Genome-wide identification and in silico gene expression analysis of the related to ABI3/VP1 (RAV) transcription factor family in barley


UÇARLI C.

BIOCELL, vol.45, no.6, pp.1673-1685, 2021 (SCI-Expanded) identifier identifier

  • Publication Type: Article / Article
  • Volume: 45 Issue: 6
  • Publication Date: 2021
  • Doi Number: 10.32604/biocell.2021.016316
  • Journal Name: BIOCELL
  • Journal Indexes: Science Citation Index Expanded (SCI-EXPANDED), Scopus, BIOSIS, CAB Abstracts, EMBASE, Veterinary Science Database
  • Page Numbers: pp.1673-1685
  • Keywords: Barley, RAV, AP2 domain, B3 domain, AP2, ERF family, Cis-acting elements, BRASSICA-NAPUS, B3 DOMAIN, ARABIDOPSIS, PROTEIN, STRESS, PREDICTION, AP2/ERF, SEQUENCE, REPRESSION, RESPONSES
  • Istanbul University Affiliated: Yes

Abstract

RAV (Related to ABI3/VP1) transcription factors are unique members of the AP2-ERF superfamily with AP2 and B3 domains and play important roles in the regulation of seed germination, plant growth, and stress response. In the study, 7 RAV genes, named HvRAVs, were identified in barley based on the available genome sequences. While five of the seven HvRAVs were located on chromosome 3, HvRAV5 and HvRAV7 were located on chromosome 1 and 4, respectively. Six of the predicted HvRAVs were intron-less, except HvRAV2, which had one intron. HvRAV proteins have shown basic, instable, and hydrophilic properties. The AP2 domain specific RAYD and WLG motifs were detected in all HvRAV proteins. Besides, B3 repression domain, R/KLFGV, is also found in the C-terminal of HvRAVs. HvRAVs were found to have stress-related cis-acting elements, including MYB, MYC, and W-BOX. HvRAV2 was predicted to have no GARE motifs, TATCCCA or TAACAA(G/A), and LTREs. Under drought conditions, the expression level of HvRAVs did not significantly change in a drought-sensitive barley genotype, whereas HvRAV5 and HvRAV7 were dramatically down-regulated in a drought-tolerant genotype. Expression of HvRAV5 was also inhibited by salinity. HvRAV7 was strongly induced by plant pathogen attack. Only HvRAV6 was induced by exogenous gibberellin application and during the germination process. Interestingly, HvRAV6 transcript was detected higher than other HvRAVs in all stress and control conditions as well as during germination. In silico analyses have shown that HvRAVs play a role in response to different abiotic and biotic stresses as well as in plant development. However, the extensive biological roles of HvRAV genes in plant development and in response to abiotic and biotic stresses need further investigation.