| Maize is one of the three major grain crops in the world and it plays a very important role in agriculture, industry and medicine, also, it is an ideal model plant in the study of inheritance and evolution. Transposable element (TE), which plays a crucial role in maize genome and contributes 85 percent to the maize genome, was first reported in maize by McClintock in 1940s, and then it came to be known.Moreover, TE activities have an impact on the physiological activity of maize. Therefore, the research of TE, as a key part in maize research, is quite meaningful.In our study, we chosen the different TE insertion frequency between temperate and tropical maize inbred lines in previous research. Then, we verified the TE insertion frequency in temperate and tropical maize inbred lines by PCR (Polymerase Chain Reaction).Materials includes 458 maize inbred lines,105 landraces and 75 teosintes. To understand how TE insertion affects agronomic traits and gene expression of maize, we analyzed the correlation between TE insertion and 27 agronomic traits which come from 80 maize inbred lines and 378 maize inbred lines in different heterotic group. Also, the correlation between TE insertion and the 273 RNA-seq data. For a further study that how TE insertion affects the response of maize to the stresses, we downloaded the RNA-seq data under four different stresses (Cold stress, Heat stress, Salt stress and UV stress) from the SRA database (Sequence Read Archive) of NCBI (National Center for Biotechnology Information). At last, we compared the FPKM value of neighboring gene between maize with TE insertion and without TE insertion. The main research results as shown below.1. To validate maize TE insertion by PCR, we chose DTM-4-225713639 and DTM-2-4101264 to study among 458 maize inbred lines. In the 80 maize inbred lines, DTM-4-225713639 insertion frequency is 0.559 in temperate maize and 0.152 in tropical maize. DTM-2-4101264 insertion frequency is 0.250 and 0.800 in temperate and tropical maize, respectively. Additional,458 maize inbred lines were used to validate TE insertion frequency, we found that DTM-4-225713639 insertion frequency is 0.423 in temperate maize inbred lines and 0.180 in tropical maize inbred lines. DTM-2-4101264 insertion frequency is 0.412 in temperate maize inbred lines and 0.685 in tropical maize inbred lines. As there were two different positions of electrophoretic band in temperate and tropical maize inbred lines, we knew that two TE insertions locus are real existence, and at the same time, the real insertion frequency matches the result of the indicate frequency by bioinformatics methods. In addition, the result shows different insertion frequency in 105 landraces and 75 teosinte lines. Two TE insertion frequency are 0.243 and 0.883 in 105 landraces. And Two TE insertion frequency are 0.029 and 0.081 in 75 teosinte lines, respectively. This shows that TE could play a crucial role in corn domestication.2. Correlation analysis between TE insertion and agronomic traits. General Linear Model (GLM) model of Tassel 3.0 software was used to analyze the correlation between DTM-4-225713639 insertion and 27 agronomic traits, also, the correlation between DTM-4-225713639 insertion and 28,850 gene expression data in 273 maize inbred lines. The result shows that DTM-4-225713639 is significantly correlated to nine agronomic traits, such as days to female flowering (DFF), days to male flowering (DMF), tassel main axis length (TML), tassel branch number (TBN), ear leaf length (ELL), ear row number (ERN), kernel width (KW), pollen shed and ear diameter (ED). The result of correlation analysis between DTM-4-225713639 insertion and 28,850 gene expression data shows that 21 gene expressions are significant correlated to DTM-4-225713639 insertion. Otherwise, gene GRMZM2G018707, which locates in 25 kilo base upstream of DTM-4-225713639, shows the FPKM values equaling 0.8981 and 1.3306 in maize with or without TE insertion, respectively. It indicates that DTM-4-225713639 could suppress the expression of gene GRMZM2G018707.3. TE insertion influences neighboring gene expression under abiotic stresses. Considering the specific location of DTM-4-225713639 in maize genome, we analyzed the expression of GRMZM2G018707 gene and GRMZM2G018673 gene under four different abiotic stresses. The results showed that the two genes with or without TE insertion, to some extent, had different expression values in maize. In other words, TE insertion could affect the response of plant to abiotic stresses. To predict the function of neighboring gene, we analyzed amino acid sequence and promoter sequence of neighboring gene. And then we found some binding elements of light responsive element, cold and drought stress responsive element in promoter of GRMZM2G018707 and GRMZM2G018673. Meanwhile, the TE sequence, which inserts the promoter of GRMZM2G018673, has a G-Box element acting. As a light responsive element and stress responsive element.In conclusion, it infers indicate that TE insertion could influence GRMZM2G018707 and GRMZM2G018673 gene-expression under light and abiotic stress. |
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