追寻栽培稻中人工选择的遗迹
文献类型：学位论文
| 作者 | 吕俊 |
| 学位类别 | 博士 |
| 答辩日期 | 2013-11 |
| 授予单位 | 中国科学院研究生院 |
| 授予地点 | 北京 |
| 导师 | 王文 |
| 关键词 | 水稻 改良 ETAS 抗旱 分蘖 |
| 其他题名 | In search of vestige of artificial selection in rice |
| 学位专业 | 遗传学 |
| 中文摘要 | 在过去的几万年中，家养动物及植物的驯化促进了人类文明的兴起。人工选择是家养动植物驯化的内在驱动力。在人工选择的作用下，野生的动植物品种的一些关键的性状被改变，成为了家养的品种。最初的家养品种一般都是在农牧性状上比较次等的地方品种（landraces）。具体到农作物上来讲，它的产量低，品质差。由于人类社会人口的增长以及人们对于食物品质需求的增长，育种者开始对作物进行改良，这是继驯化之后的人工选择的第二个阶段。在改良的过程中，育种者选择出了一些罕见的高产、优质或者抗性佳的品种，成为优异品系并在生产上进行大面积推广种植。对于这些优异品系中包含的改良相关的基因，传统上是通过QTL 作图的方法来进行定位。QTL作图法曾成功地应用于鉴定一系列的改良相关的农艺性状基因，比如控制水稻穗粒数的Gn1a，控制粒长、粒宽的GS5、GW3, 控制直立穗的DEP1等等。但是，QTL作图法由于需要构建分离群体，耗时长。于是近年来，人们越来越多地使用关联分析在不同的水稻品系中鉴定农艺性状基因。然而，对于在优异品系中存在的罕见稀有的优异等位基因，关联分析法因其对低频突变鉴定的功效低而具有局限性。在本论文的研究中，我们提出可以使用改良品系标签位点分析法（ETAS analysis）来辅助鉴定优异品系中的改良基因。本论文中我们通过对陆稻IRAT104中的一个ETAS标签位点的功能分析，证明此位点对抗旱激素脱落酸(ABA)合成以及根系生长具有显著的促进作用，并因此在陆稻品系的改良中受到强烈的人工选择。 人工选择的主要方向之一是选择对于特定生境适应的作物品种。选择适应干旱条件的农作物品种是人类长期以来进行作物改良的活动之一。包括水稻、小麦、玉米等主要粮食作物在内的驯化的禾谷类都有一些适应旱作的品种。在众多的禾本科作物中，水稻对于缺水胁迫是最敏感的。但即便如此，栽培稻在过去的人工选择中，也发展出了适应于旱地缺水的雨养种植环境的类型，这即是水稻的旱地生态型——陆稻。关于陆稻的起源是先于水稻还是晚于水稻，在学术界一直没有定论。关于陆稻适应旱地的遗传学基础也鲜有研究。在本论文中，我们通过测定全世界范围内取样的84个陆稻品种与82个水稻品种的基因组，结合前期本实验室测得的野生稻的基因组数据，第一次在全基因组的水平上阐明了陆稻与水稻的系统发育关系。我们证实陆稻很有可能起源于水稻之后，并且最初可能脱胎于粳型的水稻。我们进一步通过比较水稻与陆稻的基因组，找到了一些水陆稻显著分化的区域以及154个水陆稻分化的基因。在这154个基因中，有许多可以与水陆稻的表型分化相联系,有不少可以与抗旱的表型相联系。此外，其中有一个显著分化的基因是Os09g0410500，基因功能的注释是该基因与玉米中的teosinte branched 1（tb1） 类似。玉米中的tb1是驯化过程中导致分枝减少的重要基因。而根据我们的表型观察，陆稻相对于水稻分蘖显著地下降。所以我们推测在陆稻的改良过程中,9号染色体上的这个显著分化的tb1基因的同源基因很可能是导致陆稻分蘖降低的原因，在我们的研究中我们将此基因命名为Ostb2以区别于三号染色体上的Ostb1。 如上所言，分蘖或者分枝的性状在人工选择的过程中有显著的变化。在禾本科的不少作物中，分枝减少都是一个趋同的选择方向，如玉米、高梁、珍珠黍、小米都经历了这个过程。更少的分枝不仅有利于单个分枝上生长更大的穗子，而且方便了密植，从而提高了单位面积的作物产量。在玉米、高梁、珍珠黍、小米的驯化过程中，tb1基因都促进了分枝减少。我们在陆稻与水稻的基因组比较中，也观察到了tb1的同源基因Ostb2有显著的分化。基于我们对陆稻分蘖相对水稻变少的认识，Ostb2基因成为接下来对陆稻分枝减少的重点研究对象。本论文中，我们种植更多的水稻、陆稻品种，并进行表型定量与Ostb2的基因型鉴定工作。关联分析的结果显示Ostb2上的两个突变，indel1与SNP3都与分蘖的表型显著相关。我们进一步在一个重组自交系群体及一个近等基因系F2群体中验证了这两个突变与表型的相关性。定量PCR实验证明SNP3很可能影响了Ostb2两种剪切形式的mRNA水平，进而影响了基因功能。转基因实验正在进行，以进一步验证Ostb2及其不同形式的等位基因的功能。 |
| 英文摘要 | During the past several tens of thousands of years, human civilizations began and thrived with the domestication of plants and animals. Artificial selection is the internal driver that triggered species domestication. Under human selection, wild species were finally changed into domesticated species. The first domesticated plants or animals were called landraces, which have relatively poor agronomic characteristics, for example low yield and poor eating quality. As the expansion of human population and human needs, breeders began to improve landraces, which finally gave rise to many elite varieties with elite agronomic performances. The improvement process constitutes the second stage of artificial selection. These elite varieties probably contain some elite alleles that account for the elite traits. Traditionally, people use QTL mapping to identify those elite varieties. This approach has been proved to be useful and succeeded in identifying a series of important agronomic genes, such as Gn1a controlling seed number, GS5 and GW3 influencing seed size, and DEP1 conferring the erect panicle