Skip to main content
Log in

Genome-Wide Identification and Expression Profiling of Starch-Biosynthetic Genes in Common Wheat

  • PLANT GENETICS
  • Published:
Russian Journal of Genetics Aims and scope Submit manuscript

Abstract

Starch is synthesized through coordinated interactions of a suite of biosynthetic enzymes, including ADP-glucose pyrophosphorylases (TaAGP), granule-bound starch synthases (TaGBSS), starch synthases (TaSS), starch branching enzymes (TaSBE), and starch degradation enzymes (TaDBE). The genes involved in starch biosynthesis have not been extensively studied in common wheat. In an effort to isolate the sequences of genes responsible for starch biosynthesis in common wheat, we identified 57 genes. These genes included two types of TaAGPL located on wheat homoeologous groups 1 and 5; two types of TaAGPS located on groups 5 and 7; TaGBSSI located on chromosomes 4A, 7A, and 7D; TaGBSSII located on group 2; two types of TaISA located on groups 5 and 7; TaPUL located on group 7; three types of TaSBE located on groups 2 and 7; TaSSI located on group 7; TaSSII-1 located on group 1; TaSSII-2 located on group 6; TaSSII-3 located on group 7; TaSSIII-1 located on group 2; TaSSIII-2 located on group 1; and TaSSIV located on group 1. Wheat group 7 had the largest number of these genes. Phylogenetic analysis indicated that common wheat was closely related to Brachypodium, but relatively distant from rice and Sorghum. In silico expression-analysis in different tissues revealed that most of the genes were highly expressed in reproductive tissues, but expression was relatively low in all other tissues. Twelve genes (TaGBSSII-2, TaISA-5, TaSBE-2.1 and TaISA-7) were up-regulated after drought stress for 6 h, and only six genes (TaPUL-7 and TaISA-7) were up-regulated after heat stress for 6 h. This information will be useful for genetic manipulation of starch-biosynthesis genes to develop improved cultivars with high yield and good quality.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1.
Fig. 2.
Fig. 3.
Fig. 4.
Fig. 5.

Similar content being viewed by others

REFERENCES

  1. Stamova, B.S., Laudenciachingcuanco, D., and Beckles, D.M., Transcriptomic analysis of starch biosynthesis in the developing grain of hexaploid wheat, Int. J. Plant Genomics, 2009. https://doi.org/10.1155/2009/407426

  2. Kim, W., Johnson, J.W., Graybosch, R.A., and Gaines, C.S., Physicochemical properties and end-use quality of wheat starch as a function of waxy protein alleles, J. Cereal Sci., 2003, vol. 37, no. 2, pp. 195—204.

    Article  CAS  Google Scholar 

  3. Rasheed, A., Xia, X., Yan, Y., Appels, R., Mahmood, T., and He, Z., Wheat seed storage proteins: advances in molecular genetics, diversity and breeding applications, J. Cereal Sci., 2014, vol. 60, no. 1, pp. 11—24.

    Article  CAS  Google Scholar 

  4. Godfray, H.C.J., Beddington, J.R., Crute, I.R., Haddad, L., Lawrence, D., Muir, J.F., Pretty, J., Robinson, S., Thomas, S.M., and Toulmin, C., Food security: the challenge of feeding 9 billion people, Science, 2010, vol. 327, no. 5967, p. 812.

    Article  CAS  Google Scholar 

  5. Tetlow, I.J., Understanding storage starch biosynthesis in plants: a means to quality improvement, Can. J. Bot., 2006, vol. 84, no. 8, pp. 1167—1185.

    Article  CAS  Google Scholar 

  6. Tian, Z.X., Qian, Q., Liu, Q.Q., Yan, M.X., Liu, X.F., Yan, C.J., Liu, G.F., Gao, Z.Y., Tang, S.Z., and Zeng, D., Allelic diversities in rice starch biosynthesis lead to a diverse array of rice eating and cooking qualities, Proc. Natl. Acad. Sci. U.S.A., 2009, vol. 106, no. 51, pp. 21760—21765.

