数据需要大量的努力和时间。在过去的育种计划中，研究人员和育种家已经进行了大量的表型调查，并将结果作为遗留数据积累下来。在这项研究中，我们使用公共数据库中温带粳稻（Oryza sativa）品种的表型数据进行了 GWAS。使用遗留数据进行的 GWAS 检测到了几个已知的农业重要基因，表明遗留数据对于 GWAS 的可靠性。通过比较使用遗留数据（L-GWAS）和我们测量的表型数据（M-GWAS）进行的 GWAS，我们检测到了对农艺性状重要的可靠 QTL。这些结果表明，L-GWAS 是一种强有力的替代方法，可以重复测试以确认 M-GWAS 检测到的 QTL 的可重复性。此外，由于经常为许多性状积累了遗留数据，因此可以评估我们关注的特定性状的 QTL 对各种其他性状的多效性影响。本研究证明了使用遗留数据进行 GWAS 的有效性，并提出了使用遗留数据来加速基因组育种。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0cb6/10022637/64f644156b05/kiad018f6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0cb6/10022637/a700fd70ec98/kiad018f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0cb6/10022637/29ff5f5cb5ab/kiad018f4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0cb6/10022637/41943ad6d5f2/kiad018f5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0cb6/10022637/64f644156b05/kiad018f6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0cb6/10022637/a700fd70ec98/kiad018f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0cb6/10022637/29ff5f5cb5ab/kiad018f4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0cb6/10022637/41943ad6d5f2/kiad018f5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0cb6/10022637/64f644156b05/kiad018f6.jpg

相似文献

1
Effective use of legacy data in a genome-wide association studies improves the credibility of quantitative trait loci detection in rice.在全基因组关联研究中有效利用遗传数据可提高水稻数量性状位点检测的可信度。
Plant Physiol. 2023 Mar 17;191(3):1561-1573. doi: 10.1093/plphys/kiad018.
2
RicePilaf: a post-GWAS/QTL dashboard to integrate pangenomic, coexpression, regulatory, epigenomic, ontology, pathway, and text-mining information to provide functional insights into rice QTLs and GWAS loci.稻米煲饭：一个后 GWAS/QTL 仪表盘，用于整合泛基因组、共表达、调控、表观基因组、本体论、通路和文本挖掘信息，为水稻 QTL 和 GWAS 基因座提供功能见解。
Gigascience. 2024 Jan 2;13. doi: 10.1093/gigascience/giae013.
3
Genome-wide association study-based identification genes influencing agronomic traits in rice (Oryza sativa L.).基于全基因组关联研究鉴定影响水稻（Oryza sativa L.）农艺性状的基因。
Genomics. 2021 May;113(3):1396-1406. doi: 10.1016/j.ygeno.2021.03.016. Epub 2021 Mar 9.
4
Genome wide association mapping for grain shape traits in indica rice.籼稻粒形性状的全基因组关联图谱分析
Planta. 2016 Oct;244(4):819-30. doi: 10.1007/s00425-016-2548-9. Epub 2016 May 19.
5
Genome-wide association studies for agronomical traits in a world wide spring barley collection.在全球春大麦种质资源中进行农艺性状的全基因组关联研究。
BMC Plant Biol. 2012 Jan 27;12:16. doi: 10.1186/1471-2229-12-16.
6
Genome-Wide Association Study of Root System Development at Seedling Stage in Rice.水稻幼苗根系发育的全基因组关联研究。
Genes (Basel). 2020 Nov 25;11(12):1395. doi: 10.3390/genes11121395.
7
Multi-trait meta-analyses reveal 25 quantitative trait loci for economically important traits in Brown Swiss cattle.多性状荟萃分析揭示了 25 个与瑞士褐牛重要经济性状相关的数量性状位点。
BMC Genomics. 2019 Sep 3;20(1):695. doi: 10.1186/s12864-019-6066-6.
8
Genome wide association analysis of root hair traits in rice reveals novel genomic regions controlling epidermal cell differentiation.水稻根毛性状的全基因组关联分析揭示了控制表皮细胞分化的新的基因组区域。
BMC Plant Biol. 2023 Jan 4;23(1):6. doi: 10.1186/s12870-022-04026-5.
9
Genome-wide Association Study (GWAS) for Mesocotyl Elongation in Rice ( L.) under Multiple Culture Conditions.全基因组关联研究（GWAS）在多种培养条件下对水稻中中胚轴伸长的研究。
Genes (Basel). 2019 Dec 31;11(1):49. doi: 10.3390/genes11010049.
10
Advances in genome-wide association studies of complex traits in rice.水稻复杂性状全基因组关联研究进展。
Theor Appl Genet. 2020 May;133(5):1415-1425. doi: 10.1007/s00122-019-03473-3. Epub 2019 Nov 12.

