通过生物信息学方法筛选和杨属细胞壁特征相关的QTLs区间上的候选基因

熊荣川 译

摘要 数量性状位点（Quantitative trait locus以下简称QTL）研究是植物研究中不可或缺的一部分，常被用来描述结构化种群内部表型变化的遗传基础，以及标记辅助的繁殖结果观察。这些QTL区间在染色体上分布区域很广，包括成百上千个基因，也因此束缚了对之进行候选基因的鉴定和筛选。基因组历史、进化以及表达证据可用来缩小区间内候选基因的范围，从而方便下一步详细的功能基因组研究。我们研究的出发点是解决在QTL区间内筛选基因的方法学问题。本文提供了一种基于生物信息学的方法，用来筛选QTL区间内和表型关联可能性更高的候选基因。在研究杨属植物细胞壁特征（特别是根茎部木质素含量和S/G比率）背景下，使用这种方法得到了一套已知或潜在与细胞壁合成功能相关的基因。这些结果为进一步研究细胞壁抗性及最终利用生物质作为人类能源指明了方向。

关键词：全基因组复制；数量性状位点；植物化学；紫丁香基丙烷木质素；愈疮木基丙烷

Bioinformatics-Based Identification of Candidate Genes from QTLs Associated with Cell Wall Traits in Populus

Abstract Quantitative trait locus (QTL) studies are an integral part of plant research and are used to characterize the genetic basis of phenotypic variation observed in structured populations and inform marker-assisted breeding efforts. These QTL intervals can span large physical regions on a chromosome comprising hundreds of genes, thereby hampering candidate gene identification. Genome history, evolution, and expression evidence can be used to narrow the genes in the interval to a smaller list that is manageable for detailed downstream functional genomics characterization. Our primary motivation for the present study was to address the need for a research methodology that identifies candidate genes within a broad QTL interval. Here we present a bioinformatics-based approach for subdividing candidate genes within QTL intervals into alternate groups of high probability candidates. Application of this approach in the context of studying cell wall traits, specifically lignin content and S/G ratios of stem and root in Populus plants, resulted in manageable sets of genes of both known and putative cell wall biosynthetic function. These results provide a roadmap for future experimental work leading to identification of new genes controlling cell wall recalcitrance and, ultimately, in the utility of plant biomass as an energy feedstock. (Ranjan et al., 2010)

Keywords Populus . Whole-genome duplication . Quantitative trait loci .Wood chemistry . Syringyl lignin . Guaiacyl lignin . Biofuels

参考文献：

Ranjan P, Yin T, Zhang X, Kalluri UC, Yang X, Jawdy S,Tuskan GA (2010). "Bioinformatics-Based Identification of Candidate Genes from QTLs Associated with Cell Wall Traits in Populus." BioEnergy Research 3(2): 172-182.