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The genetic diversity and population structure of weedy rice in northeast Thailand accessed by SSR markers

Published online by Cambridge University Press:  23 October 2023

Monchita Ponsen ,
Kularb Loasatit Open the ORCID record for Kularb Loasatit [Opens in a new window] ,
Tidarat Monkham ,
Jirawat Sanitchon ,
Peerapon Moung-ngam  and
Sompong Chankaew Open the ORCID record for Sompong Chankaew [Opens in a new window]
Monchita Ponsen
Affiliation:
Graduate Research Assistant, Department of Agronomy, Faculty of Agriculture, Khon Kaen University, Khon Kaen, Thailand
Kularb Loasatit
Affiliation:
Assistant Professor, Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen, Nakhon Pathom, Thailand
Tidarat Monkham
Affiliation:
Lecturer, Department of Agronomy, Faculty of Agriculture, Khon Kaen University, Khon Kaen, Thailand
Jirawat Sanitchon
Affiliation:
Assistant Professor, Department of Agronomy, Faculty of Agriculture, Khon Kaen University, Khon Kaen, Thailand
Peerapon Moung-ngam
Affiliation:
Researcher, Pathum Thani Rice Research Center, Rangsit, Thanyaburi District, Pathum Thani, Thailand
Sompong Chankaew*
Affiliation:
Assistant Professor, Department of Agronomy, Faculty of Agriculture, Khon Kaen University, Khon Kaen, Thailand
*
Corresponding author: Sompong Chankaew; Email: somchan@kku.ac.th
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Abstract

Thailand’s northeast (NE) region is an area of high-quality cultivated rice (Oryza sativa L.) production. However, an outbreak of weedy rice has recently spread throughout the region. Weedy rice is phenotypically and morphologically similar to cultivated rice, making identification difficult. The prospective management of weedy rice in the future will involve the study of its genetic diversity and population structure in this region. This study assesses the genetic diversity and population structure of 380 weedy rice samples in the northeast of Thailand through simple sequence repeat (SSR) markers. Thirty-one SSR markers generated 213 alleles with an average of 6.87 per locus and an overall genetic diversity of 0.723. Based on its geographic origin, weedy rice in the Southern NE are showed greater genetic diversity than that in the Central NE and Northern NE areas. The outcrossing rate in all regions was relatively high, with the highest being in the Southern NE at 9.769%. According to genetic distance analysis, the clustering of weedy rice samples in northeast Thailand was not associated with the geographic region. Neighbor-joining and principal coordinate analysis revealed that the 380 weedy rice samples fell into two major clusters. Cluster I contained three weedy rice samples and four wild. In Cluster II, 377 weedy rice samples were closely related to the four cultivated rice cultivars as well as brownbeard rice (Oryza rufipogon Griffiths) wild species. The results suggest that weedy rice in northeast Thailand may have originated as a cross between cultivated and wild rice, as seen in the closely related species, O. rufipogon. Overall, the findings of this study demonstrate the high genetic diversity of weedy rice in this region. Notably, some samples adapted, performing more like cultivated rice, which may be problematic for the future production of high-quality rice in this region. The prevention of weedy rice should, therefore, be given greater consideration in future studies.

Keywords

Domesticationgeographic isolationintrogressionmigrationoutcrossingwild rice
Type
Research Article
Information
Weed Science , Volume 71 , Issue 6 , November 2023 , pp. 594 - 605
Copyright
© The Author(s), 2023. Published by Cambridge University Press on behalf of the Weed Science Society of America