引用本文的文献

1
Local haplotyping reveals insights into the genetic control of flowering time variation in wild and domesticated soybean.局部单倍型分型揭示了野生和驯化大豆开花时间变异的遗传控制机制。
Plant Genome. 2024 Dec;17(4):e20528. doi: 10.1002/tpg2.20528. Epub 2024 Nov 7.
2
How have breeders adapted rice flowering to the growing region?育种者如何使水稻开花适应种植区域？
J Integr Plant Biol. 2024 Dec;66(12):2736-2753. doi: 10.1111/jipb.13785. Epub 2024 Oct 25.
3
Redefining awn development in rice through the breeding history of Japanese awn reduction.

本文引用的文献

1
Determinant Factors and Regulatory Systems for Anthocyanin Biosynthesis in Rice Apiculi and Stigmas.水稻颖尖和柱头中花青素生物合成的决定因素及调控系统
Rice (N Y). 2021 Apr 21;14(1):37. doi: 10.1186/s12284-021-00480-1.
2
A quantitative genomics map of rice provides genetic insights and guides breeding.水稻数量基因组图谱提供遗传见解并指导育种。
Nat Genet. 2021 Feb;53(2):243-253. doi: 10.1038/s41588-020-00769-9. Epub 2021 Feb 1.
3
Status and prospects of genome-wide association studies in plants.植物全基因组关联研究的现状与展望。
通过日本芒退化的育种历史重新定义水稻芒的发育
Front Plant Sci. 2024 May 16;15:1370956. doi: 10.3389/fpls.2024.1370956. eCollection 2024.
4
Low mutation rate of spontaneous mutants enables detection of causative genes by comparing whole genome sequences.自发突变体的低突变率使得通过比较全基因组序列来检测致病基因成为可能。
Front Plant Sci. 2024 Apr 4;15:1366413. doi: 10.3389/fpls.2024.1366413. eCollection 2024.
Plant Genome. 2021 Mar;14(1):e20077. doi: 10.1002/tpg2.20077. Epub 2021 Jan 13.
4
Landraces of temperate japonica rice have superior alleles for improving culm strength associated with lodging resistance.温带粳稻地方品种具有改良茎秆强度的优异等位基因，与抗倒伏性有关。
Sci Rep. 2020 Nov 16;10(1):19855. doi: 10.1038/s41598-020-76949-8.
5
GWAS with principal component analysis identifies a gene comprehensively controlling rice architecture.GWAS 与主成分分析相结合，鉴定出一个全面控制水稻结构的基因。
Proc Natl Acad Sci U S A. 2019 Oct 15;116(42):21262-21267. doi: 10.1073/pnas.1904964116. Epub 2019 Sep 30.
6
Breeding crops to feed 10 billion.培育作物以养活 100 亿人。
Nat Biotechnol. 2019 Jul;37(7):744-754. doi: 10.1038/s41587-019-0152-9. Epub 2019 Jun 17.
7
Determining factors, regulation system, and domestication of anthocyanin biosynthesis in rice leaves.决定水稻叶片花色素苷生物合成的因素、调控系统和驯化。
New Phytol. 2019 Jul;223(2):705-721. doi: 10.1111/nph.15807. Epub 2019 Apr 23.
8
Next-Generation Sequencing Accelerates Crop Gene Discovery.下一代测序加速作物基因发现。
Trends Plant Sci. 2019 Mar;24(3):263-274. doi: 10.1016/j.tplants.2018.11.008. Epub 2018 Dec 17.
9
The C-S-A gene system regulates hull pigmentation and reveals evolution of anthocyanin biosynthesis pathway in rice.C-S-A 基因系统调控稻壳色素沉着，揭示了水稻类黄酮生物合成途径的进化。
J Exp Bot. 2018 Mar 24;69(7):1485-1498. doi: 10.1093/jxb/ery001.
10
Rice SNP-seek database update: new SNPs, indels, and queries.水稻SNP-seek数据库更新：新的单核苷酸多态性、插入缺失及查询内容。
Nucleic Acids Res. 2017 Jan 4;45(D1):D1075-D1081. doi: 10.1093/nar/gkw1135. Epub 2016 Nov 29.