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作物学报 ›› 2022, Vol. 48 ›› Issue (8): 2007-2015.doi: 10.3724/SP.J.1006.2022.12030

• 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芽期耐盐性全基因组关联分析

夏秀忠1,**(), 张宗琼1,**(), 杨行海1, 荘洁1, 曾宇2, 邓国富2, 宋国显3, 黄欲晓3, 农保选1,*(), 李丹婷1,*()   

  1. 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
    2广西农业科学院, 广西南宁 530007
    3钦州市农业科学研究所, 广西钦州 535000
  • 收稿日期:2021-04-26 接受日期:2021-11-29 出版日期:2022-08-12 网络出版日期:2021-12-24
  • 通讯作者: 农保选,李丹婷
  • 作者简介:夏秀忠, E-mail: xiaxiuzhong@163.com;
    张宗琼, E-mail: zhangzongqiong@gxaas.net, Tel: 0771-3244040第一联系人：

    ** 同等贡献

  • 基金资助:
    水稻生物学国家重点实验室开放课题(170102);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项目(Gui Nong Ke 2021JM07);广西农业科学院发展基金项目(Gui Nong Ke 2021JM49);广西农业科学院基本科研业务专项(Gui Nong Ke 2021YT030)

Genome wide association study of salt tolerance at the germination stage for core Germplasm of rice landrace in Guangxi, China

XIA Xiu-Zhong1,**(), ZHANG Zong-Qiong1,**(), YANG Xing-Hai1, ZHUANG Jie1, ZENG Yu2, DENG Guo-Fu2, SONG Guo-Xian3, HUANG Yu-Xiao3, NONG Bao-Xuang1,*(), LI Dan-Ting1,*()   

  1. 1Rice Research Institute, Guangxi Academy of Agricultural Sciences / Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning 530007, Guangxi, China
    2Guangxi Academy of Agricultural Sciences, Nanning 530007, Guangxi, China
    3Qinzhou Institute of Agricultural Sciences, Qinzhou 535000, Guangxi, China
  • Received:2021-04-26 Accepted:2021-11-29 Published:2022-08-12 Published online:2021-12-24
  • Contact: NONG Bao-Xuang,LI Dan-Ting
  • About author:First author contact:

    ** Contributed equally to this work

  • Supported by:
    Open Project Program of State Key Laboratory of Rice Biology(170102);Opening Project of Major Science and Technology Innovation Base for Guangxi(2018-05-Z06-CX04);Development Fund of Guangxi Academy of Agricultural Sciences(Gui Nong Ke 2021JM07);Development Fund of Guangxi Academy of Agricultural Sciences(Gui Nong Ke 2021JM49);Special Funds of Basic Scientific Research Foundation of Guangxi Academy of Agricultural Sciences(Gui Nong Ke 2021YT030)

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摘要：

水稻属盐敏感的作物, 盐胁迫会导致产量显著减少。我国盐渍地总面积大, 并且呈迅速增长趋势, 因此, 筛选水稻耐盐种质, 培育耐盐水稻品种十分必要。本研究在1.5% NaCl盐胁迫条件下评价419份广西水稻地方品种核心种质种子芽期的相对盐害率, 并利用全基因组关联分析鉴定耐盐位点。研究结果表明: 盐胁迫下, 种子芽期平均发芽率为57.67%, 显著低于对照92.55%, 且夏皮罗-威尔克检验(0.9301)不符合正态分布。基于208,993个SNP标记, 将419份核心种质资源分为6个亚群, 利用一般线性模型(general linear model, GLM)和混合线性模型(mixed linear model, MLM)分析分别获得129个和1个显著关联SNP, 分布在1号、2号、3号、4号、5号、6号、8号、9号和12号染色体上。在14个与水稻耐盐性显著关联区域, 有13个区域与前人定位或克隆的耐盐基因重叠。显著关联区域Chr. 8: 10,564,948~10,733,175为首次报道, 命名为qGR8。qGR8区域内含有53个基因, 其中34个经转录组数据比对获得表达谱, 比对结果推测LOC_Os08g17370为候选基因, 该基因为跨膜9超家族成员, 在耐盐亲本的根部和叶部上调表达, 可能为qGR8区域内水稻芽期耐盐的新基因。这些研究结果为耐盐新基因的克隆奠定基础, 为培育耐盐水稻品种提供新的基因资源。

