The auxin response factor gene family in allopolyploid Brassica napus

PLoS One. 2019 Apr 8;14(4):e0214885. doi: 10.1371/journal.pone.0214885. eCollection 2019.

Abstract

Auxin response factor (ARF) is a member of the plant-specific B3 DNA binding superfamily. Here, we report the results of a comprehensive analysis of ARF genes in allotetraploid Brassica napus (2n = 38, AACC). Sixty-seven ARF genes were identified in B. napus (BnARFs) and divided into four subfamilies (I-IV). Sixty-one BnARFs were distributed on all chromosomes except C02; the remaining were on Ann and Cnn. The full length of the BnARF proteins was highly conserved especially within each subfamily with all members sharing the N-terminal DNA binding domain (DBD) and the middle region (MR), and most contained the C-terminal dimerization domain (PBI). Twenty-one members had a glutamine-rich MR that may be an activator and the remaining were repressors. Accordingly, the intron patterns are highly conserved in each subfamily or clade, especially in DBD and PBI domains. Several members in subfamily III are potential targets for miR167. Many putative cis-elements involved in phytohormones, light signaling responses, and biotic and abiotic stress were identified in BnARF promoters, implying their possible roles. Most ARF proteins are likely to interact with auxin/indole-3-acetic acid (Aux/IAA) -related proteins, and members from different subfamilies generally shared many common interaction proteins. Whole genome-wide duplication (WGD) by hybridization between Brassica rapa and Brassica oleracea and segmental duplication led to gene expansion. Gene loss following WGD is biased with the An-subgenome retaining more ancestral genes than the Cn-subgenome. BnARFs have wide expression profiles across vegetative and reproductive organs during different developmental stages. No obvious expression bias was observed between An- and Cn-subgenomes. Most synteny-pair genes had similar expression patterns, indicating their functional redundancy. BnARFs were sensitive to exogenous IAA and 6-BA treatments especially subfamily III. The present study provides insights into the distribution, phylogeny, and evolution of ARF gene family.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Brassica / genetics
  • Brassica napus / genetics*
  • Brassica napus / growth & development
  • Brassica napus / metabolism
  • Chromosome Mapping
  • Evolution, Molecular
  • Gene Expression Regulation, Developmental
  • Gene Expression Regulation, Plant
  • Genes, Plant
  • Indoleacetic Acids / metabolism
  • Introns
  • Multigene Family
  • Phylogeny
  • Plant Proteins / chemistry
  • Plant Proteins / genetics
  • Plant Proteins / metabolism
  • Polyploidy
  • Promoter Regions, Genetic
  • Protein Interaction Maps
  • Sequence Homology, Amino Acid
  • Transcription Factors / chemistry
  • Transcription Factors / genetics
  • Transcription Factors / metabolism

Substances

  • Indoleacetic Acids
  • Plant Proteins
  • Transcription Factors

Grants and funding

This work was supported by the National Natural Science Foundation of China (31671727 and 31471528), the “111” Project of China (B12006), and the National Basic Research Program of China (973 Program; 2015CB150201).