基于全基因组关联分析的水稻分蘖角度和剑叶夹角的遗传基础解析

发布时间：2019-06-09 22:49

【摘要】：水稻是主要的粮食作物,随着人口的不断增加,需要不断提高产量来满足日益增长的粮食需求。株型是决定水稻群体产量的重要性状,提高水稻的种植密度是增加水稻产量的有效方法。水稻的分蘖角度和叶夹角作为塑造理想株型的两个重要农艺性状,在栽培稻群体中存在丰富的自然变异,了解其分子机制和挖掘优良的等位基因有助于培育优良品种。利用全基因组关联分析以种质群体为研究对象,可以快速有效地挖掘与表型变异紧密相关的位点,有助于全面了解复杂农艺性状的遗传机制。华中农业大学作物遗传改良国家重点实验室水稻团队对529份亚洲栽培稻包含295份籼稻和156份粳稻品种在内的种质群体进行全基因组测序,建立了关联分析平台。本研究在海南和武汉分别调查了该种质群体开花时期的分蘖角度和剑叶夹角,利用线性回归和线性混合模型方法在总群体和籼粳亚群中进行全基因组关联分析,主要研究结果如下:1.分蘖角度和剑叶夹角虽然同为影响水稻株型和产量的重要农艺性状,而基于529份亚洲栽培稻的表型数据表明两者间并不存在显著相关性。水稻分蘖角度尽管受到环境影响,但主要还是由遗传因素决定,基因与环境互作效应在粳稻亚群中相对较大。籼稻亚群的分蘖角度比粳稻亚群有更大的表型变异,其平均值也较大。水稻剑叶夹角同样主要由遗传因素决定,但基因与环境互作效应在籼稻亚群中相对较大。栽培稻的剑叶夹角相对分蘖角度具有更大的表型变异,粳稻亚群的剑叶夹角变异及平均值均大于籼稻亚群。2.通过全基因组关联分析共检测到30个控制栽培稻分蘖角度自然变异的关联位点,其中7个为海南和武汉两个环境均检测到的位点。TAC1位于q TA9c区间,与q TA8a在总群体和籼稻亚群中均关联到,且不受海南和武汉的环境影响,而在粳稻亚群中未检测到海南和武汉同时关联到的位点;其余的10和13个位点分别只在海南和武汉关联到。通过突变体表型与基因型的共分离鉴定,分离到了位于水稻第3染色体上q TA3的候选基因TAC3,该基因编码保守的假定蛋白,并在水稻的分蘖基部具有较高的表达量。已报道的控制水稻叶夹角和株高的D2/CYP90D2位于q TA1b区间,通过对该突变体的分蘖角度调查分析表明D2为该位点的候选基因。3.TAC1、TAC3和D2的核酸多态性分析表明3个基因在粳稻的驯化和遗传改良过程中均受到了选择,它们在多数粳稻品种中具有固定的基因型,而在籼稻亚群中存在不同的基因型,且不同基因型间分蘖角度存在显著性差异。4.通过全基因组关联分析共检测到62个与剑叶夹角相关的位点,其中8个关联位点在海南和武汉两个环境均检测到,4个位点与已知叶夹角相关的基因共定位。q FLA2f、q FLA3b和q FLA10c区间内均含有b HLH转录因子第16亚家族的HLHs,随后通过超量表达水稻该亚家族功能未知的基因证明Os153、Os173和Os174与前人报道的其它同源基因一样均具有调控叶夹角的功能。在水稻中超量表达同属于该亚家族的控制野生番茄柱头外露的Style2.1,转基因植株同样表现出叶片下垂的表型。结合前人研究,我们认为b HLH第16亚家族对于调控水稻叶夹角具有保守的功能。5.对本研究中检测到的剑叶夹角相关基因分别在籼粳2个亚群中进行单倍型分析并比较单倍型间的剑叶夹角,发现根据粳稻亚群构建的每个基因的单倍型间的剑叶夹角均存在显著性的差异,而根据籼稻亚群构建的每个基因(Os BRI1除外)的单倍型间的剑叶夹角都不存在显著性差异。6.在分蘖角和剑叶夹角所有全基因组关联分析检测到的位点中,只有剑叶夹角QTL q FLA8f置信区间与分蘖角度QTL q TA8a和q TA8b的置信区间部分重叠。因此,分蘖角度和叶夹角的遗传基础差异很大,没有紧密关联;分蘖角度和剑叶夹角在籼粳亚群间分别有不同的遗传调控机制。TAC1、TAC3、D2和其它新检测的基因是控制栽培稻分蘖角度自然变异的主要基因。b HLH第16亚家族成员在调控叶夹角方面具有保守的功能。本研究中鉴定的分蘖角度和叶夹角优良等位基因是培育水稻理想株型品种的优异基因资源。
[Abstract]:Rice is the main food crop, and with the increasing population, it is necessary to increase the output to meet the growing food demand. The plant type is an important trait for determining the yield of rice population, and the increase of the planting density of rice is an effective method to increase the yield of rice. The divergence angle and leaf angle of rice are two important agronomic characters for shaping the ideal plant type, and there are abundant natural variation in the cultivated rice population, so that the molecular mechanism and the excellent allele of the invention can be used for cultivating the fine variety. Using the full-genome association analysis to study the genetic mechanism of the complex agronomic characters, the site which is closely related to the phenotypic variation can be quickly and effectively excavated by using the germplasm group as the research object. The rice team of the National Key Laboratory of the Crop Genetic Improvement of the Central China Agricultural University (Huazhong Agricultural University) has set up an association analysis platform for 529 Asian cultivated rice, including 295 rice and 156 japonica rice varieties. In this study, the divergence angle and the angle of the swordleaf in the flowering period of the germplasm were investigated in Hainan and Wuhan, and the whole-genome association analysis was carried out in the total population and the non-round-grained japonica subpopulation by using the linear regression and linear mixed model method. The main results are as follows:1. The divergence angle and the angle of the swordleaf were both the important agronomic characters of the rice plant type and the yield, while the phenotypic data of 529 Asian cultivated rice showed no significant correlation between the two. The effect of the interaction between the gene and the environment is relatively large in the subpopulation of japonica rice, although it is affected by the influence of the environment. The subpopulation of rice and rice has a larger phenotypic variation than that of the subpopulation of japonica rice, and the average value of the subpopulation is also larger. The angle of the rice swordleaf is also mainly determined by the genetic factors, but the interaction effect between the gene and the environment is relatively large in the subpopulation of rice. The included angle of the swordleaf of the cultivated rice has a larger phenotypic variation with respect to the divergence angle, and the variation