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作物学报 ›› 2021, Vol. 47 ›› Issue (6): 1114-1123.doi: 10.3724/SP.J.1006.2021.02047

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

广西水稻地方品种核心种质稻瘟病抗性位点全基因组关联分析

陈灿(), 农保选(), 夏秀忠, 张宗琼, 曾宇, 冯锐, 郭辉, 邓国富, 李丹婷*(), 杨行海*()   

  1. 广西农业科学院水稻研究所/广西水稻遗传育种重点实验室, 广西南宁 530007
  • 收稿日期:2020-07-12 接受日期:2020-12-01 出版日期:2021-06-12 网络出版日期:2020-12-28
  • 通讯作者: 李丹婷,杨行海
  • 作者简介:陈灿, E-mail:chencan129@126.com|农保选, E-mail:nongbaoxuan88@gxaas.net
  • 基金资助:
    中央引导地方科技发展专项(桂科ZY19183020);广西创新驱动发展专项(AA17204045-1);广西自然科学基金项目(2020GXNSFAA259041);广西自然科学基金项目(2018GXNSFAA138124);广西自然科学基金项目(2017GXNSFBA198210);广西重大科技创新基地开放课题(2018-05-Z06-CX04);广西农业科学院发展基金(桂农科2019Z08)

Genome-wide association study of blast resistance loci in the core germplasm of rice landraces from Guangxi

CHEN Can(), NONG Bao-Xuan(), XIA Xiu-Zhong, ZHANG Zong-Qiong, ZENG Yu, FENG Rui, GUO Hui, DENG Guo-Fu, LI Dan-Ting*(), YANG Xing-Hai*()   

  1. Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning 530007, Guangxi, China
  • Received:2020-07-12 Accepted:2020-12-01 Published:2021-06-12 Published online:2020-12-28
  • Contact: LI Dan-Ting,YANG Xing-Hai
  • Supported by:
    The Special Fund of Local Science and Technology Development for the Central Guidance(桂科ZY19183020);The Guangxi Special Fund for Innovation-Driven Development(AA17204045-1);The Guangxi Natural Science Fund(2020GXNSFAA259041);The Guangxi Natural Science Fund(2018GXNSFAA138124);The Guangxi Natural Science Fund(2017GXNSFBA198210);The Opening Project of Major Science and Technology Innovation Base for Guangxi(2018-05-Z06-CX04);The Development Fund of Guangxi Academy of Agricultural Sciences(桂农科2019Z08)

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摘要：

稻瘟病是水稻重要病害之一, 严重影响水稻的产量与品质。培育抗性品种是防治稻瘟病最经济、环保的方式。稻瘟病抗性基因的鉴定与挖掘是开展抗病育种的基础与前提。本课题组前期对419份广西水稻地方品种核心种质进行简化基因组测序, 获得208,993个高质量SNP标记。本研究采用苗期喷雾接种方法, 研究了该419份核心种质对7个稻瘟病生理小种的抗性, 并根据表型和基因型数据, 利用一般线性模型(general linear model, GLM)和混合线性模型(mixed linear model, MLM)进行全基因组关联分析。2种模型下共检测到20个位点, 其中GLM检测到20个位点, MLM检测到1个位点, Chr12_10803913位点在2种模型下都检测到。17个位点与前人定位的基因/QTLs重叠, 其余3个是新位点, 分别为Chr3_18302718、Chr3_18302744及Chr5_10379127位点。在20个显著关联位点上下游各150 kb的基因组区域中共筛选出候选基因323个, 初步确定8个候选基因与抗病相关, 其中LOC_Os12g18360 (Pita)、LOC_Os12g18729 (Ptr)为已知克隆的基因, LOC_Os03g32100、LOC_Os03g32180和LOC_Os05g18090为新位点附近筛选到的候选基因。本研究结果为稻瘟病抗性位点挖掘与稻瘟病相关基因克隆提供了科学依据。

关键词: 水稻, 稻瘟病, 全基因组关联分析, 候选基因

Abstract:

Blast disease is one of the most important rice diseases, which seriously affects the yield and quality in rice. In general, breeding resistant varieties is the most economical, environmental, and friendly way to control rice blast. Identification and mining of blast resistance genes are the basis and premise of disease resistance breeding. In our previous study, 419 core germplasms from Guangxi rice landraces were sequenced using specific-locus amplified fragment sequencing (SLAF-seq) technology, and 208,993 high-quality SNPs were identified. Spray inoculation at seedling stage was used to evaluate the resistance of the 419 germplasms to 7 strains. According to phenotype and genotype data, genome-wide association study (GWAS) for rice blast was performed using general linear model (GLM) and mixed linear model (MLM). A total of 20 loci were detected under the two models, including 20 loci detected by GLM and 1 locus detected by MLM. Chr12_10803913 locus was detected in both models. There were 17 loci, overlapping with previously reported genes/QTLs, while the remaining three loci were the first reported, including Chr3_18302718, Chr3_18302744, and Chr5_10379127. A total of 323 candidate genes were screened out in the genomic regions of 150 kb upstream and downstream of 20 significantly associated loci. Eight candidate genes were preliminarily determined to be related to disease resistance. Among them, both LOC_Os12g18360 (Pita) and LOC_Os12g18729 (Ptr) were known cloned genes, LOC_Os03g32100, LOC_Os03g32180, and LOC_Os05g18090 were selected as candidate genes near the three loci. The results provided the scientific basis for the mining of rice blast resistance loci and gene cloning.

