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Comprehensive In Silico Characterization and Expression Pro-Filing of DA1/DAR Family Genes in Brassica rapa.

ABSTRACT: The DA1/DAR family genes have been shown to play important roles in regulating organ size and plant biomass in the model plant Arabidopsis and several crops. However, this family has not been characterized in Brassica rapa (B. rapa). In this study, we identified 17 DA1&DAR genes from B. rapa. Phylogenetic analysis indicated that these genes are classified into four groups. Structural and motif analysis of BrDA1&DARs discovered that the genes within the same group have similar exon-intron structures and share an equal number of conserved motifs except for BrDAR6.3 from group IV, which contains two conserved motifs. Cis-regulatory elements identified four phytohormones (Salicylic acid, Abscisic acid, Gibberellin, and auxin) and three major abiotic (Light, Low temperature, and drought) responsive elements. Further, six br-miRNAs named br-miR164a, br-miR164b, br-miR164c, br-miR164d, br-miRN360, and br-miRN366 were found which target BrDAR6.1, BrDA1.4, and BrDA1.5. BrDA1&DAR genes were highly expressed in stem, root, silique, flower, leaf, and callus tissues. Moreover, qRT-PCR analyses indicated that some of these genes were responsive to abiotic stresses or phytohormone treatments. Our findings provide a foundation for further genetic and physiological studies of BrDA1&DARs in B. rapa.

SUBMITTER: Karamat U

PROVIDER: S-EPMC9498896 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature

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Comprehensive In Silico Characterization and Expression Pro-Filing of DA1/DAR Family Genes in Brassica rapa.

Karamat Umer U Yang Rui R Ren Yuhong Y Lu Yin Y Li Na N Zhao Jianjun J

Genes 20220902 9

The DA1/DAR family genes have been shown to play important roles in regulating organ size and plant biomass in the model plant Arabidopsis and several crops. However, this family has not been characterized in Brassica rapa (B. rapa). In this study, we identified 17 DA1&DAR genes from B. rapa. Phylogenetic analysis indicated that these genes are classified into four groups. Structural and motif analysis of BrDA1&DARs discovered that the gene ...[more]

PMID: 36140744

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Project description: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.

Dataset Information

Comprehensive In Silico Characterization and Expression Pro-Filing of DA1/DAR Family Genes in Brassica rapa.

Publications

Comprehensive In Silico Characterization and Expression Pro-Filing of DA1/DAR Family Genes in <i>Brassica rapa</i>.

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