Abstract
Class III homeodomain-leucine zipper (HD-ZIP III) genes encode plant-specific transcription factors that play pivotal roles in plant growth and development. There is no systematic report on HD-ZIP III members in Brassica plants and their responses to stress are largely unknown. In this study, a total of 10, 9 and 16 HD-ZIP III genes were identified from B. rapa, B. oleracea and B. napus, respectively. The phylogenetic analysis showed that HD-ZIP III proteins were grouped into three clades: PHB/PHV, REV and CNA/HB8. Genes in the same group tended to have similar exon–intron structures. Various phytohormone-responsive elements and stress-responsive elements were detected in the promoter regions of HD-ZIP III genes. Gene expression levels in different tissues, as well as under different stress conditions, were investigated using public transcription profiling data. The HD-ZIP III genes were constitutively expressed among all the tested tissues and were highly accumulated in root and stem. In B. rapa, only one BrREV gene especially responded to heat stress, BrPHB and BrREV members were downregulated upon cold stress and most HD-ZIP III genes exhibited divergent responses to drought stress. In addition, we investigated the genetic variation at known miR165/166 complementary sites of the identified HD-ZIP III genes and found one single nucleotide polymorphism (SNP) in PHB members and two SNPs in REV members, which were further confirmed using Sanger sequencing. Taken together, these results provide information for the genome-wide characterization of HD-ZIP III genes and their stress response diversity in Brassica species.
Highlights
HD-ZIP genes encode plant-specific transcription factors that are involved in various biological processes
Thirty-five genes were identified, namely, 10 from B. rapa, 9 from B. oleracea and 16 from B. napus, and they were named after their Arabidopsis homologs
We performed a comprehensive study of HD-ZIP III genes in three
Summary
HD-ZIP genes encode plant-specific transcription factors that are involved in various biological processes. In Arabidopsis thaliana, HD-ZIP III transcription factors comprise five genes: PHABULOSA (PHB)/ATHB14, PHAVOLUTA (PHV)/ATHB9, REVOLUTA (REV), ATHB8 and CORONA (CNA)/ATHB15 [1,16]. These genes play overlapping and antagonistic yet distinct roles during development [8,16,17,18,19]. RLD1 encodes an HD-ZIP III protein in maize and a semi-dominant mutation causes the adaxialization or partial reversal of leaf polarity [20]. HD-ZIP III genes regulate the wood formation in trees
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