Genetic classification of upland rice (Oryza sativa L.) collected from minority farmers in Thailand using InDel marker
Article Sidebar
Main Article Content
Abstract
Upland rice varieties are the most appropriate for rice production in slope areas under rainfed conditions. Upland rice grows in Northern, Central and Northeast Thailand, but genetic information of this type of rice cultivated by minority farmers is still unclear. Thus, the obtained results helped upland rice breeding program. The 15 upland rice accessions were investigated using 23 InDel markers and molecular results to compare traditional morphology method. The morphological characteristics were identified with perplexing outcome and the genetic information obtained by the 25 InDel markers revealed three major groups among the 15 upland rice accessions. The upland rice accessions PLU-SU-0007, PLU-SU-0011, and PLU-SU-0012 collected from Prachuap Khiri Khan were identified as indica rice. CM-001, SU-001, and PLU-SU-002 accessions which were collected from Chiang Mai, Petchaburi, and Prachuap Khiri Khan and identified as japonica rice. The nine accessions showed closely genetic similarity to japonica rice. These data suggested that the InDel marker is an efficient method to classify ecotypes (indica or japonica) of upland rice, while morphology of seed grains failed to identify the 15 accessions. In addition, the upland rice accessions growing throughout Thailand are genetically diverse. This genetic information will provide strong opportunity for successful study of these accessions in vitro and genetic improvement of upland rice
Article Details
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.
References
Anang, B. T. and Yeboah, R. W. N. (2019). Determinants of off-farm income among smallholder rice farmers in Northern Ghana: application of double-hurdle model. Advance in Agriculture 7.
Bandumula, N. (2017). Rice production in Asia: key to global food security. Proceedings of the National Academy of Sciences, India Section B: Biological Sciences, 88:3.
Butso, O. and Isvilanonda, S. (2010). Two decades of the rice economic of Thailand. Applied Economics Journal, 17:70-92.
Chaichana, N. and Wongtaw, J. (2018). Food Security in a Cultural Dimension of the Pwo Karen Ethnic Group in Ban Thiphuye, Chalae Sub-district, Thong Phaphum District, Kanchanaburi Province. Walailak Journal of Social Science, 11:43-71.
Cheng, K. S. (1993). Discrimination of hsien (indica) and keng (japonica) subspecies in Asian cultivated rice. Kunming: Yunnan. Science and Technology Press, 1-23.
Cheng, K. S., Zhou, J. W. and Lu, Y. X. (1984). Studies on the indigenous rices in Yunnan and their utilization II: A revised classification of Asian cultivated rice. Acta Agronomica Sinica, 10:271-280.
Chang, T. (1985). Crop history and genetic conservation: rice-a case study. Iowa State Journal of Research, 59:425-455.
Changkid, N. (2008). Labour use efficiency of rice farming in Thailand with emphasis on the central plain. Suratthani Rajabhat, 1:73-82.
Da Silva, E. F., Da Silva, L. M. and Montalván, R. (2005). Crossing rate and distance in upland rice. Bragantia, 64:197-201.
Garris, A. J, Tai, T. H., Coburn, J., Kresovich, S. and McCouch, S. (2005). Genetic structure and diversity in Oryza sativa L., Genetics, 169:1631-1638.
Glaszman, J. C. (1987). Isozyme and classification of Asian rice cuitivars. Theoritical and Applied Genetics, 74:21-30.
Hu, C., Shi, J., Quan, S., Cui, B., Kleessen, S., Nikoloski Z., Tohge, T., Alexander, D., Guo, L., Lin, H., Wang, J., Cui, X., Rao, J., Luo, Q., Zhao, X., Fernie, R. A. and Zhang, D. (2014). Metabolic variation between japonica and indica rice cultivars as revealed by non-targeted metabolomics. Scientific Reports, 4:5067.
Jamjod, S., Yimyam, N., Lordkaew, S., Prom-u-thai, C. and Rerkasem, B. (2017). Characterization of on-farm rice germplasm in an area of the crop’s center of diversity. Chiang Mai University Journal of Natural Science, 16:85-98.
Keawsomnuk, P. (2017). Management of basic education for ethnic groups in highland and border regions of Thailand. Kasetsart Journal of Social Sciences, 38:97-104.
Laosutthipong, C., Seritrakul, P. and Na Chiangmai, P. (2019). Ligninbiosynthesis gene (OsPAL and Os4CL3) sequencing of native upland rice varieties from Pala U Village. Thailand. International Journal of Agricultural Technology, 15:947-958.
