Comprehensive Identification and Expression Analysis of the Members of the B-Box Gene Family of Cotton Involved in Flower bud Differentiation and Responses to Multiple Stresses

Background: B-BOX (BBX) proteins are zinc-finger transcription factors with one or two BBX domains and sometimes a CCT domain. These proteins play an essential role in regulating plant growth and development, as well as in resisting abiotic stress. So far, the BBX gene family has been widely studied in other crops. However, no one has systematically studied the BBX gene in cotton. Results: In the present study, 17, 18, 37 and 33 BBX genes were detected in Gossypium arboreum, G. raimondii, G. hirsutum and G. barbadense, respectively, via genome-wide identification. Phylogenetic analysis showed that all BBX genes were divided into 5 main categories. The protein motifs and exon/intron structures indicated that each group of BBX genes was highly conserved. Collinearity analysis revealed that the amplification of BBX gene family in Gossypium spp. was mainly through segmental replication. Nonsynonymous (Ka)/ synonymous (Ks) substitution ratios indicated that the BBX gene family had undergone purification selection throughout the long-term natural selection process. Moreover, transcriptomic data showed that some GhBBX genes were highly expressed in floral organs. Transcriptome data analysis and qRT-PCR verification showed that different GhBBX genes had different biological functions in flower bud differentiation, abiotic stress and stress response. Conclusions: Our comprehensive analysis of BBX in G. hirsutum provides a basis for further study on the molecular role of GhBBXs in regulating flowering and cotton resistance to abiotic stress.