关键词: 水稻, 核心种质, 芽期, 耐盐, 全基因组关联分析

Abstract:

Rice is a salt-sensitive crop, and salt stress can cause significant reduction in rice yield. China's total saline area is large and growing rapidly. Therefore, it is necessary to screen for the salt-tolerant rice germplasm and cultivate these varieties. In this study, we evaluated the relative salt damage rate of 419 core germplasm of Guangxi rice landraces at seed germination stage under 1.5% NaCl salt stress, and identified the salt-tolerant loci by whole-genome association analysis. The results showed that the average germination rate under salt stress was 57.67%, which was significantly 92.55% lower than that of control group, and the Shapiro-Wilk test (0.9301) found that the distribution did not conform to normal distribution. Based on 208,993 SNP markers, 419 core germplasm was divided into 6 subgroups. We used general linear model (GLM) and mixed linear model (MLM) analysis to identify 129 and 1 significantly associated SNPs, respectively, which were distributed on chromosomes 1, 2, 3, 4, 5, 6, 8, 9, and 12. Among the 14 regions that were significantly associated with rice salt tolerance, 13 regions overlapped with previously identified or cloned salt tolerance genes. The significantly associated region Chr. 8:10,564,948-10,733,175 was reported for the first time and named qGR8. There were 53 genes in qGR8 region, 34 of which were compared with transcriptome data to obtain the expression profiles. We compared the expression profiles and speculated that LOC_Os08g17370 was a candidate gene. This gene is a member of transmembrane 9 superfamily and is up-regulated in roots and leaves of salt-tolerant parent. Thus, this gene might be a novel salt-tolerant gene in qGR8 region at germination stage in rice. These results lay a foundation for cloning new genes of salt-tolerant and provide new genetic resources for breeding salt-tolerant rice varieties.

Key words: Oryza sativa L., core germplasm, germination, salt tolerance, genome-wide association study

图1

419份水稻核心种质芽期耐盐鉴定结果"

图2

连锁不平衡衰减图"

图3

种子芽期全基因组关联分析曼哈顿和QQ-plot图 (a)和(b)一般线性模型的全基因组关联分析; (c)和(d)混合线性模型的全基因组关联分析。(a)和(c)为曼哈顿图, 图中横坐标为染色体, 纵坐标为关联值的-log10 (P)值; 虚线位置(P=4.78E-07)为显著性阈值; (b)和(d)为Q-Q图, 图中X轴为P值零假设下的期望值, Y轴表示P值的观测值。"

表1

34个基因在芽期的转录丰度"

基因名称
Gene ID		 转录丰度
Transcript abundances		 描述
Description
LOC_Os08g17160 高High Plastocyanin-like domain containing protein, putative, expressed
LOC_Os08g17294 高High PSF3-Putative GINS complex subunit, expressed
LOC_Os08g17320 高High Protein kinase family protein, putative, expressed
LOC_Os08g17370 高High Transmembrane 9 superfamily member, putative, expressed
LOC_Os08g17410 高High BRASSINOSTEROID INSENSITIVE 1 precursor, putative, expressed
LOC_Os08g17510 高High Sulfotransferase domain containing protein, expressed
LOC_Os08g17600 高High SNARE domain containing protein, putative, expressed
LOC_Os08g17610 高High Expressed protein
LOC_Os08g17650 高High LYR motif containing protein, putative, expressed
LOC_Os08g17680 高High Stromal cell-drived factor 2-like protein precursor, putative, expressed
LOC_Os08g17150 低Low Expressed protein
LOC_Os08g17390 低Low Expressed protein
LOC_Os08g17400 低Low WRKY89, expressed
LOC_Os08g17430 低Low Expressed protein
LOC_Os08g17450 低Low Retrotransposon protein, putative, undassified, expressed
LOC_Os08g17500 低Low CinnamoyI-CoA reductase, putative, expressed
LOC_Os08g17520 低Low Flavanol sulfotransferase-like, putative, expressed
LOC_Os08g17655 低Low Expressed protein
LOC_Os08g17110 无No Expressed protein
LOC_Os08g17120 无No Transposon protein, putative, CACTA En/Spm sub-dass
LOC_Os08g17210 无No Transposon protein, putative, CACTA En/Spm sub-dass
LOC_Os08g17220 无No Uncharacterized PE-PGRS family protein PE PGRS54 precursor, putative, expressed
LOC_Os08g17270 无No Expressed protein
LOC_Os08g17330 无No Expressed protein
LOC_Os08g17340 无No Hypothetical protein
LOC_Os08g17350 无No Expressed protein
LOC_Os08g17360 无No Hypothetical protein
LOC_Os08g17440 无No Expressed protein
LOC_Os08g17560 无No Expressed protein
LOC_Os08g17580 无No Hypothetical protein
LOC_Os08g17620 无No Expressed protein
LOC_Os08g17630 无No Expressed protein
LOC_Os08g17640 无No Z0S8-02-C2H2 zinc finger protein, expressed
LOC_Os08g17690 无No Retrotransposon protein, putative, unclassified

