Genome-Wide Identification And Expression Analysis Of SOD Gene Family In Tomato

Tomato is mainly cultived in warm and drought areas where the soil salinity is relatively high.And it's moderately sensitive to salt,so the growth and yield are easily affected by salt and drought stress.Environment stress causes reactive oxygen species(ROS)concentration in plants,which lead to a serious of biochemical reactions,such as damaging DNA and protein,causing cell dysfunction and even death.Superoxide dismutase(SOD),as the first line of defense in the antioxidant system,can effectively remove the reactive oxygen species in plants,to protect the plant from the damage caused by environmental stress.Previous studies have shown that the activity of SOD enzyme in tomato was significantly changed under salt stress and drought stress,which indicated that SOD was closely related to the process of tomato resistance.However,there is little knowledge about the regulation mechanism gene and expression patterns of SOD genes in tomato.In this study,a system analysis was performed via the methords of bioinformatics,genetics and molecular biology to reveal the potential roles of SOD genes under various stresses.The characteristics of the SlSOD gene family were determined by analyzing gene structure,conserved motifs,chromosomal distribution,phylogenetic relationships and the expression patterns of SOD gene family members of tomato in different tissues.Besides,the expression patterns of SOD gene family were analzed under various abiotic stresses and hormonal treatments.The main findings are as follows:1.The number of SOD genes in tomato was identified at the whole genome levels,and 9 putative SOD genes were obtained,including 4 Cu/ZnSODs,4 FeSODs and 1 MnSOD.2.The locations of 9 SlSOD genes on chromosome was identified by SGN online site and found that chromosome 6 contains a gene cluster of tandem duplications(SlSOD5 and SISOD8);meanwhile,a segmental duplication was found between SISOD5(chromosome 6)and SISOD6(chromosome 3)by the PGDD database.However,homology analysis showed that the similarity of SlSOD5 and SlSOD6 protein sequences was higher than that of SlSOD5 and SlSOD8,and no homologous gene was found in the SlSOD6 gene region.3.Gene structure of 9 SlSOD genes were identified via Gene Structure Display Server software.The results showed that the number of introns and exons of 9 SlSOD genes was 4 to 8 and 5 to 9,respectively.Among them,two SlSOD genes(SlSOD5 and SISOD6)contained the number of introns and exons were 8 and 9,respectively.The SlSOD8 has the minimum number of introns and exons,which contained only about 4 and 5,respectively.In addation,two groups of SISOD genes(SlSOD1 and SISOD2,SlSOD5 and SISOD6)showed similar intron/exon configuration patterns,indicating that two groups of genes with highly conserved in evolution.4.The phylogenetic analysis revealed that the appearance of Cu/ZnSODs and Fe-MnSODs before the separation of monocotyledonous and dicotyledonous.Besides,the subfamily a was constructed by monocotyledonous and dicotyledonous plants.The results suggestted that the Cu/ZnSODs gene family in the subfamily a evolved independently after the separation of the monocotyledonous and the dicotyledonous plants.In addition,Fe-MnSODs from different plants were divided into two families,FeSODs and MnSODs,indicating that both of them evoled independently.5.The cis-elements in the promoter of each member in SISOD gene family were analyzed by PlantCare online database.The results showed that each member contained a large number of cis-elements in response to stress,hormone and light.The pairwise analysis between each member were performed,and found that each member had their specific in response to the same stress.In addition,they also had some common cis-elements and some different cis-elements which in response to the same stress.6.Published RNA-seq of microarray data was used to analyze the expression of SlSOD gene in cultivated tomato Helnz in 10 different tissues.The results showed that the members of Cu/ZnSODs and MnSOD were high expressed in all tissues,and the members of FeSODs were specific expressed in different tissues.7.qRT-PCR methord were used to analyze the expression patterns of SISOD gene family under the condition of stress(salinity and drought)and hormone treatment(NAA?SA and ABA).The results showed that three types of SlSOD gene members were involed in stress and hormone response.Although most of members were down-regulated,some members have specific expression.