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

Umer Karamat; Rui Yang; Yuhong Ren; Yin Lu; Na Li; Jianjun Zhao

doi:10.3390/genes13091577

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

Genes (Basel). 2022 Sep 2;13(9):1577. doi: 10.3390/genes13091577.

Authors

Umer Karamat¹, Rui Yang¹, Yuhong Ren¹, Yin Lu¹, Na Li¹, Jianjun Zhao¹

Affiliation

¹ State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding 071000, China.

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.

Keywords: Brassica rapa; DA1&DAR family genes; expression profiling; genome-wide.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Abscisic Acid / metabolism
Arabidopsis* / genetics
Brassica rapa* / genetics
Brassica rapa* / metabolism
Filing
Gene Expression Profiling
Gene Expression Regulation, Plant
Genome, Plant
Gibberellins / metabolism
Indoleacetic Acids / metabolism
MicroRNAs* / genetics
MicroRNAs* / metabolism
Phylogeny
Plant Growth Regulators / genetics
Plant Growth Regulators / metabolism
Salicylic Acid / metabolism

Substances

Gibberellins
Indoleacetic Acids
MicroRNAs
Plant Growth Regulators
Abscisic Acid
Salicylic Acid

Grants and funding

This work was supported by the findings from the National Natural Science Foundation of China (32172594), Hebei Provincial Department of Human Resources and Social Security (C20210363), Hebei Provincial Department of Science and Technology (216Z2904G, 21326344D), and the Natural Science Foundation of Hebei Province (C2020204111).