Genome-wide identification and analysis of the cytokinin oxidase/dehydrogenase (ckx) gene family in finger millet (Eleusine coracana)

Abstract

Cytokinin dehydrogenase/oxidase (CKX) enzymes play a key role in regulating cytokinin (CK) levels in plants by degrading the excess of this phytohormone. CKX genes have proven an attractive target for genetic engineering, as their silencing boosts cytokinin accumulation in various tissues, thereby contributing to a rapid increase in biomass and overall plant productivity. We previously reported a similar effect in finger millet (Eleusine coracana) somaclonal lines, caused by downregulation of EcCKX1 and EcCKX2. However, the CKX gene family has numerous representatives, especially in allopolyploid crop species, such as E. coracana. To date, the entire CKX gene family of E. coracana and its related species has not been characterized. We offer here, for the first time, a comprehensive genome-wide identification and analysis of a panel of CKX genes in finger millet. The functional genes identified in the E. coracana genome are compared with the previously-identified genes, EcCKX1 and EcCKX2. Exon-intron structural analysis and motif analysis of FAD- and CK-binding domains are performed. The phylogeny of the EcCKX genes suggests that CKX genes are divided into several distinct groups, corresponding to certain isotypes. Finally, the phenotypic effect of EcCKX1 and EcCKX2 in partially silencing the SE7 somaclonal line is investigated, showing that lines deficient in CKX-expression demonstrate increased grain yield and greater bushiness, enhanced biomass accumulation, and a shorter vegetation cycle.

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

“…The hormone also contributes to plant responses to a number of abiotic stresses, like salinity ( Joshi et al, 2018 ), temperature ( Bielach, Hrtyan & Tognetti, 2017 ), and drought ( Golan et al, 2016 ). CKXs encoded by a small gene family have been studied in numerous plant species, including finger millet ( Eleusine coracana ) ( Blume et al, 2022 ), rice ( Zheng et al, 2023 ), wheat ( Triticum aestivum L.), Chinese cabbage ( Liu et al, 2013 ), maize ( Zea mays L.), canola ( Brassica napus L.), and alfalfa ( Medicago sativa L.). However, there are only limited reports on CKX genes in cotton (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

“…With the continuous development of plant genomics and reverse genetics, we can provide powerful tools to study CKX genes [21]. The decipherment of the genome of L. chinensis, a representative species of the Liriodendron genus in the Magnoliophyta family, provides new insights into the phylogenetic position of magnoliophytes in angiosperms [22].…”