title: Genome-Wide Analysis and Characterization of Aux/IAA Family Genes in Brassica rapa.
abstract: Auxins are the key players in plant growth development involving leaf formation, phototropism, root, fruit and embryo development. Auxin/Indole-3-Acetic Acid (Aux/IAA) are early auxin response genes noted as transcriptional repressors in plant auxin signaling. However, many studies focus on Aux/ARF gene families and much less is known about the Aux/IAA gene family in Brassica rapa (B. rapa). Here we performed a comprehensive genome-wide analysis and identified 55 Aux/IAA genes in B. rapa using four conserved motifs of Aux/IAA family (PF02309). Chromosomal mapping of the B. rapa Aux/IAA (BrIAA) genes facilitated understanding cluster rearrangement of the crucifer building blocks in the genome. Phylogenetic analysis of BrIAA with Arabidopsis thaliana, Oryza sativa and Zea mays identified 51 sister pairs including 15 same species (BrIAA-BrIAA) and 36 cross species (BrIAA-AtIAA) IAA genes. Among the 55 BrIAA genes, expression of 43 and 45 genes were verified using Genebank B. rapa ESTs and in home developed microarray data from mature leaves of Chiifu and RcBr lines. Despite their huge morphological difference, tissue specific expression analysis of BrIAA genes between the parental lines Chiifu and RcBr showed that the genes followed a similar pattern of expression during leaf development and a different pattern during bud, flower and siliqua development stages. The response of the BrIAA genes to abiotic and auxin stress at different time intervals revealed their involvement in stress response. Single Nucleotide Polymorphisms between IAA genes of reference genome Chiifu and RcBr were focused and identified. Our study examines the scope of conservation and divergence of Aux/IAA genes and their structures in B. rapa. Analyzing the expression and structural variation between two parental lines will significantly contribute to functional genomics of Brassica crops and we belive our study would provide a foundation in understanding the Aux/IAA genes in B. rapa.
authors.affiliation: Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon, 305764, South Korea.
authors.forename: Parameswari
authors.initials: P
authors.lastname: Paul
authors.affiliation: Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon, 305764, South Korea.
authors.forename: Vignesh
authors.initials: V
authors.lastname: Dhandapani
authors.affiliation: Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon, 305764, South Korea.
authors.forename: Jana Jeevan
authors.initials: JJ
authors.lastname: Rameneni
authors.affiliation: Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon, 305764, South Korea.
authors.forename: Xiaonan
authors.initials: X
authors.lastname: Li
authors.affiliation: Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon, 305764, South Korea.
authors.forename: Ganesan
authors.initials: G
authors.lastname: Sivanandhan
authors.affiliation: Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon, 305764, South Korea.
authors.forename: Su Ryun
authors.initials: SR
authors.lastname: Choi
authors.affiliation: Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon, 305764, South Korea.
authors.forename: Wenxing
authors.initials: W
authors.lastname: Pang
authors.affiliation: Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon, 305764, South Korea.
authors.forename: Subin
authors.initials: S
authors.lastname: Im
authors.affiliation: Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon, 305764, South Korea.
authors.forename: Yong Pyo
authors.initials: YP
authors.lastname: Lim
mesh_terms: D029741:Brassica rapa / Q000235:genetics / Q000254:growth & development / Q000378:metabolism*; D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000187:drug effects*; D018745:Genome, Plant; D007210:Indoleacetic Acids / Q000494:pharmacology*; D010802:Phylogeny; D010937:Plant Growth Regulators / Q000494:pharmacology; D010940:Plant Proteins / Q000235:genetics*; D018749:RNA, Plant / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction
chemical_list: D007210:Indoleacetic Acids; D010937:Plant Growth Regulators; D010940:Plant Proteins; D018749:RNA, Plant; C030737:indoleacetic acid