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Population structure and genetic differentiation analyses reveal high level of diversity and allelic richness in crop wild relatives of AA genome species of rice (Oryza sativa L.) in India

  • Plant Genetics • Original Paper
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Abstract 

Crop wild relatives (CWRs) are vital sources of variation for genetic improvement, but their populations are few in genebanks, eroded in natural habitats and inadequately characterized. With a view to explore genetic diversity in CWRs of AA genome rice (Oryza sativa L.) species in India, we analyzed 96 accessions of 10 Oryza species by using 17 quantitative traits and 45 microsatellite markers. The morpho-quantitative traits revealed a high extent of phenotypic variation in the germplasm. Diversity index (H′) revealed a high level of within-species variability in O. nivara (H′ = 1.09) and O. rufipogon (H′ = 1.12). Principal component (PC) analysis explained 79.22% variance with five PCs. Among the traits related to phenology, morphology, and yield, days to heading showed strong positive association with days to 50% flowering (r = 0.99). However, filled grains per panicle revealed positive association with spikelet fertility (0.71) but negative with awn length (− 0.58) and panicle bearing tillers (− 0.39). Cluster analysis grouped all the accessions into three major clusters. Microsatellite analysis revealed 676 alleles with 15.02 alleles per locus. High polymorphism information content (PIC = 0.83) and Shannon’s information index (I = 2.31) indicated a high level of genetic variation in the CWRs. Structure analysis revealed four subpopulations; first and second subpopulations comprised only of O. nivara accessions, while the third subpopulation included both O. nivara and O. rufipogon accessions. Population statistics revealed a moderate level of genetic differentiation (FST = 0.14), high gene diversity (HE = 0.87), and high gene flow (Nm = 1.53) among the subpopulations. We found a high level of molecular variance among the genotypes (70%) and low among populations (11%) and within genotypes (19%). The high level of molecular and morphological variability detected in the germplasm of CWRs could be utilized for the improvement of cultivated rice.

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Data Availability

The data presented in this study are available on request from the corresponding author.

References 

  • Aggarwal RK, Brar DS, Nandi S, Huang N, Khush GS (1999) Phylogenetic relationships among Oryza species revealed by AFLP markers. Theor Appl Genet 98:1320–1328

    Article  CAS  Google Scholar 

  • Alsantely A, Gutaker R, Rodríguez MEN, Arrieta-Espinoza G, Fuchs EJ, de Oliveira AC, Tohme J, Zuccolo A, Wing RA, Fornasiero A (2023) The international Oryza map alignment project (IO MAP): the Americas-past achievements and future directions. J Exp Bot 74:1331–1342. https://doi.org/10.1093/jxb/erac490

    Article  CAS  PubMed  Google Scholar 

  • Arrieta-Espinoza G, Sanchez E, Vargas S, Lobo J, Quesada T, Espinoza AM (2005) The weedy rice complex in Costa Rica. I. morphological study of relationships between commercial rice varieties, wild Oryza relatives and weedy types. Genet Resour Crop Evol 52:575–587. https://doi.org/10.1007/s10722-004-6109-x

    Article  Google Scholar 

  • Banaticla-Hilario MCN, Sosef MS, McNally KL, Hamilton NRS, van den Berg RG (2013) Ecogeographic variation in the morphology of two Asian wild rice species, Oryza nivara and Oryza rufipogon. Int J Plant Sci 174:896–909

    Article  Google Scholar 

  • Banaticla-Hilario MCN, Van den Berg RG, Hamilton NRS, McNally KL (2013) Local differentiation amidst extensive allele sharing in Oryza nivara and O. rufipogon. Ecol Evol 3:3047–3062. https://doi.org/10.1002/ece3.689

    Article  PubMed  PubMed Central  Google Scholar 

  • Basavaraj PS, Gireesh C, Bharamappanavara M, Manoj CA, Ishwaryalakshmi LVG, Senguttuvel P, Sundaram RM, Subbarao LV, Anantha MS (2022) Genetic analysis of introgression lines of Oryza rufipogon for improvement of low phosphorous tolerance in indica rice. Indian J Genet Plant Breed 82:135–142.https://doi.org/10.31742/IJGPB.82.2.1

  • Bioversity International, IRRI, WARDA (2007) Descriptors for wild and cultivated rice (Oryza spp.). Bioversity International, Rome, Italy; International Rice Research Institute, Los Banos, Philippines; WARDA Africa Rice Center, Cotonou, Benin, pp 22–42

  • Brar DS, Khush GS (2003) Utilization of wild species of genus Oryza in rice improvement. In: Nanda JS, Sharma SD (eds) Monograph on genus Oryza, Oxford & IBH Publishing, New Delhi, pp 283–309.

  • Brar DS, Khush GS (2018) Wild relatives of rice: A valuable genetic resource for genomics and breeding research. In: Mondal TK, Henry RJ (eds) The wild Oryza genomes, Compendium of plant genomes, Springer, Cham, pp 1–25. https://doi.org/10.1007/978-3-319-71997-9_1

  • Brondani RPV, Zucchi MI, Brondani C, Rangel PHN, Oliveira Borba TCD, Rangel PN, Magalhaes MR, Vencovsky R (2005) Genetic structure of wild rice Oryza glumaepatula populations in three Brazilian biomes using microsatellite markers. Genetica 125:115–123. https://doi.org/10.1007/s10709-005-4916-4

    Article  CAS  PubMed  Google Scholar 

  • Buso GSC, Rangel PH, Ferreira ME (1998) Analysis of genetic variability of South American wild rice populations (Oryza glumaepatula) with isozymes and RAPD markers. Mol Ecol 7:107–117

