Genetic Diversity Analysis of Starch Synthesis Related Genes (SSRGs) in Rice Varieties from Thailand, Laos and Yunnan Province of China

Authors

  • Sucheela Talamphai
  • Khadija Tehseen Arshad
  • Xue Lin Tan
  • Thanai Surasilp
  • Piyama Tasanasuwan
  • Sittipun Sinumporn

DOI:

https://doi.org/10.14456/gag.2021.3

Keywords:

rice; starch; starch synthesis related genes (SSRGs); genetic variation; DNA marker

Abstract

Genetic diversity analysis of 26 rice varieties; 7 from Thailand, 14 from Laos and 5 from Yunnan, China, was conducted using DNA markers specific to starch synthesis related genes (SSRGs). Screening of 31 markers from 17 SSRGs showed 16 polymorphic makers (51.62%). All polymorphic markers contain 2 alleles, which fragment size ranges from 101-700 bp. The dendrogram was constructed based on Jaccard’s similarity coefficient using the marker data for all the rice genotypes following unweighted pair group method analysis. Examined rice varieties were divided into two major groups with a similarity coefficient of 0.68 correlated to their geographic distributions. The genetic variation of rice varieties between different countries was higher than genetic variation of rice varieties within country. Rice varieties from Laos seem to have close relationship with rice varieties from Yunnan, China. Our results showed that the SSRGs can be used as DNA makers to evaluate the genetic diversity in rice and the data generated from this study could be used in the parental selection in rice breeding program.

References

Agrawal GK, Pandey RN, Agrawal VP (1992) Isolation of DNA from Choerospondias asillaris leaves. Biotechnol. Lett 2: 19–24.
Angkhana I, Henrik B, Mats HG, Jane F, Jatupol K, Prasit W, Siam P, Pei S, Chusie T, Carla L, et al. (2016) Genetic diversity patterns of rice (Oryza sativa L.) landraces after 225 migration by Tai Lue and Akha between China and Thailand. Genet Resour Crop Ev 63: 845–858.
FAOSTAT (2013): Available at http://faostat.fao.org/; accessed on 4/03/2015.
Hannah LC, James M (2008) The complexities of starch biosynthesis in cereal endosperms. Curr Opin Biotech 19: 160–165.
James MG, Denyer K, Myers A.M (2003) Synthesis in the cereal endosperm. Curr Opin Plant Biol 6: 215–222.
Lee SK, Hwang SK, Han M, Eom JS, Kang HG, Han Y, Choi SB, Cho MH, Bhoo SH, An G, Hahn TR, Okita TW, Jeon JS, et al. (2007) Identification of the ADP-glucose pyrophosphorylase isoforms essential for starch synthesis in the leaf and seed endosperm of rice (Oryza sativa L.). Plant Mol Biol 65: 531–546.
Moonsap P, Laksanavilat N, Sinumporn S, Tasanasuwan P, Kate-Ngam S, Jantasuriyarat C (2019) Genetic diversity of Indo-China rice varieties using ISSR, SRAP and InDel markers. J of Genet 98: 80 doi: 10.1007/s12041-019-1123-0
Myers AM, Morell MK, James MG, Ball SG (2000) Recent progress toward understanding biosynthesis of the amylopectin crystal. Plant Physiol 122: 989–997.
Nakamura Y (2002) Towards a better understanding of the metabolic system for amylopectin biosynthesis in plants: Rice endosperm as a model tissue. Plant Cell Physiol 43: 718–725.
Nakamura Y, Francisco PBJ, Hosaka Y, Sato A, Sawada T, Kubo A, Fujita N (2005) Essential amino acids of starch synthase IIa differentiate amylopectin structure and starch quality between japonica and indica rice varieties. Plant Mol Biol 58: 213–227.
Sina X, Artachinda ON (2014) Review of Rice Policies in China, Thailand and Vietnam. ARE Working Paper No. 2557/1. Department of Agricultural and Resource Economics, Faculty of Economics, Kasetsart University, Bangkok.
Tian ZX, Chang-Jie Y, Qian Q (2010) Development of gene-tagged molecular makers for starch synthesis-related genes in rice. Crop Breed 33: 3768–3777.
Tian YS, Chang-Jie Y, Qian Q, Song Y, Hui-Lan X, Fang W, Jie-Fen X., Gui-Fu L, Yong-Hong W, Qiao-Quan L, Shu-Zhu T, Jia-Yang L, Ming-Hong G, et al., (2013) Mutation by DNA shuffling of 5-enolpyruvylshikimate-3-phosphate synthase from Malus domestica for improved glyphosate resistance. Plant Biotechnol 11: 829–838.
Umemoto T, Yano M, Satoh H, Shomura A, Nakamura Y (2002) Mapping of a gene responsible for the difference in amylopectin structure between japonica-type and indica-type rice varieties. Theor Appl Gent 104: 1–8.
Wanchana S, Toojinda T, Tragoonrung S, Vanavichit A (2003) Duplicated coding sequence in the waxy allele of tropical glutinous rice (Oryza sativa L.). Int J Plant Sci 6: 1193–1199.
Yan AO, Yong X, Xiao-fen C, An W, Fei T, Li-qun S, Qiao-quan L (2016) A genetic diversity assessment of starch quality traits in rice landraces from the Taihu basin, China. J Integr Agric 15(3): 493–501.

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Published

2021-04-28

Issue

Vol. 14 No. 1 (2021): JAN - APR 2021

Section

Research Articles

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