    Article  CAS  Google Scholar 

  7. Sehnke, P.C., Chung, H.J., Wu, K., and Ferl, R.J., Regulation of starch accumulation by granule-associated plant 14-3-3 proteins, Proc. Natl. Acad. Sci. U.S.A., 2001, vol. 98, no. 2, pp. 765—770.

    Article  CAS  Google Scholar 

  8. Guo, J., Dai, S., Li, H., Liu, A., Liu, C., Cheng, D., Cao, X., Chu, X., Zhai, S., Liu, J., Zhao, Z., and Song, J., Identification and expression analysis of wheat TaGF14 genes, Front. Genet., 2018, vol. 9, p. 12.

    Article  Google Scholar 

  9. Blum, A., Sinmena, B., Mayer, J., Golan, G., and Shpiler, L., Stem reserve mobilisation supports wheat-grain filling under heat stress, Funct. Plant Biol., 1994, vol. 21, no. 6, pp. 771—781.

    Article  Google Scholar 

  10. Shah, N.H. and Paulsen, G.M., Interaction of drought and high temperature on photosynthesis and grain-filling of wheat, Plant Soil, 2003, vol. 257, no. 1, pp. 219—226.

    Article  CAS  Google Scholar 

  11. International Wheat Genome Sequencing Consortium (IWGSC), A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome, Science, 2014, vol. 345, p. 1251788.

    Article  Google Scholar 

  12. Marcussen, T., Sandve, S. R., Heier, L., Spannagl, M., Pfeifer, M., Jakobsen, K.S., Wulff, B.B. H., Steuernagel, B., Mayer, K.F.X., and Olsen, O.A., Ancient hybridizations among the ancestral genomes of bread wheat, Science, 2014, vol. 345, no. 6194, p. 1250092.

    Article  Google Scholar 

  13. Keeble-Gagnère, G., Rigault, P., Tibbits, J., Pasam, R., Hayden, M., Forrest, K., Frenkel, Z., and Korol, A., Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome, BioRxiv, 2018, vol. 19, p. 112.

    Google Scholar 

  14. Goff, S.A., Ricke, D., Lan, T.H., Presting, G., Wang, R., Dunn, M., Glazebrook, J., Sessions, A., Oeller, P., and Varma, H., A draft sequence of the rice genome (Oryza sativa L. ssp. japonica), Science, 2002, vol. 296, no. 5565, pp. 92—100.

    Article  CAS  Google Scholar 

  15. Pearce, S., Vazquezgross, H., Herin, S.Y., Hane, D., Wang, Y., Gu, Y. Q., and Dubcovsky, J., WheatExp: an RNA-seq expression database for polyploid wheat, BMC Plant Biol., 2015, vol. 15, no. 1, p. 299.

    Article  Google Scholar 

  16. Borrill, P., Ramirez-Gonzalez, R., and Uauy, C., e-xpVIP: a customisable RNA-seq data analysis and visualisation platform opens up gene expression analysis, Plant Physiol., 2016, vol. 170, no. 4, p. 2172.

    Article  CAS  Google Scholar 

  17. Tamura, K., Stecher, G., Peterson, D., Filipski, A., and Kumar, S., MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0, Mol. Biol. Evol., 2013, vol. 30, pp. 2725—2729.

    Article  CAS  Google Scholar 

  18. Miura, H., Tanii, S., Nakamura, T., and Watanabe, N., Genetic control of amylose content in wheat endosperm starch and differential effects of three Wx genes, Theor. Appl. Genet., 1994, vol. 89, no. 2, pp. 276—280.

