3 Biotech

, 9:453 | Cite as

Genome-wide characterization of the UDP-glycosyltransferase gene family in upland cotton

  • Xianghui Xiao
  • Quanwei Lu
  • Ruixian Liu
  • Juwu Gong
  • Wankui Gong
  • Aiying Liu
  • Qun Ge
  • Junwen Li
  • Haihong Shang
  • Pengtao Li
  • Xiaoying Deng
  • Shaoqi Li
  • Qi Zhang
  • Doudou Niu
  • Quanjia Chen
  • Yuzhen ShiEmail author
  • Hua ZhangEmail author
  • Youlu YuanEmail author
Original Article


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.


Gossypium 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.

Author contributions

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.

Supplementary material

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Supplementary material 4 (XLS 30 kb)


  1. Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS (2009) MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res 37:202–208 (Web Server issue) CrossRefGoogle Scholar
  2. Barvkar VT (2012) Phylogenomic analysis of UDP glycosyltransferase 1 multigene family in Linum usitatissimum identified genes with varied expression patterns. BMC genomics 13(1):175CrossRefGoogle Scholar
  3. Bönisch F, Frotscher J, Stanitzek S, Rühl E, Wüst M, Bitz O, Schwab W (2014) A UDP-Glucose: monoterpenol glucosyltransferase adds to the chemical diversity of the grapevine metabolome. Plant Physiol 165(2):561CrossRefGoogle Scholar
  4. Bowles D, Lim EK, Poppenberger B, Vaistij FE (2006) Glycosyltransferases of lipophilic small molecules. Annurevplant Biol 57(57):567–597Google Scholar
  5. Caputi L, Malnoy M, Goremykin V, Nikiforova S, Martens S (2012) A genome-wide phylogenetic reconstruction of family 1 UDP-glycosyltransferases revealed the expansion of the family during the adaptation of plants to life on land. Plant J 69(6):1030–1042CrossRefGoogle Scholar
  6. Cheng J, Wei G, Zhou H, Gu C, Vimolmangkang S, Liao L, Han Y (2014) Unraveling the mechanism underlying the glycosylation and methylation of anthocyanins in peach. Plant Physiol 166(2):1044–1058CrossRefGoogle Scholar
  7. Gilbert MK, Bland JM, Shockey JM, Cao H, Hinchliffe DJ, Fang DD, Naoumkina M (2013) A transcript profiling approach reveals an abscisic acid-specific glycosyltransferase (UGT73C14) induced in developing fiber of ligon lintless-2 mutant of cotton (Gossypium hirsutum L.). PloS one 8(9):e75268CrossRefGoogle Scholar
  8. Guo AY, Zhu QH, Chen X, Luo JC (2007) GSDS: a gene structure display server. Hereditas 29(8):1023–1026CrossRefGoogle Scholar
  9. Huang C, Nie X, Shen C, You C, Li W, Zhao W, Zhang X, Lin Z (2017) Population structure and genetic basis of the agronomic traits of upland cotton in China revealed by a genome-wide association study using high-density SNPs. Plant Biotechnol J 15(11):1374–1386CrossRefGoogle Scholar
  10. Jones P, Vogt T (2001) Glycosyltransferases in secondary plant metabolism: tranquilizers and stimulant controllers. Planta 213(2):164–174CrossRefGoogle Scholar
  11. Jr SH (1992) Plant metabolism of xenobiotics. Trends Biochem Sci 17(2):82CrossRefGoogle Scholar
  12. Jung KH, An G, Ronald PC (2008) Towards a better bowl of rice: assigning function to tens of thousands of rice genes. Nat Rev Genet 9:91–101CrossRefGoogle Scholar
  13. Krzywinski M, Schein J, Birol İ, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA (2009) Circos: an information aesthetic for comparative genomics. Genome Res 19(9):1639–1645CrossRefGoogle Scholar
  14. Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35(6):1547–1549CrossRefGoogle Scholar
