Genome-Wide Identification and Characterization of Trihelix Gene Family in Asian and African Vigna Species

Shweta Kumari, Dhammaprakash Pandhari Wankhede (), Sneha Murmu, Ranjeet Maurya, Sarika Jaiswal, Anil Rai and Sunil Archak ()
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Shweta Kumari: Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute (IASRI), Pusa Campus, New Delhi 110012, India
Dhammaprakash Pandhari Wankhede: ICAR-National Bureau Plant Genetic Resources, Pusa Campus, New Delhi 110012, India
Sneha Murmu: Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute (IASRI), Pusa Campus, New Delhi 110012, India
Ranjeet Maurya: ICAR-National Bureau Plant Genetic Resources, Pusa Campus, New Delhi 110012, India
Sarika Jaiswal: Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute (IASRI), Pusa Campus, New Delhi 110012, India
Anil Rai: Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute (IASRI), Pusa Campus, New Delhi 110012, India
Sunil Archak: ICAR-National Bureau Plant Genetic Resources, Pusa Campus, New Delhi 110012, India

Agriculture, 2022, vol. 12, issue 12, 1-23

Abstract: Trihelix transcription factors play a crucial role in varied stress responses as well as in the growth and development of plants. The role of trihelix transcription factors in the non-shattering phenotype in domesticated rice is known. The Vigna group of crops has different degrees of shattering phenotypes in different species. To understand the evolutionary conservation or divergence of the trihelix gene family in important Vigna species here, the genome-wide identification and characterization of the trihelix gene family in four Vigna species including the cowpea ( Vigna unguiculata ), mung bean ( V. radiata ), adzuki bean ( V. angularis ) and rice bean ( V. umbellata ) was performed. A total of 39, 35, 41 and 50 trihelix genes were identified in the cowpea, mung bean, adzuki bean and rice bean, respectively. The trihelix genes in each of the four Vigna species were classified into five subgroups: GT, GTγ, SH4, S1P1 and GTδ. The members of each subgroup shared similar patterns of gene structure and motif across the four species. The cross-species positional relationships of the cowpea, adzuki bean and mung bean vis-a-vis rice trihelix genes were studied. Further, the Ka/Ks ratio for the trihelix genes in the four Vigna species indicated the purifying or stabilizing selection of the family. The gene expression analysis of the trihelix gene family in the cowpea showed that most of the genes express in at least some of the seed and/or pod developmental stages, although at varying degrees. Based on detailed bioinformatic analysis, a potential target for gene editing towards a possible non-shattering phenotype in the four important Vigna crops was discussed.

Keywords: trihelix transcription factor; gene family; in silico characterization; domestication; pod dehiscence (search for similar items in EconPapers)
JEL-codes: Q1 Q10 Q11 Q12 Q13 Q14 Q15 Q16 Q17 Q18 (search for similar items in EconPapers)
Date: 2022
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