Genome-wide identification and analysis of cytokinin dehydrogenase/oxidase (CKX) family genes in Brassica oleracea L. reveals their involvement in response to Plasmodiophora brassicae infections

Zhu, Mingzhao; Wang, Yong; Lu, Shujin; Yang, Limei; Zhuang, Mu; Zhang, Yangyong; Lv, Honghao; Fang, Zhiyuan; Hou, Xilin

doi:10.1016/j.hpj.2021.05.003

Cited by 25 publications

(17 citation statements)

References 47 publications

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“…thaliana , overexpression of CKX has reduced gall formation [ 179 ], indicating that more active CK metabolism in the SL root tissue might interfere with clubroot. Similar results were also obtained by Zhu et al [ 202 ], who reported significant up-and down-regulation of three CKX genes ( Bol020547, Bol028392 , and Bol045724 ) in resistant and susceptible cabbage, respectively. Cytokinin response factor 4 gene ( CRF4 ) is a component of cytokinin signaling pathway positioned close to clubroot resistance loci Crr1a and CRa was reported to mediate resistance against clubroot in B .…”

Section: Transcriptomicssupporting

confidence: 90%

“…SA biosynthesis is suppressed in resistant plants [ 231 ] B . oleracea Race 4 Roots 7 and 28 dai 36 CKX genes were identified and three genes were down- and up-regulated significantly in the susceptible and resistant materials, respectively [ 202 ] B . oleracea Isolate yeoncheon Leaves and roots 0, 3, 6, 12, 24, 72 hai and 15 and 40 dai Two BolMyro and 12 BolMBP genes were highly expressed in the susceptible line, whereas only one BolMyro and five BolMBP genes were highly induced in the resistant line [ 232 ] B .…”

Section: Transcriptomicsmentioning

confidence: 99%

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Multi-Omics Approaches to Improve Clubroot Resistance in Brassica with a Special Focus on Brassica oleracea L.

Shaw

Shen

et al. 2022

IJMS

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Brassica oleracea is an agronomically important species of the Brassicaceae family, including several nutrient-rich vegetables grown and consumed across the continents. But its sustainability is heavily constrained by a range of destructive pathogens, among which, clubroot disease, caused by a biotrophic protist Plasmodiophora brassicae, has caused significant yield and economic losses worldwide, thereby threatening global food security. To counter the pathogen attack, it demands a better understanding of the complex phenomenon of Brassica-P. brassicae pathosystem at the physiological, biochemical, molecular, and cellular levels. In recent years, multiple omics technologies with high-throughput techniques have emerged as successful in elucidating the responses to biotic and abiotic stresses. In Brassica spp., omics technologies such as genomics, transcriptomics, ncRNAomics, proteomics, and metabolomics are well documented, allowing us to gain insights into the dynamic changes that transpired during host-pathogen interactions at a deeper level. So, it is critical that we must review the recent advances in omics approaches and discuss how the current knowledge in multi-omics technologies has been able to breed high-quality clubroot-resistant B. oleracea. This review highlights the recent advances made in utilizing various omics approaches to understand the host resistance mechanisms adopted by Brassica crops in response to the P. brassicae attack. Finally, we have discussed the bottlenecks and the way forward to overcome the persisting knowledge gaps in delivering solutions to breed clubroot-resistant Brassica crops in a holistic, targeted, and precise way.

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Section: Transcriptomicssupporting

confidence: 90%

Section: Transcriptomicsmentioning

confidence: 99%

Multi-Omics Approaches to Improve Clubroot Resistance in Brassica with a Special Focus on Brassica oleracea L.

Shaw

Shen

et al. 2022

IJMS

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“…Collinearity is identified between Triticum aestivum and Aegilops tauschii as shown in (Figure 5; Supplementary Table S2). Similar results for synteny has been identified in Brassica oleracea and Arabidopsis thaliana CKX genes (Zhu et al, 2022) Promoter and Gene Ontology Analysis of CKX Gene Family…”

Section: Phylogenetic and Synteny Analysis Of The Ckx Gene Familysupporting

confidence: 81%

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

et al. 2022

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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.

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“…Polyploid dicots possess much larger panels of CKX genes, for example Glycine max has 16 genes ( Liu et al, 2021 ), while polyploid Brassica species have a much larger gene family compared to diploids. While B. rapa has only 12 CKX genes ( Liu et al, 2013 ), amphidiploid B. napus contains 23 ( Liu et al, 2018 ), while B. oleracea accounts for up to 36 CKX genes ( Zhu et al, 2022 ).…”

Section: Discussionmentioning

confidence: 99%

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

Blume

Yemets²,

Korkhovyi³

et al. 2022

Front. Genet.

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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.

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Genome-wide identification and analysis of cytokinin dehydrogenase/oxidase (CKX) family genes in Brassica oleracea L. reveals their involvement in response to Plasmodiophora brassicae infections

Cited by 25 publications

References 47 publications

Multi-Omics Approaches to Improve Clubroot Resistance in Brassica with a Special Focus on Brassica oleracea L.

Multi-Omics Approaches to Improve Clubroot Resistance in Brassica with a Special Focus on Brassica oleracea L.

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

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

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