    Article  CAS  Google Scholar 

  19. Scoles, G.J., Gill, B.S., Xin, Z.Y., Clarke, B.C., Mcintyre, C.L., Chapman, C., and Appels, R., Frequent duplication and deletion events in the 5S RNA genes and the associated spacer regions of the Triticeae, Plant Syst. Evol., 1988, vol. 160, no. 1, pp. 105—122.

    Article  CAS  Google Scholar 

  20. Tan, C.T. and Yan, L., Duplicated, deleted and translocated VRN2 genes in hexaploid wheat, Euphytica, 2016, vol. 208, pp. 277—284.

    Article  CAS  Google Scholar 

  21. Huo, N., Dong, L., Zhang, S., Wang, Y., Zhu, T., Mohr, T., Altenbach, S., Liu, Z., Dvorak, J., and Anderson, O.D., New insights into structural organization and gene duplication in a 1.75-Mb genomic region harboring the α-gliadin gene family in Aegilops tauschii, the source of wheat D genome, Plant J., 2017, vol. 92, no. 92, p. 13675.

    Article  Google Scholar 

  22. Sun, H., Lü, J., Fan, Y., Zhao, Y., Kong, F., Li, R., Wang, H., and Li, S., Quantitative trait loci (QTLs) for quality traits related to protein and starch in wheat, Prog. Nat. Sci.: Mater. Int., 2008, vol. 18, no. 7, pp. 825—831.

    Article  CAS  Google Scholar 

  23. Feng, N., He, Z., Zhang, Y., Xia, X., and Zhang, Y., QTL mapping of starch granule size in common wheat using recombinant inbred lines derived from a PH82-2/Neixiang 188 cross, Crop J., 2013, vol. 1, no. 2, pp. 166—171.

    Article  Google Scholar 

  24. Stone, P.J., Nicolas, M.E., Stone, P.J., and Nicolas, M.E., Wheat cultivars vary widely in their responses of grain yield and quality to short periods of post-anthesis heat stress, Funct. Plant Biol., 1994, vol. 21, no. 6, pp. 887—900.

    Article  Google Scholar 

  25. Fasahat, P., Rahman, S., and Ratnam, W., Genetic controls on starch amylose content in wheat and rice grains, J. Genet., 2014, vol. 93, no. 1, pp. 279—292.

    Article  CAS  Google Scholar 

  26. Nakamura, T., Yamamori, M., Hirano, H., Hidaka, S., and Nagamine, T., Production of waxy (amylose-free) wheats, Mol. Gen. Genet., 1995, vol. 248, no. 3, pp. 253—259.

    Article  CAS  Google Scholar 

  27. Slade, A.J., Fuerstenberg, S.I., Loeffler, D., Steine, M.N., and Facciotti, D., A reverse genetic, nontransgenic approach to wheat crop improvement by TILLING. Nat. Biotechnol., 2005, vol. 23, no. 1, pp. 75—81.

    Article  CAS  Google Scholar 

  28. Hazard, B., Zhang, X., Colasuonno, P., Uauy, C., Beckles, D.M., and Dubcovsky, J., Induced mutations in the starch branching enzyme II (SBEII) genes increase amylose and resistant starch content in durum wheat, Crop Sci., 2012, vol. 52, no. 4, pp. 1754—1766.

    CAS  PubMed  PubMed Central  Google Scholar 

  29. Araki, E., Miura, H., and Sawada, S., Identification of genetic loci affecting amylose content and agronomic traits on chromosome 4A of wheat, Theor. Appl. Genet., 1999, vol. 98, nos. 6—7, pp. 977—984.

    Article  CAS  Google Scholar 

  30. Hogg, A.C., Martin, J.M., Manthey, F.A., and Giroux, M.J., Nutritional and quality traits of pasta made from SSIIa null high-amylose durum wheat, Cereal Chem., 2015, vol. 92, no. 4, pp. 395—400.

