Department of Ecology, 251 Bessey Hall, Iowa State University, Ames, IA 50011, USA.
BMC Biol. 2010 Nov 15;8:139. doi: 10.1186/1741-7007-8-139.
Understanding the evolutionary genetics of modern crop phenotypes has a dual relevance to evolutionary biology and crop improvement. Modern upland cotton (Gossypium hirsutum L.) was developed following thousands of years of artificial selection from a wild form, G. hirsutum var. yucatanense, which bears a shorter, sparser, layer of single-celled, ovular trichomes ('fibre'). In order to gain an insight into the nature of the developmental genetic transformations that accompanied domestication and crop improvement, we studied the transcriptomes of cotton fibres from wild and domesticated accessions over a developmental time course.
Fibre cells were harvested between 2 and 25 days post-anthesis and encompassed the primary and secondary wall synthesis stages. Using amplified messenger RNA and a custom microarray platform designed to interrogate expression for 40,430 genes, we determined global patterns of expression during fibre development. The fibre transcriptome of domesticated cotton is far more dynamic than that of wild cotton, with over twice as many genes being differentially expressed during development (12,626 versus 5273). Remarkably, a total of 9465 genes were diagnosed as differentially expressed between wild and domesticated fibres when summed across five key developmental time points. Human selection during the initial domestication and subsequent crop improvement has resulted in a biased upregulation of components of the transcriptional network that are important for agronomically advanced fibre, especially in the early stages of development. About 15% of the differentially expressed genes in wild versus domesticated cotton fibre have no homology to the genes in databases.
We show that artificial selection during crop domestication can radically alter the transcriptional developmental network of even a single-celled structure, affecting nearly a quarter of the genes in the genome. Gene expression during fibre development within accessions and expression alteration arising from evolutionary change appears to be 'modular' - complex genic networks have been simultaneously and similarly transformed, in a coordinated fashion, as a consequence of human-mediated selection. These results highlight the complex alteration of the global gene expression machinery that resulted from human selection for a longer, stronger and finer fibre, as well as other aspects of fibre physiology that were not consciously selected. We illustrate how the data can be mined for genes that were unwittingly targeted by aboriginal and/or modern domesticators during crop improvement and/or which potentially control the improved qualities of domesticated cotton fibre.See Commentary: http://www.biomedcentral.com/1741-7007/8/137.
了解现代作物表型的进化遗传学对于进化生物学和作物改良具有双重意义。现代陆地棉（Gossypium hirsutum L.）是经过几千年的人工选择从野生种 G. hirsutum var. yucatanense 发展而来的，后者具有较短、较稀疏、单细胞、卵形的毛状体（“纤维”）。为了深入了解伴随驯化和作物改良的发育遗传转化的本质，我们在发育时间过程中研究了来自野生和驯化品种的棉花纤维的转录组。
纤维细胞在开花后 2 至 25 天收获，涵盖了初生壁和次生壁合成阶段。使用扩增的信使 RNA 和一个定制的微阵列平台，设计用于检测 40,430 个基因的表达，我们确定了纤维发育过程中的全局表达模式。驯化棉花的纤维转录组比野生棉花的转录组要活跃得多，在发育过程中有两倍以上的基因表现出差异表达（12,626 个对 5273 个）。值得注意的是，当汇总五个关键发育时间点时，野生和驯化纤维之间的差异表达基因总数达到 9465 个。人类在最初的驯化和随后的作物改良过程中的选择导致了与农艺上先进纤维重要的转录网络组件的偏上调，特别是在发育的早期阶段。在野生与驯化棉花纤维的差异表达基因中，约有 15%与数据库中的基因没有同源性。
我们表明，作物驯化过程中的人工选择可以彻底改变甚至单细胞结构的转录发育网络，影响基因组中近四分之一的基因。品种内纤维发育过程中的基因表达和进化引起的表达改变似乎是“模块化”的——复杂的基因网络已经以协调的方式同时和类似地发生转变，这是人类介导的选择的结果。这些结果突出了人类选择更长、更强和更细纤维以及其他纤维生理学方面的无意识选择所导致的全球基因表达机制的复杂改变。我们说明了如何从数据中挖掘出在作物改良过程中原始和/或现代驯化者无意中针对的基因，以及可能控制驯化棉花纤维改良品质的基因。
