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.

Evolution Analysis of the Aux/IAA Gene Family in Plants Shows Dual Origins and Variable Nuclear Localization Signals

“…Some Aux/IAAs are expressed throughout the plant, but others have tissue-specific and developmental stage-specific expression manners depending on the precise developmental context [ 42 ]. Moreover, many homologous Aux/IAAs have similar expression patterns and functions [ 17 , 43 , 44 , 45 , 46 ]. No visible defect is detected in double or triple mutants of the closely-related Aux/IAA genes, suggesting that functional redundancy is widespread in the Aux/IAA gene family [ 47 ].…”

Genome-wide analysis and transcriptomic profiling of the auxin biosynthesis, transport and signaling family genes in moso bamboo (Phyllostachys heterocycla)

“…The AUX/IAA family is significantly expanded in moso bamboo (43 members) compared with those of Arabidopsis (29 members) and rice (24 members). As reported in other species [ 47 , 48 ], AUX/IAA proteins in moso bamboo can be divided into 6 major classes (I-VI). Group I consisted of 12 PhIAA proteins, 6 OsIAA proteins, and 10 AtIAA proteins that form 12 sister pairs (4 PhIAA-OSIAA pairs, 4 PhIAA-PhIAA pairs, 4 AtIAA-AtIAA pairs).…”

Genome-wide analysis of the auxin/indoleacetic acid (Aux/IAA) gene family in allotetraploid rapeseed (Brassica napus L.)

“…For these, the protein sequences of B. oleracea (TO1000) were downloaded from the Ensembl Plants database ( http://plants.ensembl.org/index.html ). The Aux/IAA genes in B. rapa 'A' genome, the other diploid progenitor of B. napus , were obtained from a previous study [ 41 ].…”

“…In the past ten years, the release of reference genomes for different species has provided an opportunity for genome-wide identification of Aux/IAA gene families using bioinformatics approaches. Aux/IAA gene families have been isolated and analyzed from many diverse plant species, including not only A. thaliana ( Brassicaceae, 29 members) [ 32 ], but also the forest tree Populus (35 members) [ 33 ]; cereal crops such as rice (31 members) [ 34 ], sorghum (26 members) [ 35 ], maize (31 members) [ 36 ] and wheat (84 members) [ 37 ]; legume crops such as Medicago truncatula (17 members) [ 24 ], chickpea (22 members) and soybean (63 members) [ 38 ]; and some vegetable/fruit crops such as tomato (26 members) and potato (27 members) [ 39 ], cucumber (27 members) [ 40 ] and the diploid Brassica rapa (55 members) [ 41 ].…”