Science：拟南芥基因研究揭示环境对遗传多样性影响巨大

佚名

    生物谷：一项针对多种拟南芥的基因研究表明，环境因素对物种遗传多样性和基因组的影响比之前人们预期的更大。相关论文发表在7月20日的《科学》杂志上。

    除了实验室中科学家的“最爱”，世界各地还分布着多种野生拟南芥。它们的生长速度、叶子颜色以及发枝方式都是不同的。在最新的研究中，由德国马普发育生物学研究所（Max  Planck  Institute  for  Developmental  Biology）Detlef  Weigel领导的国际科学家小组，从美洲、非洲和亚洲以及其他极地和亚热带区域搜集了19种拟南芥，并将它们的基因序列（约1.2亿个碱基对）与实验室用拟南芥基因组（2000年测定完成）进行了对比研究，从而确定了相关的遗传差异。

    所得到的结果令人吃惊：它们遗传差异的广度远远超过了所谓的“改进基因组”（streamlined  genome）。研究人员发现，平均每180个碱基对中就有一个是可变的。同时研究表明，大约4%的实验室用拟南芥基因组要么与野生种类差异很大，要么完全不存在于野生种类的拟南芥中。此外，大约十分之一的野生拟南芥基因是有缺陷的，无法完成正常的功能。

    新的研究结论为科学家提出了许多新的基础性问题。Weigel表示，“或许并不存在所谓的一个物种的基因组。迄今为止，对个体DNA序列的认识并不能使科学家充分理解一个物种的遗传潜能。”此外，拟南芥基因组的可塑性也令人惊讶。尽管拟南芥的基因组中的基因数量与人类和一些作物相当，但它整个基因组的大小不及后两者的十二分之一。同时，拟南芥基因组中几乎没有重复序列和无关联的“垃圾”序列。

    进一步研究表明，拟南芥与外界环境相互作用相关（比如抵御病原体和感染）的基因，其可变性大大超过其他功能基因。Weigel认为，这一遗传特性反映出拟南芥对当地生存环境的适应性，正是这些易变基因使得拟南芥能够经受干燥和潮湿，炎热和寒冷，并调节自身的生长季节。

    新的研究成果加深了人们对环境影响遗传多样性的理解，也将有助于开发能够适应环境变化的植物品种。随着人类认识的不断发展，基因与环境的交互作用已经渐渐成为生命科学的重要研究方向。（科学网  任霄鹏/编译）

原始出处:

Science 20 July 2007:
Vol. 317. no. 5836, pp. 338 - 342
DOI: 10.1126/science.1138632

Common Sequence Polymorphisms Shaping Genetic Diversity in Arabidopsis thaliana

Richard M. Clark,1 Gabriele Schweikert,1,2,3* Christopher Toomajian,4* Stephan Ossowski,1* Georg Zeller,1,2,5* Paul Shinn,6 Norman Warthmann,1 Tina T. Hu,4 Glenn Fu,7 David A. Hinds,7 Huaming Chen,6 Kelly A. Frazer,7 Daniel H. Huson,5 Bernhard Schölkopf,3 Magnus Nordborg,4 Gunnar Rätsch,2 Joseph R. Ecker,6,8 Detlef Weigel1,8 ${dagger}$

The genomes of individuals from the same species vary in sequence as a result of different evolutionary processes. To examine the patterns of, and the forces shaping, sequence variation in Arabidopsis thaliana, we performed high-density array resequencing of 20 diverse strains (accessions). More than 1 million nonredundant single-nucleotide polymorphisms (SNPs) were identified at moderate false discovery rates (FDRs), and $~$ 4% of the genome was identified as being highly dissimilar or deleted relative to the reference genome sequence. Patterns of polymorphism are highly nonrandom among gene families, with genes mediating interaction with the biotic environment having exceptional polymorphism levels. At the chromosomal scale, regional variation in polymorphism was readily apparent. A scan for recent selective sweeps revealed several candidate regions, including a notable example in which almost all variation was removed in a 500-kilobase window. Analyzing the polymorphisms we describe in larger sets of accessions will enable a detailed understanding of forces shaping population-wide sequence variation in A. thaliana.

1 Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
2 Friedrich Miescher Laboratory of the Max Planck Society, 72076 Tübingen, Germany.
3 Department of Empirical Inference, Max Planck Institute for Biological Cybernetics, 72076 Tübingen, Germany.
4 Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.
5 Center for Bioinformatics Tübingen, Tübingen University, 72076 Tübingen, Germany.
6 Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
7 Perlegen Sciences, 2021 Stierlin Court, Mountain View, CA 94043, USA.
8 Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.

* These authors contributed equally to this work.

${dagger}$ To whom correspondence should be addressed. E-mail: weigel@weigelworld.org