Genome-wide characterization of the UDP-glycosyltransferase gene family in upland cotton
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Uridine diphosphate (UDP)-glycosyltransferases (UGTs) involved in many metabolic processes are ubiquitous in plants, animals, microorganisms and other organisms and are essential for their growth and development. Upland cotton contains a large number of UGT genes. In this study, we aimed to identify UGT family members in the genome of upland cotton (Gossypium hirsutum L.) and analyze their expression patterns. Bioinformatics methods were used to identify UGT genes from the whole genome of upland cotton (Gossypium hirsutum L. acc. TM-1). Phylogenetic analysis was conducted based on alignment of UGT proteins from upland cotton, and the gene structure, motif and chromosome localization were analyzed for the H subgroup of the UGT family. And the physical and chemical properties and expressions of the genes in the H subgroup of this family were also analyzed. A total of 274 UGT genes were identified from the whole genome of upland cotton and were divided into nine subgroups based on phylogenetic analyses. In subgroup H, 36 genes were distributed on 18 chromosomes. The subfamily genes were simple in the structure, 19 of its members contained two introns, and the others contained only one intron. The qRT-PCR results and transcriptomic data indicated that most of the genes had a wide range of tissue expression characteristics. And the phylogenetic analysis results and expression profiles of these genes revealed tissues and different UGT genes from this crop. Taking RNA-seq, RT-qPCR, and quantitative trait locus (QTL) mapping together, our results suggested that GhUGT6 and GhUGT105 in subgroup H of the GhUGT gene family could be potential candidate genes for cotton yield, and GhUGT16, GhUGT103 might play a vital role in fiber development.
KeywordsGossypium hirsutum L. GhUGT Phylogeny Structure Expression patterns Fiber development
The authors would like to thank Pengyun Chen for assistance in phylogenetic analysis, and synthetic analysis.
YY and HZ conceived and designed the experiments. XX and QL performed the experiments. YS, JG, AL, HS, WG, QG and JL contributed reagents/materials/analysis tools. Resources were provided by PL, XD, SL, QC, QZ, and DN. XX, QL and RL wrote and revised the paper.
This study was funded by the National Natural Science Foundation of China (U1804103, 31101188), the National Key R & D Program for Crop Breeding (2016YFD0100306) and the Agricultural Science and Technology Innovation Program for CAAS (CAAS-ASTIP-ICRCAAS).
Compliance with ethical standards
Conflict of interest
The authors declare that they have no competing interests.
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