中国农业科学 ›› 2019, Vol. 52 ›› Issue (3): 385-398.doi: 10.3864/j.issn.0578-1752.2019.03.001

• 作物遗传育种·种质资源·分子遗传学 •    下一篇

水稻耐淹成苗率相关性状全基因组的关联分析

孙凯,李冬秀,杨靖,董骥驰,严贤诚,罗立新,刘永柱,肖武名,王慧,陈志强,郭涛   

  1. 华南农业大学国家植物航天育种工程技术研究中心,广州 510642
  • 收稿日期:2018-09-18 接受日期:2018-11-12 出版日期:2019-02-01 发布日期:2019-02-14
  • 通讯作者: 郭涛,E-mail:guo.tao@vip.163.com。陈志强,E-mail:zqchen@scau.edu.cn
  • 作者简介:孙凯,E-mail:m15018435726_2@163.com
  • 基金资助:
    国家重点研发计划(2017YFD0100104,2016YFD0102102);广东省科技计划(2015B02031011);国家现代农业产业技术体系建设专项(CARS-01-12)

Genome-Wide Association Analysis for Rice Submergence Seedling Rate

SUN Kai,LI DongXiu,YANG Jing,DONG JiChi,YAN XianCheng,LUO LiXin,LIU YongZhu,XIAO WuMing,WANG Hui,CHEN ZhiQiang,GUO Tao   

  1. National Plant Space Breeding Engineering Technology Research Center, South China Agricultural University, Guangzhou 510642
  • Received:2018-09-18 Accepted:2018-11-12 Online:2019-02-01 Published:2019-02-14

摘要:

背景 耐淹成苗率低是限制直播稻产量的重要因素,挖掘高种子活力、低氧萌发能力强的水稻材料是提高耐淹成苗率的关键,但控制耐淹成苗率的遗传位点的挖掘仍然比较有限。目的 利用来源广泛的自然种质,分析影响耐淹成苗率的关键表型性状,挖掘相关的遗传位点和候选基因,为直播稻耐淹成苗机理研究提供一定的理论和材料基础。方法 以200份来源广泛的水稻种质为材料,在有氧环境下进行发芽试验,测量种子发芽率、发芽指数和活力指数;在低氧条件下测量芽鞘长和芽鞘直径;进行耐淹成苗试验,水深10 cm,20 d后测量耐淹成苗率。分析各性状间的相关性,挖掘影响耐淹成苗率的关键性状;利用简化基因组测序对以上6个表型进行全基因组关联分析,鉴定与性状显著关联的SNP位点,并在关联区间内筛选候选基因;对02428和YZX 2份材料进行有氧、无氧以及氧气含量转换条件下的转录组检测,结合全基因组关联分析结果,分析候选基因的表达模式差异。结果 种子活力、芽鞘表型和耐淹成苗率在200份材料间存在广泛的遗传变异,其中,芽鞘长和活力指数的变异系数最大;相关分析结果表明,芽鞘长、活力指数与耐淹成苗率呈极显著正相关;通过全基因组关联分析,共鉴定出8个与活力指数显著关联的位点,15个与芽鞘长显著关联的位点;结合基因组注释,在关联区间筛选出6个与活力指数相关的候选基因,7个与芽鞘长度相关的候选基因;进一步比较13个基因在有氧、无氧及氧气转换条件下的表达模式以及表达量的变化,发现Os02g0657000Os03g0592500Os08g0380100表达量变化显著,表现出对氧气处理的敏感性。结论 种子活力、芽鞘长与耐淹成苗率密切相关,可作为筛选高耐淹成苗水稻材料的重要性状。全基因组关联分析、转录组分析与基因表达模式比较的联合应用可提高候选基因的筛选效率。水稻耐淹成苗过程可能受到与逆境胁迫、光合作用相关基因的调控。

关键词: 水稻, 种子活力, 耐低氧萌发, 全基因组关联分析, 转录组分析

Abstract:

【Background】 The low seedling rate of direct seeding rice is an important factor limiting its yield. Mining rice materials with high seed viability and low oxygen germination ability is the key to improving the seedling rate and solving the problem of seedlings in direct seeding rice. 【Objective】 The key phenotypic traits affecting the rate of emergence and tolerance of seedlings were analyzed, and the relevant genetic loci and candidate genes were mined to provide a theoretical and material basis for the study of direct seeding rice cultivars and the mechanism of resistance to flooding. 【Method】 Using 200 rice germplasms from a wide range of sources. The germination test was carried out in an aerobic environment, and the seed viability phenotype was measured including germination rate, germination index and viability index; The coleoptile length and coleoptile diameter were measured under hypoxic conditions. The flood-tolerant seedling experiment was carried out, the water depth was 10cm, and the flood-tolerant seedling rate was measured after 20d. The correlation between various traits was analyzed, and the key traits affecting the rate of tolerance to flooding were explored. Genome-wide association analysis was performed on the above six phenotypes by simplified genome sequencing, and SNP sites significantly associated with traits were identified and within the correlation interval. Screening candidate genes related to the research purpose; transcriptome detection under the conditions of aerobic, anaerobic and oxygen content conversion of 02428 and YZX two materials, combined with genome-wide association analysis results, analysis of differences in expression patterns of candidate genes. 【Result】 Seed viability, coleoptile phenotype and seedling rate showed extensive genetic variation among 200 materials. Among them, the variation of coleoptile length and viability index was the most abundant, and the coefficient of variation was the largest. At the same time, the results of correlation analysis showed that there was a significant positive correlation between the coleoptile length, viability index and the seedling rate. Through genome-wide association analysis, 8 sites significantly associated with the viability index and 15 sites significantly associated with the coleoptile length were identified. Based on the correlation of seed growth and development and stress resistance, six candidate genes related to viability index and seven candidate genes related to the coleoptile length were screened in the relevant interval. Further comparison of 13 genes in aerobic and anaerobic the expression patterns and expression changes under oxygen conversion conditions showed that the three genes Os02g0657000, Os03g0592500 and Os08g0380100 showed different expression patterns when the oxygen content changed, and the expression amount changed significantly, showing sensitivity to oxygen treatment. 【Conclusion】 Seed viability and coleoptile length were closely related to the rate of flooding and seedling emergence, which could be used as an important trait for screening flood-tolerant rice materials. Combining genome-wide association analysis, transcriptome analysis and gene expression pattern can improve the screening efficiency of candidate genes for hypoxia tolerance germination of rice seeds; flooding tolerance of rice seedlings may be regulated by genes related to stress and photosynthesis..

Key words: rice, seed vitality, hypoxia-resistant germination, genome-wide association analysis, transcriptome analysis