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.
Highlights
The rapid development of generation sequencing technology and the decrease in cost provide us an opportunity to sequence many individuals within a species to build up the pan genome, or the sequences which, taken as a whole from all individuals, define a species
Almost half (46%, 6,726) of the expression present/absent variation (ePAV) genes expressed in more than 50% of the inbred lines have been clearly identified as regulated by expression quantitative trait loci in the previous study[5]
The ePAV genes were more likely to be regulated by distant eQTLs when compared with non-ePAV genes
Summary
The rapid development of generation sequencing technology and the decrease in cost provide us an opportunity to sequence many individuals within a species to build up the pan genome, or the sequences which, taken as a whole from all individuals, define a species. RNA sequencing (RNA-seq) has been successfully used to define the transcriptome and to find novel transcripts absent from the reference genome[10]. The construction of the maize pan-transcriptome is especially useful for the discovery of functional dispensable genes. The maize pan-transcriptome and its diversity have been studied in diverse lines[9,12], we still lack knowledge about many dispensable gene function at the genome-wide level. With the help of deep RNA-seq of kernels at 15 DAP in a diverse panel with 368 inbred lines[5], we characterized the extreme variation at the transcript level (ePAV), relative to the reference genome, and performed association studies between ePAVs and more than 600 quantitative traits. We constructed the maize pan-transcriptome and explored its contribution to phenotypic and transcriptomic diversity
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