Abstract
Genetic assessment of rice landraces is important for germplasm evaluation and genetic resource utilization. Rice landraces in peninsular Thailand have adapted to unique environmental stresses over time and have great significance as a genetic resource for crop improvement. In this study, rice landraces derived from rice research centers and farmers from different areas of peninsular Thailand were genetically assessed using 16 polymorphic InDel markers from putative stress-related genes. A total of 36 alleles were obtained. The average PIC value was 0.27/marker. The FST varied from 0.46 to 1.00. Genetic diversity was observed both within and between populations. AMOVA indicated that genetic variations occurred mainly between populations (70%) rather than within populations (30%). The dendrogram, population structure, and PCoA scatter plot clearly demonstrated the differentiation of the two major groups, i.e., landraces from upland and lowland rice ecosystems. The unique alleles of Indel1922, -2543, -6746, -7447 and -8538, which lie in genes encoding putative WAX2, heavy metal-associated domain-containing protein, GA20ox2, PTF1, and PLETHORA2, respectively, were only found in rice from upland ecosystems. Putative WAX2, GA20ox2, and PLETHORA2 are likely related to drought and salt stress. Our findings demonstrate the diversity of landraces in peninsular Thailand. The preservation of these landraces should be facilitated with effective markers to maintain all variant alleles and to protect the genetic diversity. Indel1922, -2543, -6746, -7447 and -8538 have the potential to differentiate upland rice from lowland rice. Furthermore, Indel1922, -6746 and -8538 might be effective markers for drought and salt tolerance.
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Acknowledgements
This work was supported by the government budget of Prince of Songkla University (Grant No. SCI601435S) and the Postdoctoral Fellowship from Prince of Songkla University awarded to SW. We appreciate Phatthalung Rice Research Center, Pattani Rice Research Center, Krabi Rice Research Center, Surat Thani Rice Seed Center, and the farmers for providing the rice landrace seeds used in this study. The assistance of Miss Wilasinee Moenard is gratefully acknowledged.
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SW and AP conceived and planned the work. KR prepared the plant materials. SW and SK performed genotyping. SW analyzed the data and wrote the paper. All authors read and provided helpful discussions for the manuscript. SW and AP made revisions and approved the final version of the paper.
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Whankaew, S., Kaewmanee, S., Ruttajorn, K. et al. Indel marker analysis of putative stress-related genes reveals genetic diversity and differentiation of rice landraces in peninsular Thailand. Physiol Mol Biol Plants 26, 1237–1247 (2020). https://doi.org/10.1007/s12298-020-00816-z
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DOI: https://doi.org/10.1007/s12298-020-00816-z