Abstract

BackgroundSugarcane (Saccharum) is the most critical sugar crop worldwide. As one of the most enriched transcription factor families in plants, MYB genes display a great potential to contribute to sugarcane improvement by trait modification. We have identified the sugarcane MYB gene family at a whole-genome level through systematic evolution analyses and expression profiling. R2R3-MYB is a large subfamily involved in many plant-specific processes.ResultsA total of 202 R2R3-MYB genes (356 alleles) were identified in the polyploid Saccharum spontaneum genomic sequence and classified into 15 subgroups by phylogenetic analysis. The sugarcane MYB family had more members by a comparative analysis in sorghum and significant advantages among most plants, especially grasses. Collinearity analysis revealed that 70% of the SsR2R3-MYB genes had experienced duplication events, logically suggesting the contributors to the MYB gene family expansion. Functional characterization was performed to identify 56 SsR2R3-MYB genes involved in various plant bioprocesses with expression profiling analysis on 60 RNA-seq databases. We identified 22 MYB genes specifically expressed in the stem, of which RT-qPCR validated MYB43, MYB53, MYB65, MYB78, and MYB99. Allelic expression dominance analysis implied the differential expression of alleles might be responsible for the high expression of MYB in the stem. MYB169, MYB181, MYB192 were identified as candidate C4 photosynthetic regulators by C4 expression pattern and robust circadian oscillations. Furthermore, stress expression analysis showed that MYB36, MYB48, MYB54, MYB61 actively responded to drought treatment; 19 and 10 MYB genes were involved in response to the sugarcane pokkah boeng and mosaic disease, respectively.ConclusionsThis is the first report on genome-wide analysis of the MYB gene family in sugarcane. SsMYBs probably played an essential role in stem development and the adaptation of various stress conditions. The results will provide detailed insights and rich resources to understand the functional diversity of MYB transcription factors and facilitate the breeding of essential traits in sugarcane.

Highlights

  • Sugarcane (Saccharum) is the most critical sugar crop worldwide

  • Yuan et al BMC Genomics (2021) 22:622. This is the first report on genome-wide analysis of the MYB gene family in sugarcane

  • The results will provide detailed insights and rich resources to understand the functional diversity of MYB transcription factors and facilitate the breeding of essential traits in sugarcane

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Summary

Introduction

Sugarcane (Saccharum) is the most critical sugar crop worldwide. As one of the most enriched transcription factor families in plants, MYB genes display a great potential to contribute to sugarcane improvement by trait modification. We have identified the sugarcane MYB gene family at a whole-genome level through systematic evolution analyses and expression profiling. Modern cultivated sugarcane (Saccharum spp.) is the primary source of sugar for the world. Saccharum spontaneum contributes to 10– 15% chromosomes in modern sugarcane cultivars, endowing the characteristics such as disease resistance and ratooning capacity [2]. The genome of haploid S. spontaneum has been assembled to the chromosome level and used as the reference genome of sugarcane [3]. Because of the development of multiple transcriptome models in recent times, including those for different tissues, developmental stages, and under various stress treatments, massive RNA-seq data are available, which can provide detailed insights and rich resources for studying sugarcane genes functions

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