Genome-Wide Identification, and In-Silico Expression Analysis of YABBY Gene Family in Response to Biotic and Abiotic Stresses in Potato (Solanum tuberosum)

Abstract

YABBY is among the specific transcription factor (TF) gene family in plants and plays an important role in the development of the leaves and floral organs. Its specific roles include lateral organ development, the establishment of dorsoventral polarity, and response to abiotic stress. Potato is an important crop worldwide and YABBY genes are not still identified and characterized in potato. So, little has been known about YABBY genes in potato until now. This study was carried out to perform genome-wide analysis, which will provide an in-depth analysis about the role of YABBY genes in potato. There have been seven StYAB genes identified, which are found to be located on seven different chromosomes. Through multiple sequence analyses, it has been predicted that the YABBY domain was present in all seven genes while the C2-C2 domain was found to be absent only in StYAB2. With the help of cis-element analysis, the involvement of StYAB genes in light, stress developmental, and hormonal responsiveness has been found. Furthermore, expression analysis from RNA-seq data of different potato organs indicated that all StYAB genes have a role in the vegetative growth of the potato plant. In addition to this, RNA-seq data also identified StYAB3, StYAB5, and StYAB7 genes showing expression during cadmium, and drought stress, while StYAB6 was highly expressed during a viral attack. Moreover, during the attack of Phytophthora infestans on a potato plant StYAB3, StYAB5, StYAB6, and StYAB7 showed high expression. This study provides significant knowledge about the StYAB gene structures and functions, which can later be used for gene cloning, and functional analysis; this information may be utilized by molecular biologists and plant breeders for the development of new potato lines.

Genome-wide identification and in-silico expression analysis of CCO gene family in sunflower (Helianthus annnus) against abiotic stress

“…MicroRNAs (miRNAs) are crucial regulatory molecules in plants that play a significant role in several biological processes, including plant growth, development, and responses to biotic and abiotic stress (Y. Wang et al 2023b ), (Mazhar et al 2023 ). They are highly conserved and exhibit specific functions.…”

Genome-wide identification of CCO gene family in cucumber (Cucumis sativus) and its comparative analysis with A. thaliana

“…A. thaliana , C. maxima . The synteny graph was created by using the circus module in TBTool [ 31 ]. CCO's beginning and ending positions were taken from the Cucumber genome database.…”

New Frontiers in Potato Breeding: Tinkering with Reproductive Genes and Apomixis

“…The identification and in silico analysis of potato genes involved in ovule and seed developments is now much easier and focused on available bioinformatic tools. Strategies used in other crops or in potato for certain gene families (like the YABBY family; [ 112 ]), can be implemented for recognizing reproductive genes in potato. They retrieve sequences from different databases and use genomic and gene analyses tools for gene identification (e.g., Phytozome, the PLAZA genome database, Uniprot).…”