The Transposon Of Temperate And Tropical Maize Characteristics Analysis Based On The Genome Of Maize Re- Sequencing

Transposons are widely spread in the genomes of all species. Removable transposons may cause gene mutation, gene breaking off and even chromosome rearrangement, etc. At the same time, transposons translocation activity is also one of the important factors for the formation of biological genetic diversity, so it has important influence on the genome. Transposon plays an important role in helping organisms to adapt environment stress. It not only directly regulates the expression of gene and also can provide the basis of genetic variation to help organisms to create pressure induced global regulatory networks. As one of the world’s most important crops and the model crop to study heredity and evolution, transposons accounts for over 85% of the corn genome sequence. So the analysis of the corn transposons is particularly important. Based on the 84 maize inbred lines from temperate/tropical re-sequencing, bioinformatics analysis softwares such as the RepeatMasker were used to analyses the transposon quantity and distribution of each family in B73 genome. Combined with characteristics of different types of transposon, we identified insert transposons in the genomes of 84 maize inbred lines and compared the quantity and distribution differences of different transposon types between temperate and tropical maize inbred line population. There transposons can’t find in B73, we call them non-reference transposons. Through the metabolic pathway analysis and GO analysis, the results reveal that the characteristic transposons in temperate/tropical maize inbred lines population play an important role in environmental adaptation. It will help to explore transposons differences and analyses the trends of transposon domestication in corn adapting to different environment conditions. Identification of the non-reference transposons in different maize inbred populations suggests that the transposons make important contribution for plant adopting to different environment, which has important significances and provides a new idea to learn how the transposons promoting the genome evolution and gene regulation. The main results are as follows:1. The retrotransposon content is the highest in each maize inbred line,which more than 70%. In retrotransposons, members in Gypsy and Copia family accounted for more than 90%, but these two kinds of retrotransposons distribution pattern are different. Gypsy retrotransposons are closer to the centromere position with higher insert frequency and Copia retrotransposons are in contrast. In addition, DNA transposons content is relatively low in the maize B73 genome and their distribution and recombination rate was in a positive correlation.2. Comparing the temperate/tropical inbred lines’s characteristic transposon insert site, we found that the non-reference transposons are 219.782 in temperate material, distributing in 79073 loci and 461,003 in tropical material, distributing in 142,292 loci. Each temperate material was with an average of 6,868 non-reference transposons which lightly below the average of 8.865 in a tropical material. At the same time, in the newly inserted transposons, LTR retro transposons account for 91.93%and DNA transposons for only 2.74%. It demonstrated that the LTR retrotransposons had the higher transposition activity than DNA transposons in the newly inserted transposons.3. No matter in temperate or tropical materials, newly inserted transposons are mainly distributed in both ends of the chromosomes. These transposons high-frequency inserted positions were called hot spots. These loci hotspots were used for cluster analysis and the results showed that 84 maize inbred lines clustering are consistent with their regional sources, that is, the temperate and tropical materials were gathered in the different classes. By calculating the distance between transposon insert loci in different population and the adjacent gene locus, we found that the ratio of transposon inserted into the internal gene in temperate material were higher than that in tropical materials and the distance between the inserted transposon and the nearby genes have no significant difference between temperate and tropical materials.4. The genes which are adjacent to the newly inserted transposons in temperate/tropical populations have significant differences on functions. The clustering degree of adjacent genes in temperate materials were higher than that in tropical materials in the GO functional clustering involving the degradation of hazardous substances, metabolism of different biomass and so on. In addition, the specific transposon inserted sites located in the upstream of some cold resistance genes were detected in temperate materials but not in tropical materials. The number of adjacent genes of tropical materials in synthesis metabolic pathways involving amino and nucleotide sugar metabolism, nucleotide synthesis was more than that of temperate materials. Moreover, the adjacent genes involving regulation of fructose, mannose and galactose metabolism as well as ascorbic acid metabolism only existed in tropical materials. The above results showed that transposons play an important role in corn adapting to different environments.