title: Genome-wide identification and characterization of MADS-box family genes related to organ development and stress resistance in Brassica rapa.
abstract: BACKGROUND
  MADS-box transcription factors (TFs) are important in floral organ specification as well as several other aspects of plant growth and development. Studies on stress resistance-related functions of MADS-box genes are very limited and no such functional studies in Brassica rapa have been reported. To gain insight into this gene family and to elucidate their roles in organ development and stress resistance, we performed genome-wide identification, characterization and expression analysis of MADS-box genes in B. rapa.
  
  
  RESULTS
  Whole-genome survey of B. rapa revealed 167 MADS-box genes, which were categorized into type I (Mα, Mβ and Mγ) and type II (MIKC(c) and MIKC*) based on phylogeny, protein motif structure and exon-intron organization. Expression analysis of 89 MIKC(c) and 11 MIKC* genes was then carried out. In addition to those with floral and vegetative tissue expression, we identified MADS-box genes with constitutive expression patterns at different stages of flower development. More importantly, from a low temperature-treated whole-genome microarray data set, 19 BrMADS genes were found to show variable transcript abundance in two contrasting inbred lines of B. rapa. Among these, 13 BrMADS genes were further validated and their differential expression was monitored in response to cold stress in the same two lines via qPCR expression analysis. Additionally, the set of 19 BrMADS genes was analyzed under drought and salt stress, and 8 and 6 genes were found to be induced by drought and salt, respectively.
  
  
  CONCLUSIONS
  The extensive annotation and transcriptome profiling reported in this study will be useful for understanding the involvement of MADS-box genes in stress resistance in addition to their growth and developmental functions, which ultimately provides the basis for functional characterization and exploitation of the candidate genes for genetic engineering of B. rapa.
authors.affiliation: Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 540-742, Republic of Korea. saha.18@gmail.com.
authors.forename: Gopal
authors.initials: G
authors.lastname: Saha
authors.affiliation: Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 540-742, Republic of Korea. jipark@sunchon.ac.kr.
authors.forename: Jong-In
authors.initials: JI
authors.lastname: Park
authors.affiliation: Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 540-742, Republic of Korea. my-656@hanmail.net.
authors.forename: Hee-Jeong
authors.initials: HJ
authors.lastname: Jung
authors.affiliation: Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 540-742, Republic of Korea. nasargpb@yahoo.com.
authors.forename: Nasar Uddin
authors.initials: NU
authors.lastname: Ahmed
authors.affiliation: Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 540-742, Republic of Korea. kayumagb@gmail.com.
authors.forename: Md Abdul
authors.initials: MA
authors.lastname: Kayum
authors.affiliation: Department of Agricultural Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 540-742, Republic of Korea. queen@sunchon.ac.kr.
authors.forename: Mi-Young
authors.initials: MY
authors.lastname: Chung
authors.affiliation: Department of Biology, Chungnam National University, 96 Daehangno, Gung-dong, Yuseong-gu, Daejeon, 305-764, Republic of Korea. ykhur@cnu.ac.kr.
authors.forename: Yoonkang
authors.initials: Y
authors.lastname: Hur
authors.affiliation: Department of Crop Science, Chungbuk National University, 410 Seongbongro, Heungdokgu, Cheongju, 361-763, Republic of Korea. ygcho@chungbuk.ac.kr.
authors.forename: Yong-Gu
authors.initials: YG
authors.lastname: Cho
authors.affiliation: Laboratory of Plant Reproductive Genetics, Graduate School of Life Sciences, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, 980-8577, Japan. nabe@ige.tohoku.ac.jp.
authors.forename: Masao
authors.initials: M
authors.lastname: Watanabe
authors.affiliation: Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 540-742, Republic of Korea. nis@sunchon.ac.kr.
authors.forename: Ill-Sup
authors.initials: IS
authors.lastname: Nou
mesh_terms: D020816:Amino Acid Motifs / Q000235:genetics; D017360:Arabidopsis / Q000235:genetics; D001937:Brassica / Q000235:genetics*; D002874:Chromosome Mapping; D003080:Cold Temperature; D055864:Droughts; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000187:drug effects; D018745:Genome, Plant; D026161:MADS Domain Proteins / Q000145:classification / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D012275:Oryza / Q000235:genetics; D010802:Phylogeny; D010940:Plant Proteins / Q000145:classification / Q000235:genetics*; D060888:Real-Time Polymerase Chain Reaction; D012492:Salts / Q000494:pharmacology; D013312:Stress, Physiological / Q000235:genetics
chemical_list: D026161:MADS Domain Proteins; D010940:Plant Proteins; D012492:Salts