Genome-wide identification and expression profiling of basic leucine zipper transcription factors during abiotic stresses in potato (Solanum tuberosum L.)

Authors: Halterman, Dennis; KUMAR, PANKAJ - PUNJAB AGRICULTURAL UNIVERSITY; SHARMA, DIXIT - HIMACHAL PRADESH AGRICULTURAL UNIVERSITY; KUMAR, ANKAJ - INSTITUTE OF HIMALAYAN BIORESOURCE TECHNOLOGY; VERMA, HAILENDER - HIMACHAL PRADESH AGRICULTURAL UNIVERSITY; KUMAR, ARUN - PUNJAB AGRICULTURAL UNIVERSITY

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/16/2021
Publication Date: 3/12/2021
Citation: Halterman, D.A., Kumar, P., Sharma, D., Kumar, A., Verma, H.K., Kumar, A. 2021. Genome-wide identification and expression profiling of basic leucine zipper transcription factors during abiotic stresses in potato (Solanum tuberosum L.). PLoS ONE. 16(3). Article e0247864. https://doi.org/10.1371/journal.pone.0247864.
DOI: https://doi.org/10.1371/journal.pone.0247864

Interpretive Summary: One of the biggest challenges of current times is to feed the ever-growing population amidst the climate-change scenario, with limited available resources. Abiotic stresses such as salinity, water (drought and flooding), and heat are a few of the many factors that directly impact the agronomical traits and yield of crops. Potato (Solanum tuberosum L.) is one of the most important food crops, third-largest after rice and wheat in terms of human consumption. This crop can also be used commercially as a health food because it is rich in antioxidants, minerals, and dietary fibers. However, as a consequence of global warming, a continuous increase in temperature leads to multiple stresses, including heat and salinity. Plants respond to stresses by altering expression of certain genes that allow them to adapt to the new conditions. Expression of genes are regulated, in part, by transcription factors. One type of transcription factors, named bZIP because of their molecular structure, are known to regulate gene expression during abiotic stresses in plants. In this work, we have used available sequence data on bZIPs in potato to identify candidate genes that are involved in the plant's response to abiotic stresses. This study will pave the way for future functional studies using forward and reverse genetics to improve abiotic stress tolerance in potato.

Technical Abstract: Potato (Solanum tuberosum L.) is an important food crop that is grown and consumed worldwide. The growth and productivity of this crop are severely affected by various abiotic stresses. Basic leucine zipper (bZIP) transcription factors (TFs) play crucial roles during growth and development and under stress conditions. However, systematic and in-depth identification and functional characterization of the bZIP gene family of potato is lacking. In the current study, we identified a total of 90 bZIPs (StbZIP) distributed on 12 linkage groups of potato. Based on the previous functional classification of bZIPs in Arabidopsis and rice, a phylogenetic tree of potato bZIPs was constructed and genes were categorized into various functional groups (A to I, S, and U). Analyses of the transcript sequence (RNA-seq) data led to identifying a total of 18 candidate StbZIPs [four in roots, eight in the tuber, six in mesocarp and endocarp] that were expressed in a tissue-specific manner. Differential expression analysis under the various abiotic conditions (salt, mannitol, water, and heat stress) and treatment with phytohormones (ABA, GA, IAA, and BAP) led to the identification of forty-two [thirteen under salt stress, two under mannitol stress, ten under water stress, and eighteen under heat stress], and eleven [eight and three StbZIPs upon treatment with ABA, and IAA, respectively] candidate StbZIPs, respectively. Using sequence information of candidate StbZIPs, a total of 22 SSR markers were also identified in this study. In conclusion, the genome-wide identification analysis coupled with RNA-Seq expression data led to identifying candidate StbZIPs, which are dysregulated, and may play a pivotal role under various abiotic stress conditions. This study will pave the way for future functional studies using forward and reverse genetics to improve abiotic stress tolerance in potato.