JIA-2020-2457 遗传多样性和全基因组关联分析揭示东北地区粳稻育种进程中与碾磨和外观品质相关的适应位点

doi:10.1016/S2095-3119(21)63701-2

Journal of Integrative Agriculture ›› 2022, Vol. 21 ›› Issue (6): 1539-1550.DOI: 10.1016/S2095-3119(21)63701-2

所属专题：水稻遗传育种合辑Rice Genetics · Breeding · Germplasm Resources

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JIA-2020-2457 遗传多样性和全基因组关联分析揭示东北地区粳稻育种进程中与碾磨和外观品质相关的适应位点

收稿日期:2020-12-02 接受日期:2021-04-02 出版日期:2022-06-01 发布日期:2021-04-02

Genetic diversity analysis and GWAS reveal the adaptive loci of milling and appearance quality of japonica (oryza sativa L.) in Northeast China

XU Xin, YE Jun-hua, YANG Ying-ying, LI Ruo-si, LI Zhen, WANG Shan, SUN Yan-fei, ZHANG Meng-chen, XU Qun, FENG Yue, WEI Xing-hua, YANG Yao-long

State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, P.R.China

Received:2020-12-02 Accepted:2021-04-02 Online:2022-06-01 Published:2021-04-02
About author:Correspondence YANG Yao-long, Tel: +86-571-63370539, E-mail: yangxiao182@126.com; WEI Xing-hua, Tel: +86-571-63370366, E-mail: weixinghua@caas.cn
Supported by:
This research was funded by the National Key Research and Development Program of China (2016YFD0100902–07), the Central Public-interest Scientific Institution Basal Research Fund, China (CPSIBRF-CNRRI-202101), and the Chinese Academy of Agricultural Sciences (CAAS-ASTIP-201X-CNRRI).

摘要/Abstract

摘要：

本研究以来源于辽宁、吉林和黑龙江三个省份的200个粳稻品种为实验材料，对碾磨和外观品质相关的性状进行考察。材料的系谱分析和遗传多样性分析结果表明，来自吉林省的品种遗传多样性最高。稻米品质的评价结果表明，来自辽宁省的品种具较好的碾磨品质，而来自黑龙江的品种具较好的外观品质。本研究同时用单位点和多位点的全基因组关联分析（GWAS）对碾磨和外观品质相关的基因位点进行计算，结果共检测到99个显著的SNP位点。其中，共3个SNP位点同时在混合线性模型（MLM）、mrMLM和FASTmrMLM这3种计算模型中检测到，进一步利用连锁不平衡分析获得对应的3个候选区域（qBRR-1、qBRR-9和qDEC-3），以便于后续的候选基因分析。由于候选区域内的候选基因超过300个，研究还结合基因GO分析以鉴定潜在的候选基因。此外，候选区域的遗传多样性分析结果表明，qBRR-9很可能在东北粳稻的育种过程中受到了较强的选择。这些结果为水稻育种和品质改良提供了具有参考意义的信息。

Abstract: Milling and appearance quality are important contributors to rice grain quality. Abundant genetic diversity and a suitable environment are crucial for rice improvement. In this study, we investigated the milling and appearance quality-related traits in a panel of 200 japonica rice cultivars selected from Liaoning, Jilin and Heilongjiang provinces in Northeast China. Pedigree assessment and genetic diversity analysis indicated that cultivars from Jilin harbored the highest genetic diversity among the three geographic regions. An evaluation of grain quality indicated that cultivars from Liaoning showed superior milling quality, whereas cultivars from Heilongjiang tended to exhibit superior appearance quality. Single- and multi-locus genome-wide association studies (GWAS) were conducted to identify loci associated with milling and appearance quality-related traits. Ninety-nine significant single-nucleotide polymorphisms (SNPs) were detected. Three common SNPs were detected using the mixed linear model (MLM), mrMLM, and FASTmrMLM methods. Linkage disequilibrium decay was estimated and indicated three candidate regions (qBRR-1, qBRR-9 and qDEC-3) for further candidate gene analysis. More than 300 genes were located in these candidate regions. Gene Ontology (GO) analysis was performed to discover the potential candidate genes. Genetic diversity analysis of the candidate regions revealed that qBRR-9 may have been subject to strong selection during breeding. These results provide information that will be valuable for the improvement of grain quality in rice breeding.

Key words: rice , grain quality , GWAS , genetic diversity

. JIA-2020-2457 遗传多样性和全基因组关联分析揭示东北地区粳稻育种进程中与碾磨和外观品质相关的适应位点[J]. Journal of Integrative Agriculture, 2022, 21(6): 1539-1550.

XU Xin, YE Jun-hua, YANG Ying-ying, LI Ruo-si, LI Zhen, WANG Shan, SUN Yan-fei, ZHANG Meng-chen, XU Qun, FENG Yue, WEI Xing-hua, YANG Yao-long. Genetic diversity analysis and GWAS reveal the adaptive loci of milling and appearance quality of japonica (oryza sativa L.) in Northeast China[J]. Journal of Integrative Agriculture, 2022, 21(6): 1539-1550.

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JIA-2020-2457 遗传多样性和全基因组关联分析揭示东北地区粳稻育种进程中与碾磨和外观品质相关的适应位点

Genetic diversity analysis and GWAS reveal the adaptive loci of milling and appearance quality of japonica (oryza sativa L.) in Northeast China

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