| Maize is one of the most important food and feedstuffs crops, and model crops for the research of molecular biology. At present, an increasing number of species are sequenced with the development of sequencing technology, which provides a wealth of genomic information for us. It is possible for us to explore the unknown information of molecular biology using public database combined with bioinformatics tools.Domain of unknown function (DUF) is a protein domain, and just as its name implies, the function of DUF is not currently understood. Over 20% of all protein domains are annotated as "DUF". Many of these domains are highly conserved, indicating that they play an important function in biological processes. DUF1313 family protein is found only in plants, and contains a highly conserved domain of unknown function, and plays an important role in plant growth and development. The researches and reports of this family are relatively less, for the function of this domain is still unknown.C2H2 zine finger proteins are widely distributed in higher plants and comprise a large family of plant transcription factor, members of which perform a variety of functions in plant biological processes. C2H2 zinc finger domain and its flanking sequences are the main DNA binding sites, which play an important role in regulating its target genes. Maize, as a model crop for genetic research, distribution of C2H2 zine finger in maize genome, expression patterns and function regulation of the transcription factors are poorly understood.The evolution analysis and functional prediction of the two types of gene family are analyzed in this study. The main results of this study are as follows:1. DUF 1313 gene family in plants evolutionary mechanism and function prediction of maize DUF1313 gene are analyzed in detail. The results showed that:(1) A total of 269 DUF1313 genes are identified from 81 photoautotrophic plants that from marine unicellular algae to terrestrial tall trees; (2) The prediction of the amino acid motifs of DUF1313 genes showed that four amino acid residues of DUF1313 domain occur regular variation in the evolutionary process; According to the regular variation of the four amino acid residues, the 269 DUF1313 genes from 81 species were classified into three major types:IARV-type, I(S/T/F)(K/R)V-type, and IRRV-type; (3) Phylogenetic analysis showed that the IARV-type included 17 genes from graminoids that are closely related to algae and are highly conserved. The I(S/T/F)(K/R)V-type included 69 genes, three of which are from Pinus and the others are from dicotyledonous plants. The IRRV-type includes 158 genes from monocotyledonous and dicotyledonous plants. (4) Selection pressure of DUF1313 family genes of graminoids analysis showed that four amino acid sites (codon sites) were found to have undergone positive selection in subclade B1, but no significant site had undergone positive selection in other subclades. We speculated that the family gene had been occur functional differentiation in graminoids. (5) The association analysis showed that three DUF1313 genes of differentiation earlier are significantly associated with 8 agronomic traits of maize, and a differentiation late gene is not significant; The result is consistent with t-test using 25 RILs populations; The results revealed that four DUF1313 genes of maize appeared differentiation in the evolutionary process; (6) Phylogenetic analyses revealed that the 103 accessions of maize, teosinte, and Tripsacum can be grouped into four clades based on the ELF4-like4 gene sequence similarity. Thus, this gene can be used to determine the relationships between maize and its relatives.2. Detailed analysis of the C2H2 zinc finger transcription factor family in the distribution of the maize genome, structural features, phylogenetic analysis, expression pattern and function prediction were researched. The results showed that:(1) The family genes are not evenly distributed in all regions of the maize chromosomes, and a majority are distributed in clusters at both ends of chromosomes; the copies of C2H2 zine finger of maize are mainly whole genome duplication, and part of them are tandem duplication; (2) Phylogenetic analysis of C2H2 zinc finger gene of maize showed that the gene family were classified into four groups, and group ? is plant-specific zinc finger gene, and which contains a conserved "QALGGH" sequence in DNA binding sites, named Q-type zinc finger; (3) Gene structures of plant-specific zinc finger genes are conservative with few intron insertion; Structure of protein sequence shows that structure of plant-specific zinc finger protein sequences is also relatively conservative, and contains only a single or a plurality of zinc finger domains; (4) Phylogenetic analysis of C2H2 zinc finger domains shows that the position and order of zinc finger domains of multi-zine finger gene are conservative during evolution process, and the sequences of zinc finger domains of same position are highly consistent; (5) The expression analysis of C2H2 zinc finger gene family in 11 tissues or organs of B73 inbred line at different growth stages showed that the family genes could be expressed in various tissues or organs, and were classified into three groups:high expression, differential expression, and low expression. In addition, expression analysis of the family genes at low temperature, low nitrogen, low phosphorus and drought conditions showed that expression pattern is different under different abiotic stress conditions, and it shows the diversity of expression patterns and function; (6) Function prediction of C2H2 zine finger family genes of maize showed that the gene family mainly involved in maize reproduction and development, and only a small portion of genes response to the stress of low phosphorus; (7) The association analysis of SNPs and Indels ofZMF155 gene with maize 20 agronomic traits show that these sites with ear row number traits are significantly associated. We speculate that the gene plays a key role in yield formation of maize. |
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