高粱驯化相关性状遗传结构的解析

发布时间：2017-12-27 03:27

本文关键词：高粱驯化相关性状遗传结构的解析　出处：《中国农业大学》2016年博士论文　论文类型：学位论文

【摘要】：作物的驯化始于12000年前的新石器革命,在此以后陆续有多种作物在不同地区由不同的古人类完成了驯化。作为世界五大作物之一,高粱(Sorghum bicolor (L) Moench)起源于非洲东北部的苏丹、埃塞俄比亚及其周边地区。在其驯化的过程中,高粱发生了一系列形态学和生理学巨大变化,这些变化包括落粒性的丧失、颖壳颜色和种皮颜色变化、开花期和成熟期的同步、籽粒增大以及株型更加紧凑等等。在本研究中,我们利用野生高粱SV (Sorghum virgatum)×栽培高粱Tx623组配的F2群体和F2：3群体,对高粱驯化相关性状进行了QTL定位,分别对位于10号染色体上的抽穗期主效位点以及位于9号和1号染色体上两个株高主效位点进行了精细定位,并对候选基因在高粱驯化中的作用进行了解析。本文主要研究结果如下：1.利用R/qtl软件包及272个F2单株,构建了一套包含均匀分布于高粱10条染色体上的216个SSR标记的分子遗传图谱。图谱总长1610.5 cM,相邻两个标记的平均遗传距离是7.8 cM。2.对F2群体(北京)的18个驯化相关性状及F2：3群体(海南)的6个性状进行表型调查,利用R/qtl软件包,对这些性状进行大规模的QTL定位,共检测到66个相关QTLs。这些位点分布于高粱的10条染色体上,但其分布并不均匀,在某些染色体区段上“富集”。对QTL加性效应分析表明,来自栽培种亲本的正向效应多有利于叶长、叶宽及粒重、粒宽增加等,而来自野生种亲本的正向效应多有利于株高、分蘖的增加等。3.在前期F2群体及F2；3群体初定位的基础上,我们对位于10号染色体上控制抽穗期的主效QTL-HD1进行精细定位,利用重组个体后代验证的方法将定位区间缩小到37 kb的物理区间内。在此区间内,编码CONSTANS-like蛋白的Sb10g010050对应于HDI基因,野生亲本SV的HDI基因的第一个外显子上存在一个5-bp的缺失,导致了HD1蛋白缺失了锌指结构和CCT结构功能域,从而引起蛋白功能的丧失。DNA多态性分析发现栽培种的多态性明显低于野生种,Tajima'sD检测结果表明栽培种该基因5-bp缺失位点受到轻微平衡选择(Tajima D's test=2.39, P 0.05)。比较基因组分析发现,在高粱HDl位点的对应于玉米的9号染色体、水稻的6号染色体及谷子的4号染色体区段,且在水稻6号染色体及谷子的4号染色体相关片段上都定位到了抽穗期相关QTL。对谷子的HD1基因的大规模测序发现,一个位于剪切位点的变异(GT→AT)较为常见(78/98),造成剪切位点从787bp的“GT”前移到754bp处的“GT"。关联分析在剪切位点处检测到显著关联信号(P=9.50×104)。谷子HD1基因的核酸多样性分析发现栽培谷子的DNA多样性显著降低。这些结果表明HD1基因在高粱、水稻和谷子中受到平行选择。4.根据F2和F2：3初定位结果,在9号染色体上检测到控制株高及其他性状的主效QTL(dwl)。利用连续重组后代验证的方法对其进行精细定位,将定位区间缩小到13.98 kb的物理区间内。对该区间内的两亲本的基因进行测序,发现栽培亲本Tx623的基因Sobic.009G229800第二个外显子上存在A→T的SNP变异,导致翻译提前终止。对不同来源的高粱品种候选基因测序分析发现在来自美国、印度等地的矮化栽培高粱中提前终止变异时很常见的,且这些矮化品种的DW1基因核酸序列间不存在任何变异,多样性低,说明这个A到T的突变发生在近期。然而,不存在功能位点改变的栽培高粱与野生高粱相比,DNA多样性并不存在显著降低,表明dwl基因在驯化过程中可能并未受到选择,功能位点突变可能是现代育种的结果。5.对1号染色体上的株高QTL-ph1进行精细定位,将定位区间缩小到24.5-kb的定位区间内,区间内仅存在一个基因,Sobic.001G106000(kn2),该基因编码一个KNOTTED-like转录因子。亲本DNA测序发现两个能引起编码氨基酸变化的SNP变异,但其可能并非是导致表型变异的相关功能位点。
[Abstract]:The domestication of crops began in the Neolithic Revolution 12000 years ago, after which a variety of crops have been domesticated by different kinds of ancient people in different regions. As one of the five largest crops in the world, sorghum (Sorghum bicolor (L) Moench) originated in Sultan, Ethiopia and its surrounding areas in northeastern Africa. During its domestication, sorghum has undergone a series of dramatic changes in morphology and physiology. These changes include loss of grain, the color of shell and seed coat, the synchronization of flowering and maturity, the increase of grain and the more compact plant type. In this study, we use wild sorghum SV (Sorghum virgatum) * Tx623 group with cultivation sorghum F2 population and F2:3 population, the sorghum domestication related traits were QTL, are located in heading period of major loci on chromosome 10 and chromosome 1 and 9 in two main plant height the fine mapping of loci, and the role of candidate genes in Sorghum domestication were analyzed. The main results of this study are as follows: 1.. Using R/qtl software package and 272 F2 individuals, we constructed a set of molecular genetic map containing 216 SSR markers distributed evenly on 10 chromosomes of sorghum. The total length of the map was 1610.5 cM, and the average genetic distance of two adjacent markers was 7.8 cM. 2. phenotypic investigation of 18 domesticated traits and 6 traits of F2:3 population (Hainan) in F2 group (Beijing). A large scale QTL localization of these traits was carried out by R/qtl software package, and 66 related QTLs were detected. These loci are distributed on 10 chromosomes of sorghum, but their distribution is not uniform and "enriched" on some chromosomal segments. The analysis of additive effect of QTL showed that the positive effects of parents from cultivars were more conducive to leaf length, Ye Kuan and grain weight and grain width. 