Maize pan-transcriptome provides novel insights into genome complexity and quantitative trait variation.
Maize pan-transcriptome provides novel insights into genome complexity and quantitative trait variation.
复制标题
DOI：
10.1038/srep18936
复制
发表时间：
2016-01-05
影响因子：
4.6
通讯作者：
Yan J
中科院分区：
文献类型：
--
作者：
Jin M;Liu H;He C;Fu J;Xiao Y;Wang Y;Xie W;Wang G;Yan J
基因表达变异对表型多样性的贡献很大，对于具有复杂基因组的物种，构建泛转录组被认为是必要的。然而，泛转录组的调控机制和功能后果还没有得到系统的研究。通过分析368个玉米不同自交系的RNA-SEQ数据，我们鉴定出近三分之一的核基因在表达存在和不存在变化的情况下，往往发挥调控作用，并可能受到远距离eQTL的调控。利用ePAV直接作为“基因”对15个农艺表型和526个代谢性状进行遗传配对分析，以有效地探索转录变异和表型变异之间的关系。通过改进的组装策略，发现2,355个高可信的新序列在参考基因组中缺失，总长度为1.9 Mb。随机挑选的10个新序列被基因组PCR完全验证，其中包括另外两个可能影响类黄酮和抗病的NBS_LRR候选序列。模拟分析表明，玉米全粒泛转录组正接近63,000个基因的最大值，通过建立两个测交群体和调查几个最重要的产量性状，表明这些可有可无的基因对杂种优势有贡献。为发现玉米数量性状变异提供了新的视角和资源，以更好地理解籽粒调控网络，促进玉米育种。
Gene expression variation largely contributes to phenotypic diversity and constructing pan-transcriptome is considered necessary for species with complex genomes. However, the regulation mechanisms and functional consequences of pan-transcriptome is unexplored systematically. By analyzing RNA-seq data from 368 maize diverse inbred lines, we identified almost one-third nuclear genes under expression presence and absence variation, which tend to play regulatory roles and are likely regulated by distant eQTLs. The ePAV was directly used as “genotype” to perform GWAS for 15 agronomic phenotypes and 526 metabolic traits to efficiently explore the associations between transcriptomic and phenomic variations. Through a modified assembly strategy, 2,355 high-confidence novel sequences with total 1.9 Mb lengths were found absent within reference genome. Ten randomly selected novel sequences were fully validated with genomic PCR, including another two NBS_LRR candidates potentially affect flavonoids and disease-resistance. A simulation analysis suggested that the pan-transcriptome of the maize whole kernel is approaching a maximum value of 63,000 genes, and through developing two test-cross populations and surveying several most important yield traits, the dispensable genes were shown to contribute to heterosis. Novel perspectives and resources to discover maize quantitative trait variations were provided to better understand the kernel regulation networks and to enhance maize breeding.