A team led by researchers at the National Academy of Agricultural Science, Korea, have developed a multistep screening method to identify the genes in plants using microarrays and ribonucleic acid (RNA)-seq transcriptome data. This 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. The researchers 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 this multistep screening method require further characterization and validation, this study demonstrates the power of this screening strategy after the initial identification of genes using microarrays and RNA-seq experiments.
A multistep screening method to identify genes using evolutionary transcriptome of plants
Kim CK, Lim HM, Na JK, Choi JW, Sohn SH, Park SC, Kim YH, Kim YK, Kim DY. (2014) A multistep screening method to identify genes using evolutionary transcriptome of plants. Evol Bioinform Online 10, 69-78. [article]