Single Nucleotide Polymorphisms Of Genes For Differential Expressed Proteins In Soybean Leaves During Domestication

The subject analysis22soybean leaf protein spots which based on previous proteome research. According to the results of protein sequences’ search and blast, we obtained37possible coding genes. Selecting20broad geographic representation of wild soybeans, cultivated landraces and cultivars as experimental materials, respectively. We sequenced encoding genes and analysis the single nucleotide polymorphisms of genes in population level. We used Fst values and neutral test to screen the most possible target genes which experienced artificial selection, in order to find domestication-related genes from differentially expressed proteins, and then make it become an effective method for mining domestication genes. The main results are as follows:1. Obtained difference genes in soybean leaves. According to the registry numbers of22protein spots from mass spectra, found the amino acid sequence of each protein in the NCBI, submitted the amino acid sequence to the soybean Phytozome database for proteome comparison, selected the identity above80%of the genes as possible coding genes, selected the most identity gene as possible encoding gene when identity is less than80%, obtained37soybean leaves differential gene by this method.2. Analyzed the diversity of soybean difference genes. The sequenced DNA sequences get31579bp270SNP loci. In the process of domestication and breeding, the total population theta value decreased by33.20%and3.51%, the coding region theta value decreased by58.18%and4.34%, the non-coding region of the theta value decreased by40.10%and4.13%. Domesticated coding region’s theta value is greater than non-coding region, this result is consistent with the previous findings. Based on the SNP data, we calculated the coefficient of genetic differentiation within three soybean groups and groups. Wild soybean and landraces, landraces and cultivars, wild soybean and cultivars population differentiation coefficient Fst values were0.1560,0.0132,0.1723. Gst value of the coefficient of differentiation between groups were0.1380,0.0399,0.1523. The result suggested that there is higher degree of differentiation between wild soybeans and landraces and lower degree of differentiation between the landraces and cultivars.3. Selected the candidate genes. Calculated the Fst value of37genes and found six significant differentiation genes among populations (Fst>0.45), which are Glyma02g06830.1, Glyma08g05610.1, Glyma12g12230.1, Glyma15g40140.1, Glyma15g40860.1and Glyma16g04240.3. Analyzed37differentially expressed genes by Tajima’s D, Fu and Li’s D*and Fu and Li’s F*neutral test,the result showed that there are six genes with significant difference, they are Glyma13g37880.1, Glyma10g13450.1, Glyma16g23710.1, Glyma01g38750.1, Glyma12g12230.1and Glymal4g39160.2. The studies suggest that these genes in the process of domestication breeding more strongly. The two methods selected11candidate genes.4. Analyzed the function of candidate genes. Classified11candidate genes by GO system, in the ontology of cell component, the gene products distributed in the structure of the cell membrane, cytoplasm, organelles membranes, organelles, or polymer composite body; in the ontology of molecular function, primarily with bind, catalytic activity; in the ontology of biological progress involved in metabolic pathways, cell pathway, pigmentation, and biological regulation. Searched11candidate genes’related information in database and found10proteins, the functions of those proteins are as follows. Oxygen-evolving enhancer protein1involved in the release of oxygen, change of protein conformation can improve the efficiency of photosynthesis. Ferredoxin-NADP+reductase, flavin mononucleotide dependent dehydrogenase, cytochrome b6-f complex are involved in electron transfer. G protein and GTP enzyme involved in the signal transduction process. The legume lectin played an important role in defense that can inhibit the growth and reproduction of the insects to kill pathogens. Hydroxyindole O-methyltransferase (HIOMT) and N-acetyl transferase(AANAT) participated in the synthesis of melatonin. Melatonin may be related to auxin-like function, antioxidant, free radical sweeping, as well as with plant anti-adversity functionally related. Isocitrate dehydrogenase involved in the Calvin cycle, it makes the plants transformed CO2 into glyceraldehyde3-phosphate(G3P) and improved the transformation efficiency of nutrients. Methionine synthase involved in the methionine cycle, methionine related with anti-salt stress ability in plants.