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Footnotes

Associate Editor: Mithila Jugulam, Kansas State University

References

Anderson, JA, Churchill, GA, Autrique, JE, Tanksley, SD, Sorrells, ME (1993) Optimizing parental selection for genetic linkage maps. Genome 36(1):181–186. https://doi.org/10.1139/g93-024 CrossRefGoogle ScholarPubMed
Bah, S, van der Merwe, R, Labuschagne, MT (2017) Estimation of out-crossing rates in intraspecific (Oryza sativa) and interspecific (Oryza sativa × Oryza glaberrima) rice under field conditions using agro-morphological markers. Euphytica 213:81 CrossRefGoogle Scholar
Bakti, C, Tanaka, J (2019) Detection of dominant QTLs for stigma exsertion ratio in rice derived from Oryza rufipogon accession “W0120.” Breed Sci 69:143–150 CrossRefGoogle ScholarPubMed
Bourgis, F, Guyot, R, Gherbi, H, Tailliez, E, Amabile, I, Salse, J, Lorieux, M, Delseny, M, Ghesquière, A (2008) Characterization of the major fragrance gene from an aromatic japonica rice and analysis of its diversity in Asian cultivated rice. Theor Appl Genet 117:353–368 CrossRefGoogle ScholarPubMed
Brar, DS, Khush, GS (2018) Wild relatives of rice: a valuable genetic resource for genomics and breeding research. Pages 1–25 in Mondal, T, Henry, R, eds. The Wild Oryza Genomes. Compendium of Plant Genomes. Cham, Switzerland: Springer Google Scholar
Burgos, NR, Norman, RJ, Gealy, DR, Black, HL (2006) Competitive N uptake between rice and weedy rice. Field Crops Res 99:96–105 CrossRefGoogle Scholar
Burgos, NR, Singh, V, Tseng, TM, Black, H, Young, ND, Huang, Z, Hyma, KE, Gealy, DR, Caicedo, AL (2014) The impact of herbicide-resistant rice technology on phenotypic diversity and population structure of United States weedy rice. Plant Physiol 166:1208–1220 CrossRefGoogle ScholarPubMed
Cao, Q, Lu, BR, Xia, H, Rong, J, Sala, F, Spada, A, Grassi, F (2006) Genetic diversity and origin of weedy rice (Oryza sativa f. spontanea) populations found in north-eastern China revealed by simple sequence repeat (SSR) markers. Ann Bot 98:1241–1252 CrossRefGoogle ScholarPubMed
Chauhan, BS (2013) Strategies to manage weedy rice in Asia. Crop Prot 48:51–56 CrossRefGoogle Scholar
Chin, DV (2001) Biology and management of barnyardgrass, red sprangletop and weedy rice. Weed Biol Manag 1:37–41 CrossRefGoogle Scholar
Dai, L, Dai, W, Song, X, Lu, B-R, Qiang, S (2014) A comparative study of competitiveness between different genotypes of weedy rice (Oryza sativa) and cultivated rice. Pest Manag Sci 70:113–122 CrossRefGoogle ScholarPubMed
Evanno, G, Regnaut, S, Goudet, J (2005) Detecting the number of clusters of individuals using the software structure: a simulation study. Mol Ecol 14:2611–2620 CrossRefGoogle ScholarPubMed
Gao, P, Zhang, Z, Sun, G, Yu, H, Qiang, S (2018) The within-field and between-field dispersal of weedy rice by combine harvesters. Agron Sustain Dev 38:55 CrossRefGoogle Scholar
Gealy, DR, Burgos, NR, Yeater, KM, Jackson, AK, (2015) Outcrossing potential between U.S. blackhull red rice and indica rice cultivars. Weed Sci 63:647–657. https://doi.org/10.1614/WS-D-14-00150.1 CrossRefGoogle Scholar
Gealy, D (2005) Gene movement between rice (Oryza sativa) and weedy rice (Oryza sativa)—a U.S. temperate rice perspective. Pages 323–354 in Gressel, J, ed. Crop Ferality and Volunteerism. Boca Raton, FL: CRC Press CrossRefGoogle Scholar
Gealy, DR, Agrama, HA, Eizenga, GC (2009) Exploring genetic and spatial structure of U.S. weedy red rice (Oryza sativa) in relation to rice relatives worldwide. Weed Sci 57:627–643 CrossRefGoogle Scholar
