Date Received: 19-11-2025
Date Accepted: 07-05-2026
Date Published: 25-06-2026
##submissions.doi##: https://doi.org/10.31817/tckhnnvn.2026.24.6.04
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How to Cite:
Genetic Characteristics Associated with the Morphological Traits of Pigmented Pericarp Rice Grains
,
Nguyen Minh Xuan
1
,
Bui Quang Tu
1
,
Nguyen Van Loc
1
,
Pham Van Cuong
1
,
Nguyen Thi Thuy Hanh (*)
2
Keywords
Decorticated grain, colored rice, GWAS, GS5, QTL
Abstract
This study aimed to elucidate the genetic basis underlying rice grain morphology and size, thereby providing a scientific foundation for the breeding of high-quality rice varieties that meet market demands. A genome-wide association study (GWAS) was conducted for morphological and grain structural traits in 102 pigmented pericarp rice accessions. GWAS analysis was performed using the TASSEL software, applying a mixed linear model (MLM), using 60,224 SNPs. A total of 31 quantitative trait loci (QTLs) were identified associated with the following traits: grain length, grain width, decorticated grain length, decorticated grain width, decorticated grain thickness, grain length-to-width ratio, decorticated grain length-to-width ratio, lemma color, and decorticated color. Among these, 8 loci overlapped with previously reported QTLs/genes, while 23 QTLs were novel. These results provide valuable information for molecular studies and for subsequent breeding of colored rice varieties.
References
Bradbury P.J., Zhang Z., Kroon D,.E., Casstevens T.M., Ramdoss Y. & Buckler E.S. (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics. 23(19): 2633-5. doi: 10.1093/bioinformatics/ btm308. Epub 2007 Jun 22. PMID: 17586829. Brotman Y., Llorente-Wiegand C., Oyong G., Badoni S., Misra G., Anacleto R., Parween S., Pasion E., Tiozon Jr., R.N., Anonuevo J.J., deGuzman M.K., Alseekh S., Mbanjo E.G.N., Boyd L.A., Fernie A.R. & Sreenivasulu N. (2021). The genetics underlying metabolic signatures in a brown rice diversity panel and their vital role in human nutrition. The Plant Journal. 106(2): 507-525. https://doi.org/10.1111/tpj.15182 FAO (2023). Food and Agriculture data. Truy cập từ https://www.fao.org/faostat/en/#data, ngày 12/11/2025 Furukawa T., Maekawa M., Oki T., Suda I., Iida S., Shimada H., Takamure I., & Kadowaki K. (2007). The Rc and Rd genes are involved in proanthocyanidin synthesis in rice pericarp. Plant J. 49(1): 91-102. doi: 10.1111/j.1365-313X.2006.02958.x. Jiang L., Zhong H., Jiang X., Zhang J., Huang R., Liao F., Deng Y., Liu Q., Huang Y., Wang H. & Tao Y. (2022). Identification and pleiotropic effect analysis of GSE5 on rice chalkiness and grain shape. Frontiers in Plant Science, 12, p.814928. https://doi.org/10.3389/fpls.2021.814928 Pham C.H., Do T.D., Nguyen H.T.L., Hoang N.T., Tran T.D., Vu M.T.T., Doi H.H., Bui T.G.T., & Henry R.J. (2024). Genome-wide association mapping of genes for anthocyanin and flavonoid contents in Vietnamese landraces of black rice. Euphytica 220, 11. https://doi.org/10.1007/s10681-023-03268-0