and the average value of the swordleaf angle of the subpopulation of the japonica rice are larger than the subpopulation of the rice. By means of full-genome association analysis,30 associated sites for controlling the natural variation of the divergence angle of the cultivated rice were detected,7 of which were the sites detected in both the two environments of Hainan and Wuhan. The TAC1 is located in the q-TA9c interval, and is associated with the q-TA8a in the total population and the rice subpopulation, and is not affected by Hainan and Wuhan, while the sites associated with Hainan and Wuhan are not detected in the subpopulations of japonica rice; the remaining 10 and 13 sites are only associated with Hainan and Wuhan. Through the co-separation and identification of the mutant phenotype and genotype, the candidate gene TAC3, which is located on the third chromosome of the rice, is isolated, and the gene encodes a conservative putative protein and has a higher expression level at the subbase of the rice. The included angle of the control rice leaves and the high D2/ CYP90D2 of the plant are located in the q-TA1b interval, and the analysis of the diversity angle of the mutant shows that D2 is the candidate gene of the site. The nucleic acid polymorphism analysis of TAC3 and D2 indicated that 3 genes were selected in the process of domestication and genetic improvement of japonica rice, which had a fixed genotype in most japonica rice varieties, and there were different genotypes in the subpopulation of rice. There was a significant difference in the different genotypes between different genotypes. A total of 62 sites related to the angle of the swordleaf were detected by the full-genome association analysis, of which 8 associated sites were detected in both the two environments of Hainan and Wuhan, and the four sites were co-located with the genes associated with the included angle of the known leaves. The HLHs of the 16 subfamily of the b-HLH transcription factor are contained in the q-F2f, q-F2b and q-F10c intervals, and then the Os153, Os173 and Os174 have the function of regulating the included angle of the leaves as in the other homologous genes reported by the predecessors by over-expressing the gene which is not known by the subfamily function of the rice. The over-expression in rice was the same as that of Style2.1, which controls the stigma of wild tomato belonging to the subfamily, and the transgenic plants also showed the phenotype of the leaf drooping. In combination with the previous studies, we think that the 16th sub-family of the b HLH has a conservative function for regulating the included angle of the leaves of rice. the angle of the swordleaf included in the two subpopulations of each gene detected in the study is analyzed and compared with the angle of the swordleaf between the haplotypes, and the difference of the swordleaf included angle between the haplotype of each gene constructed according to the subpopulation of the japonica rice is found to be significant, However, there was no significant difference in the angle of the swordleaf between the haplotypes of each gene (except for Os BRI1), which was constructed according to the subpopulation of rice. In all the all-genome association analysis of the angle of divergence and the angle of the swordleaf, only the one-leaf angle QTL q FLA8f confidence interval is partially overlapped with the confidence interval of the divergence angle QTL q TA8a and q TA8b. Therefore, there is a large difference in the genetic basis of the angle of divergence and the angle of the leaf, and there is no close association; the angle of the divergence and the angle of the swordleaf have different genetic control mechanisms. TAAC1, TAC3, D2 and other newly detected genes are the main genes that control the natural variation of the split angle of the cultivated rice. B The members of the 16th sub-family of HLH have a conservative function in regulating the angle of leaf. The excellent allele of the angle and leaf angle identified in this study is the excellent gene resource for cultivating the ideal plant type of rice.
【学位授予单位】：华中农业大学
【学位级别】：博士
【学位授予年份】：2017
【分类号】：S511

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