title: A multistep screening method to identify genes using evolutionary transcriptome of plants.
abstract: We introduced a multistep screening method to identify the genes in plants using microarrays and ribonucleic acid (RNA)-seq transcriptome data. Our method describes the process for identifying genes using the salt-tolerance response pathways of the potato (Solanum tuberosum) plant. Gene expression was analyzed using microarrays and RNA-seq experiments that examined three potato lines (high, intermediate, and low salt tolerance) under conditions of salt stress. We screened the orthologous genes and pathway genes involved in salinity-related biosynthetic pathways, and identified nine potato genes that were candidates for salinity-tolerance pathways. The nine genes were selected to characterize their phylogenetic reconstruction with homologous genes of Arabidopsis thaliana, and a Circos diagram was generated to understand the relationships among the selected genes. The involvement of the selected genes in salt-tolerance pathways was verified by reverse transcription polymerase chain reaction analysis. One candidate potato gene was selected for physiological validation by generating dehydration-responsive element-binding 1 (DREB1)-overexpressing transgenic potato plants. The DREB1 overexpression lines exhibited increased salt tolerance and plant growth when compared to that of the control. Although the nine genes identified by our multistep screening method require further characterization and validation, this study demonstrates the power of our screening strategy after the initial identification of genes using microarrays and RNA-seq experiments.
authors.affiliation: Genomics Division, National Academy of Agricultural Science (NAAS), Rural Development Administration (RDA), Suwon, Korea.
authors.forename: Chang-Kug
authors.initials: CK
authors.lastname: Kim
authors.affiliation: Genomics Division, National Academy of Agricultural Science (NAAS), Rural Development Administration (RDA), Suwon, Korea.
authors.forename: Hye-Min
authors.initials: HM
authors.lastname: Lim
authors.affiliation: Molecular Breeding Division, NAAS, RDA, Suwon, Korea.
authors.forename: Jong-Kuk
authors.initials: JK
authors.lastname: Na
authors.affiliation: Vegetable Science Division, National Institute of Horticultural and Herbal Science, Suwon, Korea.
authors.forename: Ji-Weon
authors.initials: JW
authors.lastname: Choi
authors.affiliation: Genomics Division, National Academy of Agricultural Science (NAAS), Rural Development Administration (RDA), Suwon, Korea.
authors.forename: Seong-Han
authors.initials: SH
authors.lastname: Sohn
authors.affiliation: The National Center for GM Crops, RDA, Suwon, Korea.
authors.forename: Soo-Chul
authors.initials: SC
authors.lastname: Park
authors.affiliation: Policy Development Office, Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, Forestry and Fisheries, Anyang, Korea.
authors.forename: Young-Hwan
authors.initials: YH
authors.lastname: Kim
authors.affiliation: School of Electrical Information Communication Engineering, Wonkwang University, Iksan, Korea.
authors.forename: Yong-Kab
authors.initials: YK
authors.lastname: Kim
authors.affiliation: Molecular Breeding Division, NAAS, RDA, Suwon, Korea.
authors.forename: Dool-Yi
authors.initials: DY
authors.lastname: Kim
keywords: RNA-seq; microarray; multistep method; salt tolerance