Evolutionary Response to Parallel Selective Pressures in Cultivated Rice

描述（由申请人提供）：独立的谱系如何在遗传水平上对类似的选择压力作出反应？选择是影响相同的基因，还是不同的基因产生相同的结果？我将解决这些问题使用选择增加淀粉含量在独立起源的驯化水稻（稻属）作为一个模型系统。大米特别适合这项研究，原因有三。首先，驯化水稻有三个起源;其中两个起源导致了广泛种植的亚洲水稻的形成（O。sativa），第三次导致非洲稻（O. glaberrima）。第二，控制淀粉生物合成的基因已经被鉴定和很好地表征。第三，水稻有两个完全测序的基因组，这使得遗传研究非常容易。因此，该系统将进化历史和遗传资源结合起来，这将使解决平行选择下的进化问题成为一个可行的目标。这项研究建议有三个具体目标：1）确定和比较非洲与亚洲水稻驯化的基因组后果，并确定非洲驯化水稻的种群结构和地理起源，2）确定每个驯化谱系中淀粉生物合成基因座处等位基因相对于野生祖先的起源，并将这些候选基因与全基因组中性基因座组进行比较，和3）确定和比较在栽培稻的三个起源中控制淀粉生物合成的基因中的选择标记。我将通过对栽培物种及其野生祖先的彻底取样，结合中性位点、控制淀粉生物合成的位点和淀粉合成位点周围区域的基因片段的测序来解决这些问题。将使用当前的群体遗传学和系统发育技术基于核苷酸变异的相似性和模式分析序列数据。这种分析，结合广泛的序列数据集，将区分人口因素与选择对感兴趣的基因的影响，这在大多数其他系统中很难实现。结合起来，该项目的三个组成部分将提供有价值的洞察力的遗传反应的独立谱系平行选择。该项目对公共卫生具有重要意义，因为人类病原体在广泛的地理区域以同质药物治疗的形式经历类似的选择性压力。了解类似选择压力的遗传结果可以使我们预测病原体对平行选择的反应，并预测潜在的危险情况，包括在相同选择制度下独立谱系之间的重组。

DESCRIPTION (provided by applicant): How do independent lineages respond to similar selective pressures at the genetic level? Does selection affect the same genes, or different genes for the same result? I will address these questions using selection for increased starch content across independent origins of domesticated rice (genus Oryza) as a model system. Rice is uniquely appropriate for this study for three reasons. First, there have been three origins of domesticated rice; two of these origins resulted in the formation of the widely cultivated Asian rice (O. sativa), and the third resulted in the formation of African rice (O. glaberrima). Second, the genes controlling starch biosynthesis have been identified and well characterized. Third, there are two fully sequenced genomes available for rice, making genetic studies extremely tractable. Thus, the system presents a combination of evolutionary history and genetic resources that will make addressing the question of evolution under parallel selection a viable objective. This research proposal has three specific aims: 1) to determine and compare the genomic consequences of domestication in African vs. Asian rice, and to determine the population structure and geographic origin of domesticated rice in Africa, 2) to determine the origin of alleles at starch biosynthesis loci in each domesticated lineage relative to the wild progenitors and to compare these candidate genes to a genome-wide panel of neutral loci, and 3) to determine and compare the signature of selection in genes controlling starch biosynthesis across the three origins of cultivated rice. I will address these questions using thorough sampling of the cultivated species and their wild progenitors combined with sequencing of neutral loci, loci controlling starch biosynthesis, and gene fragments from the regions surrounding starch synthesis loci. Sequence data will be analyzed based on similarity and patterns of nucleotide variation using current population genetic and phylogenetic techniques. This analysis, in combination with an extensive sequence data set, will differentiate the effects of demographic factors from those of selection on genes of interest, something that is difficult to accomplish in most other systems. In combination, the three components of the project will provide valuable insight into the genetic response of independent lineages to parallel selection. The project has important implications for public health, as human pathogens experience similar selective pressures in the form of homogeneous drug treatments across broad geographical areas. Understanding the genetic results of similar selective pressures can allow us to predict the response of pathogens to parallel selection and also to anticipate potentially dangerous scenarios involving recombination among independent lineages subject to the same selective regimes.