trait, etc. However, QTL mapping is labor and time consuming, taking several years to construct the segregating population. In the recent years, more and more people take advantage of association analysis to identify agronomic genes, but this approach has little power in identifying rare elite alleles. In this dissertation, we proposed a new approach for guiding mining rare elite alleles in elite varieties, which we named ETAS analysis. Using this approach, we identified an important ETAS in the famous upland rice variety, IRAT104. Functional analysis shows that this ETAS allele increases the ABA level and enhances the root development in upland rice. This adaptive phenotype might probably be the reason why it was selected for upland agriculture. One of the main purposes of artificial selection is to enhance crops’ adaption to specific cultural environments. So far, breeders have been able to breed many upland rice varieties that adapt to dry land cultivation. However, it remains an open question that whether upland or irrigated rice emerge first in the evolution. Moreover, the genetic mechanisms underlying dry land adaption of upland rice have been hardly investigated. In second part of this study, we sequenced the genomes of 84 upland rice accessions and 82 irrigated rice accessions sampled around the world. By incorporating the genomic data of wild rice sequenced previously by our lab, we revealed the whole genome phylogenetic relationship between upland, irrigated and wild rice accessions. Our results show that upland rice probably came from improvement using irrigated japonica as basic materials. Furthermore, we did population genetics analysis by comparing the upland and irrigated rice genomes thereby to identify some ecotype differentiated regions (EDRs). Within these EDRs, we identified 154 ecotype differentiated genes (EDGs), many of which could be linked to the phenotypic differentiation between upland and irrigated rice. Among these EDGs, we were very interested in one gene, Os09g0410500, annotated as “similar to teosinte branched one (tb1)”. In our study, we named Os09g0410500 as Ostb2 so as to differentiate it from another homolog, Ostb1, on rice chromosome03. Tiller branching is an important trait that has been shaped radically during artificial selection of gramineous crops. The reduction of branches seems to be the convergent direction of artificial selection in many crops. For example, the tillering ability of maize, sorghum, pearl millet and foxtail millet all decrease after domestication. Fewer tillers could enhance the yield of single panicle and simultaneously permit close planting, therefore increase production per acre. During the domestication of maize, sorghum, pearl millet and foxtail millet, tb1 locus all contributes to their tiller decrease. In our study, we focus the tb1 homolog in rice, Ostb2, and study it |
| 语种 | 中文 |
| 公开日期 | 2014-06-06 |
| 源URL | [http://159.226.149.42:8088/handle/152453/7887]  |
| 专题 | 昆明动物研究所_基因起源组 |
| 推荐引用方式 GB/T 7714 | 吕俊. 追寻栽培稻中人工选择的遗迹[D]. 北京. 中国科学院研究生院. 2013. |
入库方式： OAI收割
来源：昆明动物研究所
浏览0
下载0
收藏0
其他版本
除非特别说明，本系统中所有内容都受版权保护，并保留所有权利。