  15. Li Y, Baldauf S, Lim EK, Bowles DJ (2001) Phylogenetic analysis of the UDP-glycosyltransferase multigene family of Arabidopsis thaliana. J Biol Chem 276(6):4338CrossRefGoogle Scholar
  16. Lim EK, Bowles DJ (2004) A class of plant glycosyltransferases involved in cellular homeostasis. EMBO J 23(15):2915CrossRefGoogle Scholar
  17. Lin JS, Huang XX, Li Q, Cao Y, Bao Y, Meng XF, Li YJ, Fu C, Hou BK (2016) UDP-glycosyltransferase 72B1 catalyzes the glucose conjugation of monolignols and is essential for the normal cell wall lignification in Arabidopsis thaliana. Plant J 88(1):26–42CrossRefGoogle Scholar
  18. Liu R, Gong J, Xiao X, Zhang Z, Li J, Liu A, Lu Q, Shang H, Shi Y, Ge Q, Iqbal MS, Deng X, Li S, Pan J, Duan L, Zhang Q, Jiang X, Zou X, Hafeez A, Chen Q, Geng H, Gong W, Yuan Y (2018) GWAS analysis and QTL identification of fiber quality traits and yield components in upland cotton using enriched high-density SNP markers. Front Plant Sci 9:1067. CrossRefPubMedPubMedCentralGoogle Scholar
  19. Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods (San Diego, Calif) 25(4):402–408. CrossRefGoogle Scholar
  20. Lu Q (2017) Fine mapping and candidate gene identification of qFL-12-2 in chromosome introgression line carrying Gossypium barbadense chromosomal segments in Gossypium hirsutum background. PhD. Shanxi Agriculture UniversityGoogle Scholar
  21. Lu Q, Shi Y, Xiao X, Li P, Gong J, Gong W, Liu A, Shang H, Li J, Ge Q (2017) Transcriptome analysis suggests that chromosome introgression fragments from sea Island cotton (Gossypium barbadense) increase fiber strength in upland cotton (Gossypium hirsutum). G3 7(10):3469–3479CrossRefGoogle Scholar
  22. Mackenzie PI, Owens IS, Burchell B, Bock KW, Bairoch A, Bélanger A, Fournelgigleux S, Green M, Hum DW, Iyanagi T (1997) The UDP glycosyltransferase gene superfamily: recommended nomenclature update based on evolutionary divergence. Pharmacogenetics 7(4):255CrossRefGoogle Scholar
  23. Montefiori M, Espley RV, Stevenson D, Cooney J, Datson PM, Saiz A, Atkinson RG, Hellens RP, Allan AC (2011) Identification and characterisation of F3GT1 and F3GGT1, two glycosyltransferases responsible for anthocyanin biosynthesis in red-fleshed kiwifruit (Actinidia chinensis). Plant J 65(1):106–118CrossRefGoogle Scholar
  24. Moon S, Kim SR, Zhao G, Yi J, Yoo Y, Jin P, Lee SW, Jung KH, Zhang D, An G (2013) Rice glycosyltransferase1 encodes a glycosyltransferase essential for pollen wall formation. Plant Physiol 161(2):663–675CrossRefGoogle Scholar
  25. Ono E, Homma Y, Horikawa M, Kunikane-Doi S, Imai H, Takahashi S, Kawai Y, Ishiguro M, Fukui Y, Nakayama T (2010) Functional differentiation of the glycosyltransferases that contribute to the chemical diversity of bioactive flavonol glycosides in grapevines (Vitis vinifera). Plant Cell 22(8):2856–2871CrossRefGoogle Scholar
  26. Paquette S, Møller BL, Bak S (2003) On the origin of family 1 plant glycosyltransferases. Phytochemistry 62(3):399–413CrossRefGoogle Scholar
  27. Paquette SM, Jensen K, Bak S (2009) A web-based resource for the Arabidopsis P450, cytochromes b5, NADPH-cytochrome P450 reductases, and family 1 glycosyltransferases. Phytochemistry 70(17–18):1940–1947CrossRefGoogle Scholar
  28. Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R (2005) InterProScan: protein domains identifier. Nucleic Acids Research 33:W116–W120 (Web Server issue) CrossRefGoogle Scholar
  29. Ren ZY, Yu DQ, Yang ZE, Li CF, Qanmber G, Li Y, Li J, Liu Z, Lu LL, Wang LL (2017) Genome-wide identification of the MIKC-Type MADS-Box gene family in Gossypium hirsutum L. Unravels their roles in flowering. Front. Plant Sci 8:384Google Scholar
