中国农业科学 ›› 2017, Vol. 50 ›› Issue (14): 2635-2646.doi: 10.3864/j.issn.0578-1752.2017.14.001

• 作物遗传育种·种质资源·分子遗传学 •    下一篇

不同氮处理下水稻剑叶叶宽的全基因组关联分析

高易宏,燕金香,涂政军,冷语佳,陈龙,黄李超,代丽萍,张光恒,朱丽,胡江,任德勇,郭龙彪,钱前,王丹英,曾大力   

  1. 中国水稻研究所/水稻生物学国家重点实验室,杭州 310006
  • 收稿日期:2017-01-12 出版日期:2017-07-16 发布日期:2017-07-16
  • 通讯作者: 曾大力,E-mail:dalizeng@126.com。王丹英,E-mail:wangdanying@caas.cn
  • 作者简介:高易宏,E-mail:gaoyihong93@163.com;燕金香,E-mail:2911669220@qq.com;高易宏和燕金香为同等贡献作者。
  • 基金资助:
    国家自然科学基金(91435105、31661143006、31371581)、中国农业科学院科技创新工程项目

Genome-Wide Association Analysis on Flag Leaf Width Under Different Nitrogen Levels in Rice

GAO YiHong, YAN JinXiang, TU ZhengJun, LENG YuJia, CHEN Long, HUANG LiChao, DAI LiPing, ZHANG GuangHeng, ZHU Li, HU Jiang, REN DeYong, GUO LongBiao, QIAN Qian, WANG DanYing, ZENG DaLi   

  1. China National Rice Research Institute/State Key Laboratory of Rice Biology, HangZhou 310006
  • Received:2017-01-12 Online:2017-07-16 Published:2017-07-16

摘要: 【目的】探索水稻剑叶叶宽调控及其对氮肥响应的遗传机理,为氮高效水稻新品种的培育提供新的种质资源和基因标记。【方法】以134份水稻地方种质资源为关联分析材料,通过基因组重测序发掘获得了3 356 591个分布于全基因组的高密度SNP位点(single nucleotide polymorphism,SNP)。在大田栽培条件下,以施氮量为主区,品种为裂区的设计,设计低氮(不施氮肥,N0)、正常氮(纯氮96 kg·hm-2,N1)和高氮(纯氮192 kg·hm-2,N2)3种氮肥处理。于水稻成熟期分别调查水稻剑叶叶宽在低、中、高3种氮肥处理下的表现及响应,结合EMMAX软件计算群体亲缘关系矩阵和EIGENSOFT软件分析群体结构,采用纳入亲缘关系矩阵及群体结构的混合线性模型开展全基因组关联分析。【结果】水稻剑叶叶宽在N0、N1、N2 3种氮肥处理下均呈正态分布,并表现丰富的变异。剑叶叶宽受品种差异及氮水平的影响,且与施氮水平呈显著正相关。在N0、N1、N2氮处理下共检测到14个与剑叶叶宽显著相关的SNP位点。其中,低氮处理下检测到的SNP位点的最小等位基因频率均大于0.46,表明此类SNP在关联群体中广泛存在;中氮和高氮水平下检测到的SNP位点的最小等位基因频率均较小,是一类较为稀有的SNP位点。位于第12染色体上的一个SNP(chr12:15 066 507)位点在正常氮及高氮处理下均被检测到,在高氮处理下还检测到的另一显著性位点,其候选区间内包含一候选基因LOC_Os12g25660,该基因与业已报道的叶宽性状相关基因OsBR6ox同属于细胞色素P450家族。根据不同氮处理下剑叶叶宽的响应,鉴定出20与低氮响应有关的SNP位点,8个位点与高氮响应有关。其中与高氮响应的显著性位点中,位于第1染色体显著性峰候选区间包含业已克隆的与氮素利用相关的基因OsATG7。【结论】通过全基因组关联分析共检测到42个与剑叶叶宽及其在不同氮处理下叶宽响应相关的显著性关联位点。

关键词: 水稻, 全基因组关联分析, 叶宽, 氮肥

Abstract: 【Objective】 The objective of this experiment is to study the genetic mechanism of flag leaf width and its response to different nitrogen fertilizer rates, and provide advantageous germplasm resources and genetic markers for the improvement of nitrogen use efficiency in rice breeding. 【Method】 Based on re-sequencing of 134 rice landraces, a total of 3 356 591 SNPs distributed on the whole genome were identified. Three different nitrogen levels were assigned as the main plot in the split-plot design, and rice landraces are assigned at random to the subplots within each whole plot. Three nitrogen levels including low nitrogen (no nitrogen fertilizer), normal nitrogen (96 kg·hm-2) and high nitrogen (192 kg·hm-2) were applied under normal field cultivation, respectively. The EMMAX method was used to analyze the genetic relationship and EIGENSOFT was employed to detect the population structure. The mixed linear model was used to detect the potential genome-wide association between single nucleotide polymorphisms (SNPs) and the flag leaf width performance or response under low, medium and high nitrogen treatments. 【Result】The results showed that the flag leaf width displayed normal distribution in N0, N1 and N2 treatments, respectively. The variation of flag leaf width caused by the varietal differences and the different nitrogen levels, and the significant positive correlation between nitrogen fertilizer and flag leaf width were detected at all nitrogen levels. A total of 14 SNPs on five chromosomes presented significant association with the flag leaf width under three different nitrogen levels. The estimated minimum allele frequency was 0.46 at low nitrogen level, which indicate those loci are widely distributed in the association population. While the estimated minimum allele frequencies were lower at normal nitrogen and high nitrogen levels. One SNP located on chromosome 12 was found both at normal nitrogen and high nitrogen levels. Besides, another SNP on chromosome 12 was also detected at high nitrogen. Its flank contained a candidate gene LOC_Os12g25660, which belongs to the super-family of cytochrome P450. It is a homologous gene of OsBR6ox which was confirmed in regulating the flag leaf width in rice. Based on the variation of leaf width at different nitrogen levels, twenty SNPs and eight SNPs were identified to low nitrogen and high nitrogen response, respectively. Among them, the nitrogen utilization related gene, OsATG7, was associated with high nitrogen response on chromosome 1. 【Conclusion】 In this study, a total of 42 SNPs associated with flag leaf width and response to different nitrogen were identified based on the genome-wide association analysis.

Key words: Oryza sativa, genome-wide association study, leaf width, nitrogen fertilizer