title: Screening and identification of soybean seed-specific genes by using integrated bioinformatics of digital differential display, microarray, and RNA-seq data.
abstract: Soybean is one of the most economically important crops in the world. Soybean seeds have abundant protein and lipid content and very high economic value. In this study, a total of 184 seed-specific genes were obtained using online microarray databases, DDD, and RNA-seq data. The reported seed-specific genes in soybean and the 184 seed-specific genes analyzed in this paper were compared. Of the screened genes, 26 were common to both previous reports and the current screening. Meanwhile, 90 of the 184 genes have homologous counterparts in Arabidopsis, among which 24 have seed-specific expression, as indicated by microarray data for Arabidopsis. Furthermore, promoter analysis showed that almost all seed-specific genes contain at least one seed specific-related element. Seed-specific element Skn-1 motif exists in most, if not all, of the seed-specific genes screened. Five genes were randomly selected from 184 soybean seed specific gene pool and their expressions were quantified using quantitative real time polymerase chain reaction (qRT-PCR) to further confirm the specificity of the screened genes. The results indicated that all five genes showed seed-specific expression. Moreover, the identification of genes with seed-specific expression screened in this study provides information valuable to the in-depth study of soybean.
authors.affiliation: College of Life Sciences, Capital Normal University, Beijing 100048, China. Electronic address: yinguangjundejia@gmail.com.
authors.forename: Guangjun
authors.initials: G
authors.lastname: Yin
authors.affiliation: Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455, USA. Electronic address: xuxxx812@umn.edu.
authors.forename: Hongliang
authors.initials: H
authors.lastname: Xu
authors.affiliation: College of Life Sciences, Capital Normal University, Beijing 100048, China. Electronic address: liujingyi627@163.com.
authors.forename: Jingyi
authors.initials: J
authors.lastname: Liu
authors.affiliation: College of Life Sciences, Capital Normal University, Beijing 100048, China. Electronic address: wangclx@163.com.
authors.forename: Cong
authors.initials: C
authors.lastname: Gao
authors.affiliation: Plant Biotechnology Institute, National Research Council Canada, Saskatoon S7N 0W9, Canada. Electronic address: Jinyue.Sun@nrc-cnrc.gc.ca.
authors.forename: Jinyue
authors.initials: J
authors.lastname: Sun
authors.affiliation: College of Life Sciences, Capital Normal University, Beijing 100048, China. Electronic address: yanym2004@163.com.
authors.forename: Yueming
authors.initials: Y
authors.lastname: Yan
authors.affiliation: College of Life Sciences, Capital Normal University, Beijing 100048, China. Electronic address: yingkaohu@yahoo.com.
authors.forename: Yingkao
authors.initials: Y
authors.lastname: Hu
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism; D030561:Databases, Nucleic Acid; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000502:physiology*; D017343:Genes, Plant / Q000502:physiology*; D005820:Genetic Testing / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012639:Seeds / Q000235:genetics / Q000378:metabolism; D013025:Glycine max / Q000235:genetics / Q000378:metabolism
keywords: Digital differential display; Microarray; RNA-seq; Seed-specific genes; Soybean