Limnirankul, B., Promburom, P. and Thongngam, K. (2015). Community participation in developing and accessing household food security in the highlands of Northern Thailnd. Agriculture and Agricultural Science Procedia, 5:52-59.
Lu, B. R., Cai, X. and Xin, J. (2009). Efficient indica and japonica rice identification based on the InDel molecular method: Its implication in rice breeding and evolutionary research. Progress in Natural Science, 19:1241-1252.
Lu, L., Shao, D., Qiu, X., Sun, L., Yan, W., Zhou, X., Yang, L., He, Y., Yu, S. and Xing, Y. (2013). National variation and artificial selection in four genes determine grain shape in rice. New Physiologist Doi:10.1111/nph.12430.
Mariam, A. L., Masahuling, B. and Jamilah, I. (1991). Hill paddy cultivation in Sabah. Sabah Society Journal, 9:284-289.
Morishima, H. and Oka, H. (1981). Phylogenetic differentiation of cultivated rice, XXII. Numerical evaluation of the indica-japonica differentiation. Japanese Journal of Breeding, 31:402-413.
Oka, H. I. (1988). Origin of cultivated rice, Elsevier, Tokyo.
Okodua, H. (2018). Assessing the impact of rice sector policy reforms on the income mobility of rural households in Nigeria. The Open Agriculture Journal, 12:174-184.
Okubo, K. (2014). Morphological evaluation of the trace of grain detachment in Japonica rice cultivars with different shattering habits. Plant Production Science, 17:291-297.
Perret, S., Thanawong, K., Basset-Mens, C. and Mungkung, R. (2013). The environmental impacts of lowland paddy rice: a case study comparison between rainfed and irrigate rice in Thailand. Cahiers Agricultures, 22:369-377.
Pusadee, T., Oupkaew, P., Rerkasem, B., Jamjod, S. and Schaal, B. (2014). Natural and human-mediated selection in a landrace of Thai rice (Oryza sativa L.). Annals of Applied Biology, 165:280-292.
Saito, K., Asai, H., Zhao, D., Laborte, A. G. and Grenier, C. (2018). Progress in varietal improvement for increasing upland rice productivity in the tropics. Plant production Science, 21:145-158.
Sato, Y. I. (1985). Genetic control of apiculus hair length. Rice Genetics Newsletter, 2:72-74.
Shen, Y. J., Jiang, H., Jin, J. P., Zhang, Z. B., Xi. B., He, Y. Y., Wang, G., Wang, C., Qian, L. and Li, X. (2004). Development of genome-wide DNA polymorphism database for map-based cloning of rice genes. Plant Physiology, 135:1198-1205. doi: 10.1104/pp.103.038463.
Silva, F., Stevens, C.J., Weisskopf, A., Castillo, C., Qin, L., Bevan A. and Fuller, D.Q. (2015). Modelling the geographical origin of rice cultivation in Asia using the rice Archaeological Database. PLOS ONE, 10:e0137024.
Tonini, A. and Cabrera, E. (2011). Globalizing rice research for a changing world. Los Banos, Philippines: International Rice Research Institute. Technical Bulletin, 15 10:e0137024.
Unthong, A., Kaosa-ard, M. and Punkiew, N. (2007). Factors affecting upland farmers’ choice of local rice varieties in Thailand. Kasetsart University Journal of Economics, 14:70-85.
Xingxing, C., Liu, J., Qiu, Y., Zhao, W., Song, Z. and Lu, B. R. (2007). Differentiation of Indica-Japonica rice revealed by insertion/deletion (InDel) fragments obtained from the comparative genomic study of DNA sequences between 93-11 (Indica) and Nipponbare (Japonica). Frontiers of Biology in China, 2:291-296. 10.1007/s11515-007-0042-2.
Yang, T., Zhang, S., Hu, Y., Wu, F., Hu, Q., Chen, G. and Xu, G. (2014). The role of a potassium transporter OsHAK5 in potassium acquisition and transport from roots to shoots in rice at low potassium supply levels. Plant Physiology, 166:945-959.
Zhang, W., Wu, L., Wu, X., Ding, Y., Li, G., Li, J., Weng, F., Liu, Z., Tang, S., Ding, C. and Wang, S. (2016). Lodging Resistance of Japonica Rice (Oryza Sativa L.): Morphological and Anatomical Traits due to top-Dressing Nitrogen Application Rates. Rice (N Y), 9:3.