title: Characterization and expression profiling of MYB transcription factors against stresses and during male organ development in Chinese cabbage (Brassica rapa ssp. pekinensis).
abstract: MYB proteins comprise a large family of plant transcription factors that play regulatory roles in different biological processes such as plant development, metabolism, and defense responses. To gain insight into this gene superfamily and to elucidate its roles in stress resistance, we performed a comprehensive genome-wide identification, characterization, and expression analysis of MYB genes in Chinese cabbage (Brassica rapa ssp. pekinensis). We identified 475 Chinese cabbage MYB genes, among which most were from R2R3-MYB (256 genes) and MYB-related (202) subfamilies. Analysis of sequence characteristics, phylogenetic classification, and protein motif structures confirmed the existence of several categories (1R, 2R, 3R, 4R, and 5R) of Chinese cabbage MYB genes, which is comparable with MYB genes of other crops. An extensive in silico functional analysis, based on established functional properties of MYB genes from different crop species, revealed 11 and four functional clades within the Chinese cabbage R2R3-MYB and MYB-related subfamilies, respectively. In this study, we reported a MYB-like group within the MYB-related subfamily contains 77 MYB genes. Expression analysis using low temperature-treated whole-genome microarray data revealed variable transcript abundance of 1R/2R/3R/4R/5R-MYB genes in 11 clusters between two inbred lines of Chinese cabbage, Chiifu and Kenshin, which differ in cold tolerance. In further validation tests, we used qRT-PCR to examine the cold-responsive expression patterns of 27 BrMYB genes; surprisingly, the MYB-related genes were induced more highly than the R2R3-MYB genes. In addition, we identified 10 genes with corresponsive expression patterns from a set of salt-, drought-, ABA-, JA-, and SA-induced R2R3-MYB genes. We identified 11 R2R3-MYBs functioning in resistance against biotic stress, including 10 against Fusarium oxysporum f.sp. conglutinans and one against Pectobacterium carotovoram subsp. caratovorum. Furthermore, based on organ-specific expression data, we identified nine R2R3-MYBs that were constitutively expressed in male reproductive tissue, which may provide an important key for studying male sterility in Chinese cabbage. The extensive annotation and transcriptome profiling reported in this study will be useful for understanding the involvement of MYB genes in stress resistance in addition to their growth regulatory functions, ultimately providing the basis for functional characterization and exploitation of the candidate MYB genes for genetic engineering of Chinese cabbage.
authors.affiliation: Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam, 540-950, South Korea.
authors.forename: Gopal
authors.initials: G
authors.lastname: Saha
authors.affiliation: Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam, 540-950, South Korea.
authors.forename: Jong-In
authors.initials: JI
authors.lastname: Park
authors.affiliation: Department of Genetics and Plant Breeding, Patuakhali Science and Technology University, Dumki, Patuakhali, 8602, Bangladesh.
authors.forename: Nasar Uddin
authors.initials: NU
authors.lastname: Ahmed
authors.affiliation: Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam, 540-950, South Korea.
authors.forename: Md Abdul
authors.initials: MA
authors.lastname: Kayum
authors.affiliation: Department of Horticulture, Hankyong National University, Ansung, Kyonggi-do, 456-749, South Korea.
authors.forename: Kwon-Kyoo
authors.initials: KK
authors.lastname: Kang
authors.affiliation: Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam, 540-950, South Korea. Electronic address: nis@sunchon.ac.kr.
authors.forename: Ill-Sup
authors.initials: IS
authors.lastname: Nou
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D029741:Brassica rapa / Q000187:drug effects / Q000235:genetics* / Q000254:growth & development / Q000502:physiology; D016000:Cluster Analysis; D003198:Computer Simulation; D035264:Flowers / Q000187:drug effects / Q000235:genetics / Q000254:growth & development*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000187:drug effects; D017343:Genes, Plant; D020411:Oligonucleotide Array Sequence Analysis; D038081:Organogenesis / Q000187:drug effects / Q000235:genetics*; D010802:Phylogeny; D010937:Plant Growth Regulators / Q000494:pharmacology; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D060888:Real-Time Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D013312:Stress, Physiological / Q000187:drug effects / Q000235:genetics*; D014157:Transcription Factors / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism
chemical_list: D010937:Plant Growth Regulators; D010940:Plant Proteins; D014157:Transcription Factors
keywords: Abiotic and biotic stress; Chiifu; Gene expression; Kenshin; MYB-Related; R2R3-MYB