Phytochrome-interacting factor (PIF) in rapeseed (Brassica napus L.): Genome-wide identification, evolution and expression analyses during abiotic stress, light quality and vernalization

Wenqian Li; Yan Liu; Weiping Wang; Juncen Liu; Mingyao Yao; Mei Guan; Chunyun Guan; Xin He

doi:10.1016/j.ijbiomac.2021.03.055

Phytochrome-interacting factor (PIF) in rapeseed (Brassica napus L.): Genome-wide identification, evolution and expression analyses during abiotic stress, light quality and vernalization

Int J Biol Macromol. 2021 Jun 1:180:14-27. doi: 10.1016/j.ijbiomac.2021.03.055. Epub 2021 Mar 13.

Authors

Wenqian Li¹, Yan Liu¹, Weiping Wang¹, Juncen Liu¹, Mingyao Yao¹, Mei Guan², Chunyun Guan³, Xin He⁴

Affiliations

¹ Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, Hunan 410128, China.
² Oil Crops Research, Hunan Agricultural University, Changsha, Hunan 410128, China; Hunan Branch of National Oilseed Crops Improvement Center, Changsha, Hunan 410128, China.
³ Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, Hunan 410128, China; Oil Crops Research, Hunan Agricultural University, Changsha, Hunan 410128, China; Hunan Branch of National Oilseed Crops Improvement Center, Changsha, Hunan 410128, China.
⁴ Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, Hunan 410128, China; Oil Crops Research, Hunan Agricultural University, Changsha, Hunan 410128, China; Hunan Branch of National Oilseed Crops Improvement Center, Changsha, Hunan 410128, China. Electronic address: hexinzhsh@126.com.

PMID: 33722620
DOI: 10.1016/j.ijbiomac.2021.03.055

Abstract

Phytochrome-interacting factors (PIFs) are members of basic helix-loop-helix (bHLH) transcription factors and the primary partners of phytochromes (PHY) in light signaling. PIFs interact with the P_fr forms of phytochrome to play an important role in the pathways of response to light and temperature in plants. In this study, 30, 12, and 16 potential PIF genes were identified in Brassica napus, Brassica rapa, Brassica oleracea, respectively, which could be divided into three subgroups. The Br/Bo/BnaPIF genes are intron-rich and similar to the PIF genes in Arabidopsis. However, unlike the AtPIFs that exist in multiple alternative-splicing forms, the majority of Br/Bo/BnaPIF genes have no alternative-splicing forms. A total of 52 Br/Bo/BnaPIF proteins have both the conserved active PHYB binding (APB) and bHLH domains. The Ka/Ks ratio revealed that most BnaPIFs underwent purifying selection. A promoter analysis found that light-related, abscisic acid-related and MYB-binding sites were the most abundant in the promoters of BnaPIFs. BnaPIF genes displayed different spatiotemporal patterns of expression and were regulated by light quality, circadian rhythms, cold, heat, and vernalization. Our results are useful for understanding the biological functions of PIF proteins in rapeseed.

Keywords: Cold; Heat; Phytochrome-interacting factors; Rapeseed; Vernalization.

MeSH terms

Basic Helix-Loop-Helix Transcription Factors / genetics*
Basic Helix-Loop-Helix Transcription Factors / metabolism
Binding Sites
Brassica napus / genetics*
Brassica napus / metabolism*
Brassica rapa / genetics*
Brassica rapa / metabolism*
Gene Expression Regulation, Plant / radiation effects
Genes, Plant
Light*
Phylogeny*
Phytochrome / metabolism
Plant Proteins / genetics*
Plant Proteins / metabolism
Promoter Regions, Genetic
Protein Binding
Signal Transduction / genetics
Stress, Physiological / genetics*
Synteny
Transcriptome / radiation effects

Substances

Basic Helix-Loop-Helix Transcription Factors
Plant Proteins
Phytochrome