基于全基因組關(guān)聯(lián)分析的水稻分蘗角度和劍葉夾角的遺傳基礎(chǔ)解析
發(fā)布時(shí)間：2019-06-09 22:49
【摘要】：水稻是主要的糧食作物,隨著人口的不斷增加,需要不斷提高產(chǎn)量來(lái)滿(mǎn)足日益增長(zhǎng)的糧食需求。株型是決定水稻群體產(chǎn)量的重要性狀,提高水稻的種植密度是增加水稻產(chǎn)量的有效方法。水稻的分蘗角度和葉夾角作為塑造理想株型的兩個(gè)重要農(nóng)藝性狀,在栽培稻群體中存在豐富的自然變異,了解其分子機(jī)制和挖掘優(yōu)良的等位基因有助于培育優(yōu)良品種。利用全基因組關(guān)聯(lián)分析以種質(zhì)群體為研究對(duì)象,可以快速有效地挖掘與表型變異緊密相關(guān)的位點(diǎn),有助于全面了解復(fù)雜農(nóng)藝性狀的遺傳機(jī)制。華中農(nóng)業(yè)大學(xué)作物遺傳改良國(guó)家重點(diǎn)實(shí)驗(yàn)室水稻團(tuán)隊(duì)對(duì)529份亞洲栽培稻包含295份秈稻和156份粳稻品種在內(nèi)的種質(zhì)群體進(jìn)行全基因組測(cè)序,建立了關(guān)聯(lián)分析平臺(tái)。本研究在海南和武漢分別調(diào)查了該種質(zhì)群體開(kāi)花時(shí)期的分蘗角度和劍葉夾角,利用線性回歸和線性混合模型方法在總?cè)后w和秈粳亞群中進(jìn)行全基因組關(guān)聯(lián)分析,主要研究結(jié)果如下:1.分蘗角度和劍葉夾角雖然同為影響水稻株型和產(chǎn)量的重要農(nóng)藝性狀,而基于529份亞洲栽培稻的表型數(shù)據(jù)表明兩者間并不存在顯著相關(guān)性。水稻分蘗角度盡管受到環(huán)境影響,但主要還是由遺傳因素決定,基因與環(huán)境互作效應(yīng)在粳稻亞群中相對(duì)較大。秈稻亞群的分蘗角度比粳稻亞群有更大的表型變異,其平均值也較大。水稻劍葉夾角同樣主要由遺傳因素決定,但基因與環(huán)境互作效應(yīng)在秈稻亞群中相對(duì)較大。栽培稻的劍葉夾角相對(duì)分蘗角度具有更大的表型變異,粳稻亞群的劍葉夾角變異及平均值均大于秈稻亞群。2.通過(guò)全基因組關(guān)聯(lián)分析共檢測(cè)到30個(gè)控制栽培稻分蘗角度自然變異的關(guān)聯(lián)位點(diǎn),其中7個(gè)為海南和武漢兩個(gè)環(huán)境均檢測(cè)到的位點(diǎn)。TAC1位于q TA9c區(qū)間,與q TA8a在總?cè)后w和秈稻亞群中均關(guān)聯(lián)到,且不受海南和武漢的環(huán)境影響,而在粳稻亞群中未檢測(cè)到海南和武漢同時(shí)關(guān)聯(lián)到的位點(diǎn);其余的10和13個(gè)位點(diǎn)分別只在海南和武漢關(guān)聯(lián)到。通過(guò)突變體表型與基因型的共分離鑒定,分離到了位于水稻第3染色體上q TA3的候選基因TAC3,該基因編碼保守的假定蛋白,并在水稻的分蘗基部具有較高的表達(dá)量。已報(bào)道的控制水稻葉夾角和株高的D2/CYP90D2位于q TA1b區(qū)間,通過(guò)對(duì)該突變體的分蘗角度調(diào)查分析表明D2為該位點(diǎn)的候選基因。3.TAC1、TAC3和D2的核酸多態(tài)性分析表明3個(gè)基因在粳稻的馴化和遺傳改良過(guò)程中均受到了選擇,它們?cè)诙鄶?shù)粳稻品種中具有固定的基因型,而在秈稻亞群中存在不同的基因型,且不同基因型間分蘗角度存在顯著性差異。4.通過(guò)全基因組關(guān)聯(lián)分析共檢測(cè)到62個(gè)與劍葉夾角相關(guān)的位點(diǎn),其中8個(gè)關(guān)聯(lián)位點(diǎn)在海南和武漢兩個(gè)環(huán)境均檢測(cè)到,4個(gè)位點(diǎn)與已知葉夾角相關(guān)的基因共定位。q FLA2f、q FLA3b和q FLA10c區(qū)間內(nèi)均含有b HLH轉(zhuǎn)錄因子第16亞家族的HLHs,隨后通過(guò)超量表達(dá)水稻該亞家族功能未知的基因證明Os153、Os173和Os174與前人報(bào)道的其它同源基因一樣均具有調(diào)控葉夾角的功能。在水稻中超量表達(dá)同屬于該亞家族的控制野生番茄柱頭外露的Style2.1,轉(zhuǎn)基因植株同樣表現(xiàn)出葉片下垂的表型。結(jié)合前人研究,我們認(rèn)為b HLH第16亞家族對(duì)于調(diào)控水稻葉夾角具有保守的功能。5.對(duì)本研究中檢測(cè)到的劍葉夾角相關(guān)基因分別在秈粳2個(gè)亞群中進(jìn)行單倍型分析并比較單倍型間的劍葉夾角,發(fā)現(xiàn)根據(jù)粳稻亞群構(gòu)建的每個(gè)基因的單倍型間的劍葉夾角均存在顯著性的差異,而根據(jù)秈稻亞群構(gòu)建的每個(gè)基因(Os BRI1除外)的單倍型間的劍葉夾角都不存在顯著性差異。6.在分蘗角和劍葉夾角所有全基因組關(guān)聯(lián)分析檢測(cè)到的位點(diǎn)中,只有劍葉夾角QTL q FLA8f置信區(qū)間與分蘗角度QTL q TA8a和q TA8b的置信區(qū)間部分重疊。因此,分蘗角度和葉夾角的遺傳基礎(chǔ)差異很大,沒(méi)有緊密關(guān)聯(lián);分蘗角度和劍葉夾角在秈粳亞群間分別有不同的遺傳調(diào)控機(jī)制。TAC1、TAC3、D2和其它新檢測(cè)的基因是控制栽培稻分蘗角度自然變異的主要基因。b HLH第16亞家族成員在調(diào)控葉夾角方面具有保守的功能。本研究中鑒定的分蘗角度和葉夾角優(yōu)良等位基因是培育水稻理想株型品種的優(yōu)異基因資源。
[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.
【學(xué)位授予單位】：華中農(nóng)業(yè)大學(xué)
【學(xué)位級(jí)別】：博士
【學(xué)位授予年份】：2017
【分類(lèi)號(hào)】：S511
本文編號(hào)：2495954
[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.
【學(xué)位授予單位】：華中農(nóng)業(yè)大學(xué)
【學(xué)位級(jí)別】：博士
【學(xué)位授予年份】：2017
【分類(lèi)號(hào)】：S511
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