Phạm Văn Cường, Nguyễn Quốc Trung, Đinh Mai Thùy Linh, Bùi Hồng Nhung, Trần Thị Hiên, Tăng Thị Hạnh, & Nguyễn Văn Hoan. (2021). Kết quả chọn tạo giống lúa triển vọng DCG93 có năng suất cao, phôi to và vỏ lụa dày phục vụ chế biến dầu cám gạo ở Việt Nam. Tạp chí Nông nghiệp và Phát triển nông thôn. 11:10-19. ISSN.1859-4581. Phan N.T.H., Pham C.V., Tang H.T., Nguyen L.V. & Bertin P. (2023). Integration of genome-wide association studies reveal loci associated with salt tolerance score of rice at the seedling stage. Journal of Applied Genetics, 64(4): 603-614. https://doi.org/10.1007/s13353-023-00775-7 Ponce K., Zhang Y., Guo L., Leng Y. & Ye G. (2020). Genome-Wide Association Study of Grain Size Traits in Indica Rice Multiparent Advanced Generation Intercross (MAGIC) Population. Frontiers in Plant Science. Vol. 11. https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2020.00395 Singh N., Majumder S., Singh O.N., Vikram P., Singh A.K. & Singh S. (2015). A large-effect QTL for grain weight in rice on chromosome 10. Australian Journal of Crop Science. 9(5): 372-377. Tổng cục Thống kê (2023). Sản xuất nông, lâm nghiệp và thủy sản năm 2023. Truy cập từ https://www.nso.gov.vn/du-lieu-va-so-lieu-thong-ke/2024/01/san-xuat-nong-lam-nghiep-va-thuy-san-nam-2023-ket-qua-dat-duoc-va-kho-khan-thach-thuc-dan-xen/ ngày 15/11/2025 Tran V.Q., Nguyen V.L., Nguyen Q.T, Tran T.H., Le V.H. & Ngo, T. H.T. (2024). Genetic diversity and genetic analysis for pigmented pericarps in rice (Oryza sativa L.). Vegetos. 37(6): 2413-2422. https://doi.org/10.1007/s42535-023-00721-2 Wang N., Chen H., Qian Y., Liang Z., Zheng G., Xiang J., Feng T., Li M., Zeng W., Bao Y. & Liu E. (2023). Genome-wide association study of rice grain shape and chalkiness in a worldwide collection of Xian accessions. Plants. 12(3): 419. https://doi.org/10.3390/plants12030419 Yang W., Hao Q., Liang J., Tan Q., Luan X., Lin S., Zhu H., Bu S., Liu Z., Liu G., Wang S., Zhang G. Fine Mapping of Two Major Quantitative Trait Loci for Rice Chalkiness With High Temperature-Enhanced Additive Effects. (2022). Frontiers in Plant Science.13: 957863. doi: 10.3389/fpls.2022.957863. Yaobin Q., Peng C., Yichen C., Yue F., Derun H., Tingxu H., Xianjun S. & Jiezheng Y. (2018). QTL-Seq identified a major QTL for grain length and weight in rice using near isogenic F2 population. Rice Science. 25(3): 121-131. https://doi.org/10.1016/j.rsci.2018.04.001 Zhang T., Wang S., Sun S., Zhang Y., Li J., You J., Su T., Chen W., Ling Y., He G., Zhao F. (2020). Analysis of QTL for Grain Size in a Rice Chromosome Segment Substitution Line Z1392 with Long Grains and Fine Mapping of qGL-6. Rice (N Y).13(1): 40. doi: 10.1186/s12284-020-00399-z. Zhu B.F., Si L., Wang Z., Zhou Y., Zhu J., Shangguan Y., Lu D., Fan D., Li C., Lin H., Qian Q., Sang T., Zhou B., Minobe Y., & Han B. (2011). Genetic control of a transition from black to straw-white seed hull in rice domestication. Plant Physiol.155(3): 1301-11. doi: 10.1104/pp.110.168500. Zhu Q., Yu S., Zeng D., Liu H., Wang H., Yang Z., Xie X., Shen R., Tan J., Li H., Zhao X., Zhang Q., Chen Y., Guo J., Chen L., & Liu Y.-G. (2017). Development of “Purple Endosperm Rice” by Engineering Anthocyanin Biosynthesis in the Endosperm with a High-Efficiency Transgene Stacking System. Molecular Plant. 10(7): 918-929. https://doi.org/10.1016/j.molp.2017.05.008.