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Transcriptome-referenced association study of clove shape traits in garlic.
DNA Research ( IF 4.1 ) Pub Date : 2018-08-08 , DOI: 10.1093/dnares/dsy027
Xiaojun Chen 1 , Xia Liu 2 , Siyuan Zhu 1 , Shouwei Tang 1 , Shiyong Mei 1 , Jing Chen 2 , Shan Li 2 , Mengdi Liu 2 , Yuejiao Gu 2 , Qiuzhong Dai 1 , Touming Liu 1
Affiliation  

Genome-wide association studies are a powerful approach for identifying genes related to complex traits in organisms, but are limited by the requirement for a reference genome sequence of the species under study. To circumvent this problem, we propose a transcriptome-referenced association study (TRAS) that utilizes a transcriptome generated by single-molecule long-read sequencing as a reference sequence to score population variation at both transcript sequence and expression levels. Candidate transcripts are identified when both scores are associated with a trait and their potential interactions are ascertained by expression quantitative trait loci analysis. Applying this method to characterize garlic clove shape traits in 102 landraces, we identified 22 candidate transcripts, most of which showed extensive interactions. Eight transcripts were long non-coding RNAs (lncRNAs), and the others were proteins involved mainly in carbohydrate metabolism, protein degradation, etc. TRAS, as an efficient tool for association study independent of a reference genome, extends the applicability of association studies to a broad range of species.

中文翻译:

转录组参考关联研究大蒜的丁香形状性状。

全基因组关联研究是鉴定与生物复杂性状相关的基因的有力方法,但受研究物种对参考基因组序列的要求所限制。为了解决这个问题,我们提出了转录组参考关联研究(TRAS),该研究利用单分子长序列测序产生的转录组作为参考序列来对转录本序列和表达水平的种群变异进行​​评分。当两个分数都与一个性状相关联并且通过表达定量性状基因座分析确定它们的潜在相互作用时,将鉴定候选转录本。应用此方法表征102个地方品种的蒜瓣形状特征,我们鉴定了22个候选转录本,其中大多数表现出广泛的相互作用。
更新日期:2019-11-01
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