Comparative Analysis Of Annual Teosinte And Maize Transcriptomes And Identification Of Genes Associated With Maize Domestication

Maize(Zea mays L.) is one of the most important food crops and displays the highest global grain production, it is also a central forage staple as well as an important source of biofuel and other industrial materials. The ever growing population of the world and drastic reduction in arable land along with dynamic climatic changes significantly influence crop yield. Therefore, utilizing the wild teosinte resources for dissecting relevant information about maize is the corner stone to meet global food requirement. On the other hand, using this information to enhance resistance against both biotic and abiotic stresses is extremely important to increase per unit area production of this crop. In this study, six teosinte collections and ten maize inbred lines were used for RNA sequencing at the seedling stage. Teosinte transcriptome was de novo assembled, and a set of unigenes were used for functional annotation. Sequence diversity between maize and teosinte was also characterizaed based on sequence alignment, and a set of conserved and divergence unigenes were identified. Alternative splicing landscape difference between maize and teosinte orthologous genes was also dissected and the results indicated that maize domestication was inclined to increase the alternative splicing compexity in order to adapt different environmental stimuli. The main achievements of this study are as follows:1. 98,431 unigenes were de novo assembled based on teosinte seedling RNA sequencing data. Of which N50 and N90 was 1,170 bp and 322 bp separately, with an average length of 770 bp. Functional annotations about these unigenes were performed by sequence comparision to the KEGG, GO and Pfam database, 62,989(63.99%) unigenes were annotated.2. Sequence diversity analysis indicated that ~75% tsosinte unigenes were highly conserved between maize and teosinte. Meanwhile, we also inentified that approminately 10% teosinte unigenes were specifically expressed in teosinte seedling stage, of which 721 unigenes were supported by gene models of four plant species. 571 unigenes were located in the inter-genic regions of maize genome which showed evidence-based expressed presence/absence variations(e PAVs).3. Based on these sequencing data, we first mapped these cleaning reads to maize B73 reference genome. A total of 58,897 SNPs and 270,024 Indels were identified based on our investigation. Phylogenetic analysis indicated that samples from temperate maize inbred lines, tropical maize inbred lines, and different teosinte subspecies could be clearly separated. On the other hand, based on these reconstructed teosinte transctiptome sequences, a total of 14,659 simple sequence repeat lociwere indentified and 11,286 primer pairs were designed specifically to teosinte geome. This data can facilitate teosinte genomics and genetics studies for future.4. In maize and teosinte, 13,593 orthologous genes were identified. Orthologous genes’ alterntive splicing landscape was dissected between annual teosinte and maize, which indicated that two main AS types(intron retention and alternative acceptor) contributed to more than 60% of the AS events in the two species. The average unique AS events of each alternatively spliced gene in maize(4.12) was higher than that in teosinte(2.26). Moreover, 94 genes generating 98 retained introns with transposable element(TE) sequences were detected in maize. This was far more than 9 retained introns with TEs detected in teosinte so far. These results indicated that TE insertion might be an important mechanism for intron retention in maize. Additionally, the AS levels of 3,864 genes were significantly different between maize and teosinte. Most genes(2,766, 71.58%) inclined to increase the alternative splicing leveles during maize domestication and improvement. Of these, 151 AS level-altered genes that are involved in transcriptional regulation and in stress responses are located in regions that have been targets of selection during maize improvement. These genes were inferred to be putatively improved genes.A set of teosinte transcriptome data can help for further intensive and extensive teosinte studies for identification of favorable genes. By comparsion of alternative splicing difference between maize and teosinte, the maize domestication and improvement can be studied in a comprehensive manner.