Identification, Structural Analysis, and Expression Profile of Genes Related to Starch Metabolism in Cassava (Manihot esculenta Crantz)

Date Received: Jun 15, 2019

Date Published: Aug 30, 2019

DOI: https://doi.org/10.31817/vjas.2019.2.2.02

Views

2420

Download

437

How to Cite:

Ha, C. D., Loc, N., Uyen, L. T., Thu, P., & Thu, P. T. (2019). Identification, Structural Analysis, and Expression Profile of Genes Related to Starch Metabolism in Cassava (Manihot esculenta Crantz). Vietnam Journal of Agricultural Sciences, 2(2), 370–375. https://doi.org/10.31817/vjas.2019.2.2.02

Identification, Structural Analysis, and Expression Profile of Genes Related to Starch Metabolism in Cassava (Manihot esculenta Crantz)

Chu Duc Ha (*) 1 , Nguyen Van Loc 2 , Lai Thi Uyen 1, 3 , Pham Phuong Thu 4   , Pham Thi Ly Thu 1

  • Corresponding author: nvloc@vnua.edu.vn
  • 1 Agricultural Genetics Institute, Vietnam Academy of Agricultural Sciences, Hanoi 129810, Vietnam
  • 2 VNUA
  • 3 Faculty of Agronomy, Vietnam National University of Agriculture, Hanoi 131000, Vietnam
  • 4 Faculty of Biology-Agricultural Technology, Hanoi Pedagogical University 2, Vinh Phuc 283460, Vietnam

    • Keywords

    Starch metabolism, identification, gene family, UGPase, bioinformatics, cassava

    Abstract


    Starch metabolism is known to be an important pathway in the growth and development of plants. This study was conducted to investigate the genome-wide identification and structural analysis of genes encoding uridine diphosphate glucose pyrophosphorylase (UGPase), a key enzyme in starch synthesis in cassava, and to analyze the expression profiles of these genes based on publicly available RNA-seq data. A total of 11 members were found in the UGPase gene family (MeUGP) in cassava. Ten of the MeUGP genes were successfully mapped onto the chromosomes of the current cassava genome assembly. Based on their nucleotide sequences, the lengths of the genomic DNA sequences of the MeUGP genes ranged from 3,200 to 11,601bp, while the size of the coding sequence (CDS) varied from 831 to 3,654bp. According to the recent RNA-seq data, we found that a majority of the MeUGP genes were expressed in at least 1 tissue under normal conditions. Interestingly, MeUGP4 was greatly expressed in the shoot apical meristem, while MeUGP10 was more specific in the root apical meristem. The expression profiles of these MeUGP genes should be carried out in various conditions in further studies.

    References

    Awoleye F., van Duren M., Dolezel J. & Novak F. J. (1994). Nuclear DNA content and in vitro induced somatic polyploidization cassava (Manihot esculenta Crantz) breeding. Euphytica. 76(3): 195-202.

    Bredeson J. V., Lyons J. B., Prochnik S. E., Wu G. A., Ha C. M., Edsinger-Gonzales E., Grimwood J., Schmutz J., Rabbi I. Y., Egesi C., Nauluvula P., Lebot V., Ndunguru J., Mkamilo G., Bart R. S., Setter T. L., Gleadow R. M., Kulakow P., Ferguson M. E., Rounsley S. & Rokhsar D. S. (2016). Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity. Nature Biotechnology. 34(5): 562-570.

    Ceballos H., Iglesias C. A., Pérez J. C. & Dixon A. G. O. (2004). Cassava breeding: Opportunities and challenges. Plant Molecular Biology. 56(4): 503-516.

    Chen X., Xia J., Xia Z., Zhang H., Zeng C., Lu C., Zhang W. & Wang W. (2015). Potential functions of microRNAs in starch metabolism and development revealed by miRNA transcriptome profiling of cassava cultivars and their wild progenitor. BMC Plant Biology. 15(1): 33.

    Cutting W. A. (1978). Cassava - A valuable food but a possible poison. Tropical Doctor. 8(3): 102-103.

    Ha C. D., Dung T. L., Huyen T. T. & Thu L. P. (2017). Evolutionary analysis and expression profiling of the sweet sugar transporter gene family in cassava (Manihot esculenta Crantz). The Journal of Science of Hanoi National University of Education. 62(10): 91-99 (in Vietnamese).

    Emanuel B. S. and Shaikh T. H. (2001). Segmental duplications: an 'expanding' role in genomic instability and disease. Nature Reviews Genetics. 2(10): 791-800.

    Finn R. D., Coggill P., Eberhardt R. Y., Eddy S. R., Mistry J., Mitchell A. L., Potter S. C., Punta M., Qureshi M., Sangrador-Vegas A., Salazar G. A., Tate J. & Bateman A. (2016). The Pfam protein families database: Towards a more sustainable future. Nucleic Acids Research. 44(D1): D279-D285.

    Goodstein D. M., Shu S., Howson R., Neupane R., Hayes R. D., Fazo J., Mitros T., Dirks W., Hellsten U., Putnam N. & Rokhsar D. S. (2012). Phytozome: A comparative platform for green plant genomics. Nucleic Acids Research. 40(Database issue): D1178-D1186.

    Gorlova O., Fedorov A., Logothetis C., Amos C. & Gorlov I. (2014). Genes with a large intronic burden show greater evolutionary conservation on the protein level. BMC Evolutionary Biology. 14(1): 50.

    Hall T. A. (1999). BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series. 41: 95-98.

    Hu B., Jin J., Guo A. Y., Zhang H., Luo J. & Gao G. (2015). GSDS 2.0: An upgraded gene feature visualization server. Bioinformatics. 31(8): 1296-1297.

    Kumar S., Stecher G. & Tamura K. (2016). MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution. 33(7): 1870-1874.

    Li Y. Z., Zhao J. Y., Wu S. M., Fan X. W., Luo X. L. & Chen B. S. (2016). Characters related to higher starch accumulation in cassava storage roots. Scientific Reports. 6: 19823.

    Saithong T., Rongsirikul O., Kalapanulak S., Chiewchankaset P., Siriwat W., Netrphan S., Suksangpanomrung M., Meechai A. & Cheevadhanarak S. (2013). Starch biosynthesis in cassava: a genome-based pathway reconstruction and its exploitation in data integration. BMC System Biology. 7: 75.

    Van Harsselaar J. K., Lorenz J., Senning M., Sonnewald U. & Sonnewald S. (2017). Genome-wide analysis of starch metabolism genes in potato (Solanum tuberosum L.). BMC Genomics. 18(1): 37.

    Wang X., Chang L., Tong Z., Wang D., Yin Q., Wang D., Jin X., Yang Q., Wang L., Sun Y., Huang Q., Guo A. & Peng M. (2016). Proteomics profiling reveals carbohydrate metabolic enzymes and 14-3-3 proteins play important roles for starch accumulation during cassava root tuberization. Scientific Reports. 6: 19643.

    Wilson M. C., Mutka A. M., Hummel A. W., Berry J., Chauhan R. D., Vijayaraghavan A., Taylor N. J., Voytas D. F., Chitwood D. H. & Bart R. S. (2017). Gene expression atlas for the food security crop cassava. New Phytologist. 213(4): 1632-1641.