Abstract
Main conclusion
Genome-wide identification reveals 55 PvuGRAS genes belonging to 16 subfamilies and their gene structures and evolutionary relationships were characterized. Expression analyses highlight their prominence in plant growth, development and abiotic stress responses.
Abstract
GRAS proteins comprise a plant-specific transcription factor family involved in multiple growth regulatory pathways and environmental cues including abiotic/biotic stresses. Despite its crucial importance, characterization of this gene family is still elusive in common bean. A systematic genome-wide scan identified 55 PvuGRAS genes unevenly anchored to the 11 common bean chromosomes. Segmental duplication appeared to be the key driving force behind expansion of this gene family that underwent purifying selection during evolution. Computational investigation unraveled their intronless organization and identified similar motif composition within the same subfamily. Phylogenetic analyses clustered the PvuGRAS proteins into 16 phylogenetic clades and established extensive orthologous relationships with Arabidopsis and rice. Analysis of the upstream promoter region uncovered cis-elements responsive to growth, development, and abiotic stresses that may account for their differential expression. The identified SSRs could serve as putative molecular markers facilitating future breeding programs. 37 PvuGRAS transcripts were post-transcriptionally regulated by different miRNA families, miR171 being the major player preferentially targeting members of the HAM subfamily. Global expression profile based on RNA-seq data indicates a clade specific expression pattern in various tissues and developmental stages. Additionally, nine PvuGRAS genes were chosen for further qPCR analyses under drought, salt, and cold stress suggesting their involvement in acclimation to environmental stimuli. Combined, the present results significantly contribute to the current understanding of the complexity and biological function of the PvuGRAS gene family. The resources generated will provide a solid foundation in future endeavors for genetic improvement in common bean.
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Abbreviations
- FPKM:
-
Fragments per kilobase per million mapped reads
- SSR:
-
Simple sequence repeats
- TF:
-
Transcription factor
- TFBS:
-
Transcription factor binding site
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The authors are thankful to the Principal, Ramakishna Mission Vivekananda Centenary College, Rahara, Kolkata (India) for providing necessary infrastructure. The financial requirements were borne by the authors and no additional funding was received from any organization.
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Conceived and designed the experiments: AK, PL, and SB; performed the experiments: PL, SB, AC, and AK; analyzed the data: PL, SB, AC, and AK; wrote the paper: SB and AK; all authors read and approved the final manuscript.
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Laskar, P., Bhattacharya, S., Chaudhuri, A. et al. Exploring the GRAS gene family in common bean (Phaseolus vulgaris L.): characterization, evolutionary relationships, and expression analyses in response to abiotic stresses. Planta 254, 84 (2021). https://doi.org/10.1007/s00425-021-03725-x
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DOI: https://doi.org/10.1007/s00425-021-03725-x