Genomic analysis of SBP gene family in Saccharum spontaneum reveals their association with vegetative and reproductive development

Yanhui Liu,Yuan Qin,Xiaoping Niu,Huihuang Chen,Lulu Wang,Mohammad Aslam,Li-Ang Yao,Man Zhang,Youmei Huang

doi:10.1186/s12864-021-08090-3

Yanhui Liu, Yuan Qin + Show 7 more

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https://doi.org/10.1186/s12864-021-08090-3

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Abstract

BackgroundSQUAMOSA promoter binding proteins (SBPs) genes encode a family of plant-specific transcription factors involved in various growth and development processes, including flower and fruit development, leaf initiation, phase transition, and embryonic development. The SBP gene family has been identified and characterized in many species, but no systematic analysis of the SBP gene family has been carried out in sugarcane.ResultsIn the present study, a total of 50 sequences for 30 SBP genes were identified by the genome-wide analysis and designated SsSBP1 to SsSBP30 based on their chromosomal distribution. According to the phylogenetic tree, gene structure and motif features, the SsSBP genes were classified into eight groups (I to VIII). By synteny analysis, 27 homologous gene pairs existed in SsSBP genes, and 37 orthologous gene pairs between sugarcane and sorghum were found. Expression analysis in different tissues, including vegetative and reproductive organs, showed differential expression patterns of SsSBP genes, indicating their functional diversity in the various developmental processes. Additionally, 22 SsSBP genes were predicted as the potential targets of miR156. The differential expression pattern of miR156 exhibited a negative correlation of transcription levels between miR156 and the SsSBP gene in different tissues.ConclusionsThe sugarcane genome possesses 30 SsSBP genes, and they shared similar gene structures and motif features in their subfamily. Based on the transcriptional and qRT-PCR analysis, most SsSBP genes were found to regulate the leaf initial and female reproductive development. The present study comprehensively and systematically analyzed SBP genes in sugarcane and provided a foundation for further studies on the functional characteristics of SsSBP genes during different development processes.

Highlights

SQUAMOSA promoter binding proteins (SBPs) genes encode a family of plant-specific transcription factors involved in various growth and development processes, including flower and fruit development, leaf initiation, phase transition, and embryonic development
Identification and characterization of SBP genes in S. spontaneum To identify of SBP genes in sugarcane, the HMM profile of the SBP domain was used as a query to search the sugarcane genome database and BLASTP program
The alignment results showed that all SsSBP proteins contained the complete SBP domain and possessed the typical characteristics of SBP domain with two Zinc motifs (Zn1 and Zn2) and one nuclear localization signal (NLS) (Fig. 1)

Summary

Introduction

SQUAMOSA promoter binding proteins (SBPs) genes encode a family of plant-specific transcription factors involved in various growth and development processes, including flower and fruit development, leaf initiation, phase transition, and embryonic development. The SQUAMOSA promoter binding (like) proteins (SBPs/SPLs) represent a major family of plant-specific transcription factors. SPL8 and other SPL genes influence gynoecium patterning through mediating auxin homeostasis [17] In monocot plants, such as rice and maize, SBP genes are reported to modulate essential developmental processes. SBP proteins encoding genes, unbranched and unbranched, affect plant architecture and yield traits by regulating the lateral primordia initiation [21]

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