    Article  CAS  Google Scholar 

  31. Schönhofen, A., Zhang, X., and Dubcovsky, J., Combined mutations in five wheat STARCH BRANCHING ENZYME II genes improve resistant starch but affect grain yield and bread-making quality, J. Cereal Sci., 2017, vol. 75, pp. 165—174.

    Article  Google Scholar 

  32. Avni, R., Nave, M., Barad, O., Baruch, K., Twardziok, S.O., Gundlach, H., Hale, I., Mascher, M., Spannagl, M., and Wiebe, K., Wild emmer genome architecture and diversity elucidate wheat evolution and domestication, Science, 2017, vol. 357, no. 6346, p. 93.

    Article  CAS  Google Scholar 

  33. LLuo, M.C., Gu, Y.Q., Puiu, D., Wang, H., Twardziok, S.O., Deal, K.R., Huo, N., Zhu, T., Wang, L., and Wang, Y., Genome sequence of the progenitor of the wheat D genome Aegilops tauschii, Nature, 2017, vol. 551, no. 7681, p. 498.

    Article  Google Scholar 

  34. Tseng, E., Underwood, J.G., and Tseng, E., Full length cDNA sequencing on the PacBio® RS, J. Biomol. Tech., 2013, vol. 24, p. S45.

    PubMed Central  Google Scholar 

  35. Knecht, A.C., Campbell, M.T., Caprez, A., Swanson, D.R., and Walia, H., Image harvest: an open-source platform for high-throughput plant image processing and analysis, J. Exp. Bot., 2016, vol. 67, pp. 3587—3599.

    Article  CAS  Google Scholar 

  36. Ahmad, H.I., Ahmad, M.J., Asif, A.R., Adnan, M., Iqbal, M.K., Mehmood, K., Muhammad, S.A., Bhuiyan, A.A., Elokil, A., and Du, X., A review of CRISPR-based genome editing: survival, evolution and challenges, Curr. Issues Mol. Biol., 2018, vol. 28, pp. 47—68.

    Article  Google Scholar 

  37. Zadoks, J.C., Chang, T.T., and Konzak, C.F., A decimal code for the growth stages of cereals, Weed Res., 1974, vol. 14, pp. 415—421.

    Article  Google Scholar 

Download references

ACKNOWLEDGMENTS

The authors thank Robert McIntosh, University of Sydney Plant Breeding Institute-Cobbitty, PB4011, Narellan, NSW 2567, Australia, and Xiwen Cai, University of North Dakota State University, Fargo, ND 58102, for review of the manuscript before submission. This work was supported by the Natural Science Foundation of Shandong province, NSF of China, National Key Research and Development Program, Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, and Chuang Xin Gong Cheng of the Shandong Academy of Agricultural Sciences.

Funding

Agricultural Variety Improvement Project of Shandong Province (2019LZGC001), Natural Science Foundation of Shandong province (ZR2018BC031), NSF of China (31471487), National Key Research and Development Program (2016YFD0100500 and 2017YFD0100600), Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China (JRK2018005) and Chuang Xin Gong Cheng of the Shandong Academy of Agricultural Sciences (CXGC2018E01).

Author information

Authors and Affiliations

Authors

Contributions

J.M. Song and J. Guo conceived and designed the experiments. J. Guo, H.S. Li and A.F. Liu performed the experiments. J. Guo and H.S. Li analyzed the data. X.Y. Cao, D.G. Cheng, C. Liu, J.M. Song and J.J. Liu contributed reagents/materials/analysis tools. J. Guo wrote the paper.

Corresponding authors

Correspondence to J. Guo or J. Song.

Ethics declarations

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

This article does not contain any studies involving animals or human participants performed by any of the authors.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Guo, J., Li, H., Liu, J. et al. Genome-Wide Identification and Expression Profiling of Starch-Biosynthetic Genes in Common Wheat. Russ J Genet 56, 1445–1456 (2020). https://doi.org/10.1134/S102279542012008X

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1134/S102279542012008X

Keywords:

Navigation