  30. Song C, Hong X, Zhao S, Liu J, Schulenburg K, Huang FC, Franz-Oberdorf K, Schwab W (2016a) Glucosylation of 4-Hydroxy-2,5-Dimethyl-3(2H)-Furanone, the key strawberry flavor compound in strawberry fruit. Plant Physiol 171(1):139–151CrossRefGoogle Scholar
  31. Song C, Zhao S, Hong X, Liu J, Schulenburg K, Schwab W (2016b) A UDP-glucosyltransferase functions in both acylphloroglucinol glucoside and anthocyanin biosynthesis in strawberry (Fragaria x ananassa). Plant J Cell Mol Biol 85(6):730–742CrossRefGoogle Scholar
  32. Sturn A, Quackenbush J, Trajanoski Z (2002) Genesis: cluster analysis of microarray data. Bioinformatics 18(1):207–208CrossRefGoogle Scholar
  33. Tan Z, Zhang Z, Sun X, Li Q, Sun Y, Yang P, Wang W, Liu X, Chen C, Liu D (2018) Genetic map construction and fiber quality QTL mapping using the CottonSNP80K array in upland cotton. Front Plant Sci 9:225CrossRefGoogle Scholar
  34. Wu B, Gao L, Gao J, Xu Y, Liu H, Cao X, Zhang B, Chen K (2017) Genome-Wide identification, expression patterns, and functional analysis of UDP glycosyltransferase family in peach (Prunus persica L. Batsch). Front. Plant Sci 8:389Google Scholar
  35. Yauk YK, Ged C, Wang MY, Matich AJ, Tessarotto L, Cooney JM, Chervin C, Atkinson RG (2015) Manipulation of flavour and aroma compound sequestration and release using a glycosyltransferase with specificity for terpene alcohols. Plant J 80(2):317–330CrossRefGoogle Scholar
  36. Yonekura-Sakakibara K, Hanada K (2011) An evolutionary view of functional diversity in family1 glycosyltransferases. Plant J Cell Mol Biol 66(1):182–193CrossRefGoogle Scholar
  37. Yonekurasakakibara K, Fukushima A, Nakabayashi R, Hanada K, Matsuda F, Sugawara S, Inoue E, Kuromori T, Ito T, Shinozaki K (2012) Two glycosyltransferases involved in anthocyanin modification delineated by transcriptome independent component analysis in Arabidopsis thaliana. Plant J 69(1):154–167CrossRefGoogle Scholar
  38. Zhang T, Hu Y, Jiang W, Fang L, Guan X, Chen J, Zhang J, Saski CA, Scheffler BE, Stelly DM (2015) Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement. Nat Biotechnol 33(5):531–537CrossRefGoogle Scholar
  39. Zhang Z, Shang H, Shi Y, Huang L, Li J, Ge Q, Gong J, Liu A, Chen T, Wang D, Wang Y, Palanga KK, Muhammad J, Li W, Lu Q, Deng X, Tan Y, Song W, Cai J, Li P, Rashid H, Gong W, Yuan Y (2016) Construction of a high-density genetic map by specific locus amplified fragment sequencing (SLAF-seq) and its application to Quantitative Trait Loci (QTL) analysis for boll weight in upland cotton (Gossypium hirsutum). BMC Plant Biol 16:79. CrossRefPubMedPubMedCentralGoogle Scholar
  40. Zhang Z, Ge Q, Liu A, Li J, Gong J, Shang H, Shi Y, Chen T, Wang Y, Palanga KK, Muhammad J, Lu Q, Deng X, Tan Y, Liu R, Zou X, Rashid H, Iqbal MS, Gong W, Yuan Y (2017) Construction of a high-density genetic map and its application to qtl identification for fiber strength in upland cotton. Crop Sci 57(2):774. CrossRefGoogle Scholar

Copyright information

© King Abdulaziz City for Science and Technology 2019

Authors and Affiliations

  1. 1.College of AgronomyXinjiang Agricultural UniversityUrumqiChina
  2. 2.State Key Laboratory of Cotton BiologyInstitute of Cotton Research, Chinese Academy of Agricultural SciencesAnyangChina
  3. 3.School of Biotechnology and Food EngineeringAnyang Institute of TechnologyAnyangChina

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