Gressel, J, ed (2005) Crop Ferality and Volunteerism. Boca Raton, FL: CRC Press. 448 pCrossRefGoogle Scholar
Goudet, J (2002) FSTAT (Version 2.9.3.2): a computer program to calculate F-statistics. J Hered 86:485–486 CrossRefGoogle Scholar
Hobas, S, Gaggiotti, O, ConGRESS Consortium, Bertorelle, G (2013) Sample planning optimization tool for conservation and population genetics (SPOTG): a software for choosing the appropriate number of markers and samples. Methods Ecol Evol 4:299–303 Google Scholar
Ives, CGRG, Tereza, COB, Valmir, GM, Aldo, MJ (2014) Distribution of weedy red rice (Oryza sativa) resistant to imidazolinone herbicides and its relationship to rice cultivars and wild Oryza species. Weed Sci 62:280–293 Google Scholar
Jena, KK (2010) The species of the genus Oryza and transfer of useful genes from wild species into cultivated rice, O. sativa. Breed Sci 60:518–523 CrossRefGoogle Scholar
Jiang, Z, Xia, H, Basso, B, Lu, BR (2012) Introgression from cultivated rice influences genetic differentiation of weedy rice populations at a local spatial scale. Theor Appl Genet 124:309–322 CrossRefGoogle Scholar
Jing, W, Jiang, L, Zhang, WW, Zhai, HQ, Wan, JM (2008) Mapping QTL for seed dormancy in weedy rice. Acta Agron Sin 34:737–742 Google Scholar
Kane, NC, Baack, EJ (2007) The origins of weedy rice. Mol Ecol 16:4419–4648. https://doi.org/10.1111/j.1365-294X.2007.03520.x CrossRefGoogle ScholarPubMed
Khush, GS (1997) Origin, dispersal, cultivation and variation of rice. Plant Mol Biol 35:25–34 CrossRefGoogle ScholarPubMed
Kovach, MJ, Calingacion, MN, Fitzgerald, MA, McCouch, SR. (2009) The origin and evolution of fragrance in rice (Oryza sativa L.). Proc Natl Acad Sci USA 106:14444–14449 CrossRefGoogle ScholarPubMed
Langella, O (1999) Populations: A Free Population Genetic Software. Version 1.2.32. https://mybiosoftware.com/populations-population-genetic-software.html. Accessed: August 19, 2022Google Scholar
Li, Z, Gui, R, Yu, X, Liang, C, Cui, J, Zhao, X, Zhang, X, Yu, P, Chen, W, Sun, J (2022) Genetic basis of the early heading of high-latitude weedy rice. Front Plant Sci 13:1059197 CrossRefGoogle ScholarPubMed
Lodhi, MA, Ye, GN, Weeden, NF, Reisch, BI (1994) A simple and efficient method for DNA extraction from grapevine cultivars and Vitis species. Plant Mol Biol Rep 12:6–13 CrossRefGoogle Scholar
Londo, JP, Schaal, BA (2007) Origins and population genetics of weedy red rice in the USA. Mol Ecol 16:4523–4535 CrossRefGoogle ScholarPubMed
Lou, J, Yue, GH, Yang, WQ, Mei, HW, Luo, LJ, Lu, HJ (2014) Mapping QTLs influencing stigma exsertion in rice. Bulg J Agric Sci 20:1450–1456 Google Scholar
Maneechote, C, Jamjod, S, Rerkasem, B (2004) Invasion of weedy rice in rice fields in Thailand: problems and management. Int Rice Res Notes 29:20–22 Google Scholar
Muto, C, Ishikawa, R, Olsen, KM, Kawano, K, Bounphanousay, C, Matoh, T, Sato, YI (2016) Genetic diversity of the wx flanking region in rice landraces in northern Laos. Breed Sci 66:580–590 CrossRefGoogle ScholarPubMed
Nazareno, AG, Bemmels, JB, Dick, CW, Lohmann, LG (2017) Minimum sample sizes for population genomics: an empirical study from an Amazonian plant species. Mol Ecol Resour 17:1136–1147 CrossRefGoogle ScholarPubMed
Nettuwakul, C, Pongtongkam, P, Thongpan, A, Peyachoknagul, S (2007) Detection of photoperiod responsive gene in KDML 105 Rice (Oryza sativa L.) using cDNA-SRAP technique. Kasetsart J Nat Sci 41:651–659 Google Scholar