3., on the basis of early F2 population and F2 and 3 population initial location, we fine positioned the dominant QTL-HD1 on chromosome 10, and reduced the location interval to 37 KB by using the method of recombinant offspring. In this interval, the Sb10g010050 encoding CONSTANS-like protein corresponds to HDI gene. There is a deletion of 5-bp on the first exon of HDI gene of wild parent SV, which results in the loss of zinc finger structure and CCT functional domain, which results in the loss of protein function. DNA polymorphism analysis showed that the polymorphism of cultivated species was significantly lower than that of wild species. Tajima'sD detection showed that the 5-bp deletion site of cultivated species was slightly balanced (Tajima D's test=2.39, P 0.05). Comparative genomic analysis revealed that there was a heading related QTL in maize sorghum HDl locus corresponding to maize chromosome 9, rice chromosome 6 and millet chromosome 4, and on chromosome 4 of rice chromosome 6 and millet. A large-scale sequencing of HD1 gene in Millet showed that a mutation located at the shear site (GT to AT) was more common (78/98), causing the shear site to move from 787bp GT to 754bp at 754bp. A significant correlation signal (P=9.50 x 104) was detected at the shear site by correlation analysis. The analysis of nucleic acid diversity of the HD1 gene of millet showed that the DNA diversity of cultivated millet was significantly reduced. These results showed that the HD1 gene was selected in sorghum, rice and millet. 4. according to the initial results of F2 and F2:3, the main effect QTL (DWL) of control plant height and other traits were detected on chromosome 9. The positioning interval is narrowed to the 13.98 KB physical interval by using the method of continuous recombined verification. According to the sequencing of the two parents in the interval, it was found that there existed SNP variation of A to T on the second exons of the parental gene Tx623 Sobic.009G229800, leading to the early termination of the translation. The sorghum candidate gene sequencing analysis found in different sources from the United States, India and other places of dwarfing cultivation sorghum early termination mutation is common, and these dwarf varieties of DW1 gene sequence, no mutation, low diversity, the A to T mutation in the near future. However, there was no significant decrease in DNA diversity in cultivated sorghum compared with wild sorghum without functional site change, indicating that DWL gene may not be selected during domestication. Functional site mutation may be the result of modern breeding. 5. fine mapping of plant height QTL-ph1 on chromosome 1, narrowing the location interval to the 24.5-kb location interval. There is only one gene, Sobic.001G106000 (kn2), which encodes a KNOTTED-like transcription factor. Parent DNA sequencing found two SNP mutations that could cause the changes in encoded amino acids, but may not be related functional sites that lead to phenotypic variation.
【学位授予单位】：中国农业大学
【学位级别】：博士
【学位授予年份】：2016
【分类号】：S514

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