Genome-Wide Analysis and Evolutionary Perspective of the Cytokinin Dehydrogenase Gene Family in Wheat (Triticum aestivum L.)

Abstract

Cytokinin dehydrogenase (CKX; EC.1.5.99.12) regulates the level of cytokinin (CK) in plants and is involved in CK regulatory activities. In different plants, a small gene family encodes CKX proteins with varied numbers of members. These genes are expanded in the genome mainly due to segmental duplication events. Despite their biological importance, CKX genes in Triticum aestivum have yet to be studied in depth. A total of 11 CKX subfamilies were identified with similar gene structures, motifs, domains, cis-acting elements, and an average signal peptide of 25 amino acid length was found. Introns, ranging from one to four, were present in the coding regions at a similar interval in major CKX genes. Putative cis-elements such as abscisic acid, auxin, salicylic acid, and low-temperature-, drought-, and light-responsive cis-regulatory elements were found in the promoter region of majority CKX genes. Variation in the expression pattern of CKX genes were identified across different tissues in Triticum. Phylogenetic analysis shows that the same subfamily of CKX clustered into a similar clade that reflects their evolutionary relationship. We performed a genome-wide identification of CKX family members in the Triticum aestivum genome to get their chromosomal location, gene structure, cis-element, phylogeny, synteny, and tissue- and stage-specific expression along with gene ontology. This study has also elaborately described the tissue- and stage-specific expression and is the resource for further analysis of CKX in the regulation of biotic and abiotic stress resistance, growth, and development in Triticum and other cereals to endeavor for higher production and proper management.

Genomic insights into CKX genes: key players in cotton fibre development and abiotic stress responses

“…The abundance of elements in the promoter region of GhCKX genes suggests the functional diversity of these genes in cotton. Furthermore, GhCKX genes harbor cis -elements in their promoter regions associated with a stress response (low-temperature and drought response) and hormone response elements (salicylic acid response, auxin response, abscisic acid response, gibberellin response, and methyl jasmonate (MeJA) response elements) were consistent with prior studies in soybean ( Du et al, 2023 ) and wheat ( Jain et al, 2022 ). The occurrence of different elements in the GhCKX genes’ promoter region indicate their functional diversity in cotton…”

“…The analysis of GhCKX gene structures show that they have multiple introns and exons, and the CKX members of a subgroup, that are closely related, have similar gene structure and domain composition, which may indicate comparable developmental functions in the plant. Previous studies have found that the number of exons/introns of CKX gene family members ranges from 1 to 4 in wheat ( Jain et al, 2022 ), and from 1 to 10 in soybean ( Du et al, 2023 ). In this study, the number of exons/introns in G. hirsutum ranged from 8 to 18, which is consistent with the number of exons/introns in Phaseolus vulgaris ( Zhang et al, 2023 ), suggesting that the exons/introns of CKX genes were deleted or inserted during the evolution of G. hirsutum .…”

“…CKX genes are encoded by a multigene family, and have been phylogenetically and functionally characterized in a variety of plants species, such as such as Arabidopsis thaliana ( Schmülling et al, 2003 ), Oryza sativa ( Zheng et al, 2023 ), Glycine max L., Nicotiana tabacum ( Zheng et al, 2023 ), Medicago truncatula ( Wang et al, 2021 ), Triticum aestivum ( Jain et al, 2022 ), finger millet ( Eleusine coracana) ( Blume et al, 2022 ), Liriodendron chinense ( Sun et al, 2023 ), Brassica oleracea ( Zhu et al, 2022 ) and Brassica napus ( Liu et al, 2018 ), which underline their indispensable role in plant growth and development. Several studies have indicated a correlation between cotton fibre elongation and cytokinin concentration, wherein cytokinins promote fibre differentiation before flowering but inhibit fibre elongation after flowering ( Chen et al, 1997 ).…”

Genome-Wide Identification and Abiotic-Stress-Responsive Expression of CKX Gene Family in Liriodendron chinense

“…CKX7 was expressed at low levels in leaf, inflorescence, and spike tissues. CKX4 and CKX5 were expressed at higher levels in leaf tissues [13]. CKX3 and CKX11 were expressed at different levels in all the tissues studied, while CKX10 was expressed at lower levels in all tissues except leaves [13].…”

“…CKX4 and CKX5 were expressed at higher levels in leaf tissues [13]. CKX3 and CKX11 were expressed at different levels in all the tissues studied, while CKX10 was expressed at lower levels in all tissues except leaves [13]. BjuCKX11 and BjuCKX13 were significantly up-regulated in the S2 phase, which had the highest expression levels among the four periods, while the highest expression levels of BjuCKX12 and BjuCKX14 occurred in the S4 phase [14].…”