Genome-wide exploration of C2H2 zinc finger family in durum wheat (Triticum turgidum ssp. Durum): insights into the roles in biological processes especially stress response

Members of the AP2/ERF transcription factor family play critical roles in plant development, biosynthesis of key metabolites, and stress response. A detailed study was performed to identify TtAP2s/ERFs in the durum wheat (Triticum turgidum ssp. durum) genome, which resulted in the identification of 271 genes distributed on chromosomes 1A-7B. By carrying 27 genes, chromosome 6A had the highest number of TtAP2s/ERFs. Furthermore, a duplication assay of TtAP2s/ERFs demonstrated that 70 duplicated gene pairs had undergone purifying selection. According to RNA-seq analysis, the highest expression levels in all tissues and in response to stimuli were associated with DRF and ERF subfamily genes. In addition, the results revealed that TtAP2/ERF genes have tissue-specific expression patterns, and most TtAP2/ERF genes were significantly induced in the root tissue. Additionally, 13 TtAP2/ERF genes (six ERFs, three DREBs, two DRFs, one AP2, and one RAV) were selected for further analysis via qRT-PCR of their potential in coping with drought and salinity stresses. The TtAP2/ERF genes belonging to the DREB subfamily were markedly induced under both drought-stress and salinity-stress conditions. Furthermore, docking simulations revealed several residues in the pocket sites of the proteins associated with the stress response, which may be useful in future site-directed mutagenesis studies to increase the stress tolerance of durum wheat. This study could provide valuable insights for further evolutionary and functional assays of this important gene family in durum wheat.

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Genome wide identification and functional assignments of C2H2 Zinc-finger family transcription factors in Dichanthelium oligosanthes

Bioinformation ◽

10.6026/97320630015689 ◽

2019 ◽

Vol 15 (9) ◽

pp. 689-696 ◽

Cited By ~ 1

Author(s):

Raj Kumar Joshi ◽

Keyword(s):

Transcription Factors ◽

Zinc Finger ◽

C2h2 Zinc Finger ◽

Genome Wide

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Genome-Wide Analysis of C2H2 Zinc-Finger Family Transcription Factors and Their Responses to Abiotic Stresses in Poplar (Populus trichocarpa)

PLoS ONE ◽

10.1371/journal.pone.0134753 ◽

2015 ◽

Vol 10 (8) ◽

pp. e0134753 ◽

Cited By ~ 40

Author(s):

Quangang Liu ◽

Zhanchao Wang ◽

Xuemei Xu ◽

Haizhen Zhang ◽

Chenghao Li

Keyword(s):

Transcription Factors ◽

Zinc Finger ◽

Abiotic Stresses ◽

Populus Trichocarpa ◽

C2h2 Zinc Finger ◽

Genome Wide Analysis ◽

Genome Wide

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Genome-Wide Association Mapping of Prostrate/Erect Growth Habit in Winter Durum Wheat

International Journal of Molecular Sciences ◽

10.3390/ijms21020394 ◽

2020 ◽

Vol 21 (2) ◽

pp. 394 ◽

Cited By ~ 2

Author(s):

Daniela Marone ◽

Monica Rodriguez ◽

Sergio Saia ◽

Roberto Papa ◽

Domenico Rau ◽

...

Keyword(s):

Plant Growth ◽

Association Mapping ◽

Durum Wheat ◽

Candidate Genes ◽

Zinc Finger ◽

Growth Habit ◽

Genome Wide Association ◽

Genome Wide ◽

Plant Growth Habit ◽

Tiller Angle

By selecting for prostrate growth habit of the juvenile phase of the cycle, durum wheat cultivars could be developed with improved competitive ability against weeds, and better soil coverage to reduce the soil water lost by evaporation. A panel of 184 durum wheat (Triticum turgidum subsp. durum) genotypes, previously genotyped with DArT-seq markers, was used to perform association mapping analysis of prostrate/erect growth habit trait and to identify candidate genes. Phenotypic data of plant growth habit were recorded during three consecutive growing seasons (2014–2016), two different growth conditions (field trial and greenhouse) and two sowing periods (autumn and spring). Genome-wide association study revealed significant marker-trait associations, twelve of which were specific for a single environment/year, 4 consistent in two environments, and two MTAs for the LSmeans were identified across all environments, on chromosomes 2B and 5A. The co-localization of some MTAs identified in this study with known vernalization and photoperiod genes demonstrated that the sensitivity to vernalization and photoperiod response are actually not only key components of spring/winter growth habit, but they play also an important role in defining the magnitude of the tiller angle during the tillering stage. Many zinc-finger transcription factors, such as C2H2 or CCCH-domain zinc finger proteins, known to be involved in plant growth habit and in leaf angle regulation were found as among the most likely candidate genes. The highest numbers of candidate genes putatively related to the trait were found on chromosomes 3A, 4B, 5A and 6A. Moreover, a bioinformatic approach has been considered to search for functional ortholog genes in wheat by using the sequence of rice and barley tiller angle-related genes. The information generated could be used to improve the understanding of the mechanisms that regulate the prostrate/erect growth habit in wheat and the adaptive potential of durum wheat under resource-limited environmental conditions.

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