Key words: rice, blast disease, genome-wide association study (GWAS), candidate genes

表1

不同稻瘟病小种接种下水稻苗期叶瘟抗性级别统计分析"

小种
Strain		 抗级
Range		 平均值±标准差
Mean±SE		 变异系数
CV (%)
ZA9 1-9 5.03±1.49 29.62
ZA13 1-8 5.72±1.36 23.78
ZB1 1-7 4.29±1.44 33.57
ZB9 1-8 4.83±1.54 31.88
ZB13 1-7 3.80±1.53 40.26
ZC3 1-8 4.84±1.62 33.47
ZC13 1-7 2.93±1.40 47.78

图1

关联群体在7个不同稻瘟病生理小种接种下的叶瘟抗性级别分布"

图2

3个菌种下水稻稻瘟病抗性的全基因组关联研究 A、B、C分别表示GLM模型ZB9、ZC3、ZC13的曼哈顿图。D表示MLM模型ZC3的曼哈顿图。E、F、G分别表示GLM模型ZB9、ZC3、ZC13的QQ图。H表示MLM模型ZC3的QQ图。图中实心倒三角形为本文中显著性关联位点。"

表2

水稻稻瘟病显著关联的SNP位点及已定位的基因/QTL"

小种
Strain		 染色体
Chr.		 位置
Position		 P值
P-value		 上游位点
Upstream loci		 下游位点
Downstream loci		 模型
Model		 已知基因/QTL
Known genes/QTLs
ZB9 1 10,443,043 1.63E-06 10,293,043 10,593,043 GLM Pi-h2(t)
ZC3 1 8,116,727 1.54E-07 7,966,727 8,266,727 GLM Pi-sj9
ZC3 1 8,116,887 2.91E-07 7,966,887 8,266,887 GLM Pi-sj9
ZC3 3 18,302,718 3.60E-08 18,152,718 18,452,718 GLM
ZC3 3 18,302,744 1.35E-08 18,152,744 18,452,744 GLM
ZC3 5 10,379,127 2.32E-07 10,229,127 10,529,127 GLM
ZB9 8 6,776,078 4.99E-07 6,626,078 6,926,078 GLM Pizh, Pi42
小种
Strain		 染色体
Chr.		 位置
Position		 P值
P-value		 上游位点
Upstream loci		 下游位点
Downstream loci		 模型
Model		 已知基因/QTL
Known genes/QTLs
ZC13 12 10,917,077 9.44E-08 10,767,077 11,067,077 GLM Pi12, Pi157, Pi19(t), Pi20, Pi31(t), Pi42(t), Pi6(t), Pita, Pita2, Pi67, Pi39(t), Pi58(t), Pi57, Ptr
ZC13 12 10,919,541 3.98E-07 10,769,541 11,069,541 GLM
ZC3 12 10,629,609 6.56E-08 10,479,609 107,79,609 GLM
ZC3 12 10,796,961 1.84E-07 10,646,961 10,946,961 GLM
ZC3 12 10,801,871 1.30E-07 10,651,871 10,951,871 GLM
ZC3 12 10,803,744 7.39E-09 10,653,744 10,953,744 GLM
ZC3 12 10,803,791 3.45E-08 10,653,791 10,953,791 GLM
ZC3 12 10,803,913 9.20E-10 10,653,913 10,953,913 GLM
ZC3 12 10,816,142 4.90E-09 10,666,142 10,966,142 GLM
ZC3 12 10,816,145 8.24E-09 10,666,145 10,966,145 GLM
ZC3 12 10,816,166 8.24E-09 10,666,166 10,966,166 GLM
ZC3 12 10,816,338 8.01E-09 10,666,338 10,966,338 GLM
ZC3 12 10,926,790 2.35E-07 10,776,790 11,076,790 GLM
ZC3 12 10,803,913 3.93E-07 10,653,913 10,953,913 MLM

表3

候选基因信息"

基因名称
Gene name		 物理位置
Physical position		 基因注释
Gene annotation
LOC_Os01g14550 8,159,849-8,161,554 Pathogen-related protein, putative, expressed
LOC_Os01g14590 8,175,375-8,177,889 Pathogen-related protein, putative, expressed
LOC_Os03g32100 18,367,156-18,368,378 Spotted leaf 11, putative, expressed
LOC_Os03g32180 18,410,063-18,411,482 Polygalacturonase inhibitor 1 precursor, putative, expressed
LOC_Os05g18090 10,404,235-10,407,571 SHR5-receptor-like kinase, putative, expressed
LOC_Os12g18360 10,606,359-10,612,068 NB-ARC domain containing protein, expressed
LOC_Os12g18374 10,624,037-10,633,368 NB-ARC domain containing protein, expressed
LOC_Os12g18729 10,822,534-10,833,768 Expressed protein

图3

已定位的稻瘟病抗性基因与关联位点 倒三角形所指关联位点或关联位点所在区域。A: 1号染色体上已定位的稻瘟病基因; B: 12号染色体上与显著关联位点区域重叠的稻瘟病基因。"

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