Pinglei, G, Zhang, Z, Sun, G, Yu, H, Qiang, S (2018) The within-field and between-field dispersal of weedy rice by combine harvesters. Agron Sustain Dev 38:55 Google Scholar
Prathepha, P (2003) Characterization of Waxy microsatellite classes that are closely linked to the rice Waxy gene and amylose content in Thai rice germplasm. Songklanakarin J Sci Technol 25:1–8 Google Scholar
Prathepha, P (2009a) The badh2 allele of the fragrance (fgr/BADH2) gene is present in the gene population of weedy rice (Oryza sativa f. spontanea) from Thailand. Am-Eurasian J Agric Environ Sci 5:603–608 Google Scholar
Prathepha, P (2009b) Pericarp color and haplotype diversity in weedy rice (O. sativa f. spontanea) from Thailand. Pak J Biol Sci 12:1075–1079 CrossRefGoogle Scholar
Prathepha, P (2011) Microsatellite analysis of weedy rice (Oryza sativa f. spontanea) from Thailand and Lao PDR. Aust J Crop Sci 5:270 Google Scholar
Pritchard, JK, Stephens, M, Donnelly, P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959 CrossRefGoogle ScholarPubMed
Pusadee, T, Schaal, BA, Rerkasem, B, Jamjod, S (2013) Population structure of the primary gene pool of Oryza sativa in Thailand. Genet Resour Crop Evol 60:335–353 CrossRefGoogle Scholar
Ratnasekera, D, Perera, UIP, He, Z, Senanayake, SGJN, Wijesekara, GAW, Lu, B-R (2014) High level of variation among Sri Lankan weedy rice populations, as estimated by morphological characterization. Weed Biol Manag 14:68–75 CrossRefGoogle Scholar
Reagon, M, Thurber, CS, Gross, BL, Olsen, KM, Jia, Y, Caicedo, AL (2010) Genomic patterns of nucleotide diversity in divergent populations of U.S. weedy rice. BMC Evol Biol 10:180 CrossRefGoogle ScholarPubMed
Roma-Burgos, N, San Sudo, M, Olsen, K, Werle, I, Song, B. (2021) Weedy rice (Oryza spp.): what’s in a name? Weed Sci 69:505–513 CrossRefGoogle Scholar
Rosenberger, K, Schumacher, E, Brown, A, Hoban, S (2021) Proportional sampling strategy often captures more genetic diversity when population sizes vary. Biol Conserv 261:109261 CrossRefGoogle Scholar
Shivrain, VK, Burgos, NR, Agrama, HA, Lawton-Rauh, A, Lu, B, Sales, MA, Boyett, V, Gealy, DR, Moldenhauer, KAK (2010) Genetic diversity of weedy red rice (Oryza sativa) in Arkansas, USA. Weed Res 50:289–302 CrossRefGoogle Scholar
Song, Z, Lu, B, Zhu, Y, Chen, J (2002) Pollen competition between cultivated and wild rice species (Oryza sativa and O. rufipogon). New Phytol 153:289–296 CrossRefGoogle Scholar
Song, ZP, Lu, B, Zhu, YG, Chen, JK (2003) Gene flow from cultivated rice to the wild species Oryza rufipogon under experimental field conditions. New Phytol 157:657–665 CrossRefGoogle Scholar
Sudianto, E, Neik, TX, Tam, SM, Chuah, TS, Idris, AA, Olsen, KM, Song, BK (2016) Morphology of Malaysian weedy rice (Oryza sativa): diversity, origin and implications for weed management. Weed Sci 64:501–512 CrossRefGoogle Scholar
Sujariya, S, Jongdee, B, Fukai, S (2023) Estimation of flowering time and its effect on grain yield of photoperiod sensitive varieties in rainfed lowland rice in Northeast Thailand. Field Crops Res 302:109075 CrossRefGoogle Scholar
Sun, J, Qian, Q, Ma, D, Xu, Z, Liu, D, Du, H, Chen, W (2013) Introgression and selection shaping the genome and adaptive loci of weedy rice in northern China. New Phytol 197:290–299 CrossRefGoogle ScholarPubMed
Swain, R, Mohapatra, S, Roy, P, Swain, D, Singh, ON, Meher, J, Dash, SK, Rao, GJN, Subudhi, HN (2017) Assessment of genetic diversity in wild rice of eastern India using SSR markers. J Agric Sci 9:239 Google Scholar
