Genome-wide identification, phylogeny, and expression analysis of GRF transcription factors in pineapple (Ananas comosus)

Wen Yi; Aiping Luan; Chaoyang Liu; Jing Wu; Wei Zhang; Ziqin Zhong; Zhengpeng Wang; Mingzhe Yang; Chengjie Chen; Yehua He

doi:10.3389/fpls.2023.1159223

Genome-wide identification, phylogeny, and expression analysis of GRF transcription factors in pineapple (Ananas comosus)

Front Plant Sci. 2023 Apr 14:14:1159223. doi: 10.3389/fpls.2023.1159223. eCollection 2023.

Authors

Affiliations

¹ Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Areas, College of Horticulture, South China Agricultural University, Guangzhou, China.
² Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.

Abstract

Background: Pineapple is the only commercially grown fruit crop in the Bromeliaceae family and has significant agricultural, industrial, economic, and ornamental value. GRF (growth-regulating factor) proteins are important transcription factors that have evolved in seed plants (embryophytes). They contain two conserved domains, QLQ (Gln, Leu, Gln) and WRC (Trp, Arg, Cys), and regulate multiple aspects of plant growth and stress response, including floral organ development, leaf growth, and hormone responses. The GRF family has been characterized in a number of plant species, but little is known about this family in pineapple and other bromeliads.

Main discoveries: We identified eight GRF transcription factor genes in pineapple, and phylogenetic analysis placed them into five subfamilies (I, III, IV, V, VI). Segmental duplication appeared to be the major contributor to expansion of the AcGRF family, and the family has undergone strong purifying selection during evolution. Relative to that of other gene families, the gene structure of the GRF family showed less conservation. Analysis of promoter cis-elements suggested that AcGRF genes are widely involved in plant growth and development. Transcriptome data and qRT-PCR results showed that, with the exception of AcGRF5, the AcGRFs were preferentially expressed in the early stage of floral organ development and AcGRF2 was strongly expressed in ovules. Gibberellin treatment significantly induced AcGRF7/8 expression, suggesting that these two genes may be involved in the molecular regulatory pathway by which gibberellin promotes pineapple fruit expansion.

Conclusion: AcGRF proteins appear to play a role in the regulation of floral organ development and the response to gibberellin. The information reported here provides a foundation for further study of the functions of AcGRF genes and the traits they regulate.

Keywords: GRF gene family; expression analysis; flower organ; phylogeny analysis; pineapple.

Grants and funding

This research was funded by the National Natural Science Foundation of China(32272677, 31901355), Special Project of Rural Revitalization Strategy in Guangdong Province(2022-NPY-00-031), the National Key R&D Program of China (2018YFD1000500).