title: Maize pan-transcriptome provides novel insights into genome complexity and quantitative trait variation.
abstract: 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.
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Minliang
authors.initials: M
authors.lastname: Jin
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Haijun
authors.initials: H
authors.lastname: Liu
authors.affiliation: College of Agriculture and Biotechnology, China Agricultural University, Beijing 100193, China.|Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
authors.forename: Cheng
authors.initials: C
authors.lastname: He
authors.affiliation: Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
authors.forename: Junjie
authors.initials: J
authors.lastname: Fu
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Yingjie
authors.initials: Y
authors.lastname: Xiao
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Yuebin
authors.initials: Y
authors.lastname: Wang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Weibo
authors.initials: W
authors.lastname: Xie
authors.affiliation: Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
authors.forename: Guoying
authors.initials: G
authors.lastname: Wang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Jianbing
authors.initials: J
authors.lastname: Yan
mesh_terms: D019295:Computational Biology / Q000379:methods; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D017343:Genes, Plant; D018745:Genome, Plant; D023281:Genomics; D058977:Molecular Sequence Annotation; D010641:Phenotype; D019655:Quantitative Trait, Heritable; D059467:Transcriptome; D003313:Zea mays / Q000235:genetics*