图4

不同发育阶段候选基因的表达模式 (a) 34个基因对种子芽期的反应; (b) 基于来自GENEVESTIGATOR的mRNA-seq数据和Affymetrix微阵列数据集, “OS-nnnnn”是指实验ID; (c) 详细查看选择扰动(绝对表达水平)。"

表2

芽期耐盐相关的14个显著关联QTL及候选基因分析"

QTL SNP数量
Number of SNPs		 范围
Range		 峰值SNP
Peak SNP		 P值
P-value		 候选基因
Candidate gene		 基因描述
Gene description
qGR1.1 2 23,752,956-23,786,838 23,752,956 2.33E-08 SIDP361[23] DUF1644蛋白
DUF1644 protein gene
qGR1.2 6 31,534,965-31,593,365 31,534,965 1.09E-07 OsERF922[24] ERF转录因子
ERF transcription factor
qGR3.1 3 1,874,033-1,874,036 1,874,033 2.22E-07 ONAC022[25] 胁迫响应型NAC转录因子基因
Overexpression of a stress-responsive NAC
qGR3.2 16 16,671,741-17,432,153 16,671,952 2.81E-10 OsHAP2E[26] 血红素激活蛋白; 核因子Y; CCAAT结合因子
Heme activator protein gene; nuclear factor Y; CCAAT binding factor
qGR3.3 2 20,621,667-20,925,341 20,621,667 2.00E-07 OsHAK16[27,28] 钾转运蛋白
Potassium transporter
qGR3.4 3 26,339,090-26,393,672 26,339,090 2.89E-09 OsBIHD1[29] 同源异型基因
Rice homeodomain gene
qGR3.5 5 31,937,083-32,488,239 31,982,396 1.32E-10 OsGASR1[30] 赤霉素刺激转录基因
GA-stimulated transcript-related gene; Oryza sativa gibberellic acid stimulated rice 1
qGR4.1 5 17,564,210-19,871,791 17,626,425 8.53E-08 OsHAK1[31] 钾离子转运蛋白
Potassium transporter
qGR4.2 5 24,215,216-24,282,470 24,282,470 2.26E-08 OsBADH1[32] 甜菜碱醛脱氢酶
Betaine aldehyde dehydrogenase
qGR4.3 43 27,473,283-27,958,451 27,907,711 9.60E-13 OsGPX1[33] 线粒体谷胱甘肽过氧化物酶
Mitochondrial glutathione peroxidase
qGR5 9 19,208,151-19,330,003 19,329,999 7.44E-08 SERF1[34] 盐应答的ERF转录因子
Salt-responsive ERF 1
qGR6 12 1,607,061-1,822,395 1,661,829 1.07E-09 OsSIK1[35] 类受体激酶基因; 胁迫诱导的蛋白激酶基因
Receptor-like kinase; stress-induced protein kinase gene 1
qGR8 4 10,564,948-10,733,175 10,564,948 4.24E-08 New gene 未知
Unknown
qGR12 3 21,374,803-22,039,414 21,374,803 7.63E-08 WSL12[36] 白色条纹叶基因
White stripe leaf 12
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