Takano-Kai, N, Doi, K, Yoshimura, A (2011) GS3 participates in stigma exsertion as well as seed length in rice. Breed Sci 61:244–250 CrossRefGoogle Scholar
Tamura, K, Stecher, G, Peterson, D, Filipski, A, Kumar, S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729 CrossRefGoogle ScholarPubMed
Tan, Q, Bu, S, Chen, G, Yan, Z, Chang, Z, Zhu, H, Yang, W, Zhan, P, Lin, S, Xiong, L, Chen, S, Liu, G, Liu, Z, Wang, S, Zhang, G (2022) Reconstruction of the high stigma exsertion rate trait in rice by pyramiding multiple QTLs. Front Plant Sci 13:921700 CrossRefGoogle ScholarPubMed
Tan, Q, Wang, C, Luan, X, Zheng, L, Ni, Y, Yang, W, Yang, Z, Zhu, H, Zeng, R, Liu, G, Wang, S, Zhang, G (2021) Dissection of closely linked QTLs controlling stigma exsertion rate in rice by substitution mapping. Theor Appl Genet 134:1253–1262 CrossRefGoogle ScholarPubMed
Thanasilungura, K, Kranto, S, Monkham, T, Chankaew, S, Sanitchon, J (2020) Improvement of a RD6 rice variety for blast resistance and salt tolerance through marker-assisted backcrossing. Agronomy 10:1118 CrossRefGoogle Scholar
Tian, Z, Qian, Q, Liu, Q, Yan, M, Liu, X, Yan, C, Liu, G, Gao, Z, Tang, S, Zeng, D, Wang, Y, Yu, J, Gu, M, Li, J (2009) Allelic diversities in rice starch biosynthesis lead to a diverse array of rice eating and cooking qualities. Proc Natl Acad Sci USA 106:21760–21765 CrossRefGoogle ScholarPubMed
Vilayheuang, K, Machida-Hirano, R, Bounphanousay, C, Watanabe, KN (2016) Genetic diversity and population structure of ‘Khao Kai Noi’, a Lao rice (Oryza sativa L.) landrace, revealed by microsatellite DNA markers. Breed Sci 66:204–212 CrossRefGoogle Scholar
Weir, BS (1996) Genetic Data Analysis II: Methods for Discrete Population Genetic Data. Sunderland, Massachusetts: Sinauer Associates. 445 pGoogle Scholar
Wongtamee, A, Maneechote, C, Pusadee, T, Rerkasem, B, Jamjod, S (2015) The dynamics of spatial and temporal population genetic structure of weedy rice (Oryza sativa f. spontanea Baker). Genet Res Crop Evol 64:23–39 CrossRefGoogle Scholar
Xia, HB, Wang, W, Xia, H, Zhao, W, Lu, BR (2011) Conspecific crop–weed introgression influences evolution of weedy rice (Oryza sativa f. spontanea) across a geographical range. PLoS ONE 6:e16189 CrossRefGoogle ScholarPubMed
Yan, WG, Li, Y, Agrama, HA, Luo, D, Gao, F, Lu, X, Ren, G (2009) Association mapping of stigma and spikelet characteristics in rice (Oryza sativa L.). Mol Breed 24:277–292 CrossRefGoogle ScholarPubMed
Zhang, C, Zhu, J, Chen, S, Fan, X, Li, Q, Lu, Y, Wang, M, Yu, H, Yi, C, Tang, S, Gu, M, Liu, Q (2019) Wx lv, the ancestral allele of rice Waxy gene. Mol Plant 12:1157–1166 CrossRefGoogle ScholarPubMed
Zhang, L, Dai, W, Wu, C, Song, X, Qiang, S (2012) Genetic diversity and origin of Japonica- and Indica-like rice biotypes of weedy rice in the Guangdong and Liaoning provinces of China. Genet Res Crop Evol 59:399–410 Google Scholar
Zhang, L, Zhu, Q, Wu, Z, Ross-Ibarra, J, Gaut, BS, Ge, S, Sang, T (2009) Selection on grain shattering genes and rates of rice domestication. New Phytol 184:708–720 CrossRefGoogle ScholarPubMed
Zhu, BF, Si, L, Wang, Z, Jingjie, YZ, 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. 155:1301–1311 CrossRefGoogle ScholarPubMed
Zou, T, Zhao, H, Li, X, Zheng, M, Zhang, S, Sun, L, He, N, Pan, X, Liu, Z, Fu, X (2020) QTLs detection and pyramiding for stigma exsertion rate in wild rice species by using the single-segment substitution lines. Mol Breed 40:74 CrossRefGoogle Scholar
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