    Article  CAS  Google Scholar 

  • Chen Y, Fan Y, Yang W, Ding G, Xi J, Zhang F (2022) Development and verification of SSR markers from drought stress-responsive miRNAs in Dongxiang wild rice (Oryza rufipogon Griff.). Funct Integr Genomics 22:1153–1157. https://doi.org/10.1007/s10142-022-00891-3

    Article  CAS  PubMed  Google Scholar 

  • Choudhury DR, Singh N, Singh AK, Kumar S, Srinivasan K, Tyagi RK, Ahmad A, Singh NK, Singh R (2014) Analysis of genetic diversity and population structure of rice germplasm from north-eastern region of India and development of a core germplasm set. PLoS ONE 9:e113094. https://doi.org/10.1371/journal.pone.0113094

    Article  CAS  Google Scholar 

  • Chouhan SK, Singh AK, Singh A, Singh SP, Singh NK, Singh PK (2014) Agro-morphological diversity in wild rice accessions of Eastern Indo-Gangetic region of India. Bangladesh J Bot 43:337–344

    Article  Google Scholar 

  • Dong YB, Pei XW, Yuan QH, Wu HJ, Wang XJ, Jia SR, Peng YF (2010) Ecological, morphological and genetic diversity in Oryza rufipogon Griff. (Poaceae) from Hainan Island. China Genet Resour Crop Evol 57:915–926. https://doi.org/10.1007/s10722-009-9523-2

    Article  Google Scholar 

  • Earl DA, VonHoldt BM (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 4:359–361

    Article  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Fornasiero A, Wing RA, Ronald P (2022) Rice domestication. Curr Biol 32:20–24

    Article  Google Scholar 

  • Gao LZ, Zhang CH, Jia JZ (2005) Cross-species transferability of rice microsatellites in its wild relatives and the potential for conservation genetic studies. Genet Resour Crop Evol 52:931–940

    Article  CAS  Google Scholar 

  • Ge S, Oliveira GC, Schaal BA, Gao LZ, Hong DY (1999) RAPD variation within and between natural populations of the wild rice Oryza rufipogon from China and Brazil. Heredity 82:638–644

    Article  CAS  PubMed  Google Scholar 

  • Ge S, Sang T, Lu BR, Hong DY (1999) Phylogeny of rice genomes with emphasis on origins of allotetraploid species. Proc Natl Acad Sci USA 96:14400–14405

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gu B, Zhou T, Luo J, Liu H, Wang Y, Shangguan Y, Zhu J, Li Y, Sang T, Wang Z, Han B (2015) An-2 encodes a cytokinin synthesis enzyme that regulates awn length and grain production in rice. Mol Plant 8:1635–1650. https://doi.org/10.1016/j.molp.2015.08.001

    Article  CAS  PubMed  Google Scholar 

  • Haritha G, Sudhakar T, Chandra D, Ram T, Divya B, Sarla N (2016) Informative ISSR markers help identify genetically distinct accessions of Oryza rufipogon in yield improvement. Rice Sci 23:225–241. https://doi.org/10.1016/j.rsci.2016.08.001

    Article  Google Scholar 

  • Ishikawa R, Castillo CC, Htun TM, Numaguchi K, Inoue K, Oka Y, Ogasawara M, Sugiyama S, Takama N, Orn C, Inoue C, Nonomura KI, Allaby R, Fuller DQ, Ishii T (2022) A stepwise route to domesticate rice by controlling seed shattering and panicle shape. Proc Natl Acad Sci USA 119:e2121692119. https://doi.org/10.1073/pnas.2121692119

    Article  CAS  PubMed  PubMed Central  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. https://doi.org/10.1270/jsbbs.60.518

    Article  Google Scholar 

  • Jin J, Hua L, Zhu Z, Tan L, Zhao X, Zhang W, Liu F, Fu Y, Cai H, Sun X, Gu P, Xie D, Sun C (2016) GAD1 encodes a secreted peptide that regulates grain number, grain length and awn development in rice domestication. Plant Cell 28:2453–2463. https://doi.org/10.1105/tpc.16.00379

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Joseph L, Kuriachan P, Kalyanaraman K (1999) Collection and evaluation of the tetraploid Oryza officinalis Wall ex Watt (O. malampuzhaensis Krish.et Chand.) endemic to Western Ghats. India Genet Resour Crop Evol 46:531–541

    Article  Google Scholar 

  • Joshi SP, Gupta VS, Aggarwal RK, Ranjekar PK, Brar DS (2000) Genetic diversity and phylogenetic relationship as revealed by inter simple sequence repeat (ISSR) polymorphism in the genus Oryza. Theor Appl Genet 100:1311–1320

    Article  CAS  Google Scholar 

  • Juliano AB, Naredo MEB, Jackson MT (1998) Taxonomic status of Oryza glumaepatula Steud. I. Comparative morphological studies of New World diploids and Asian AA genomes species. Genet Resour Crop Evol 45:197–203

    Article  Google Scholar 

  • Juneja S, Das A, Joshi SV, Sharma S, Vikal Y, Patra BC, Bharaj TS, Sidhu JS, Singh K (2006) Oryza nivara (Sharma et Shastry) the progenitor of O. sativa (L.) subspecies indica harbours rich genetic diversity as measured by SSR markers. Curr Sci 91:1079–1085

    CAS  Google Scholar 

  • Kakar N, Bheemanahalli R, Jumaa S, Redoña E, Warburton ML, Reddy KR (2021) Assessment of agro-morphological, physiological and yield traits diversity among tropical rice. PeerJ 9:e11752. https://doi.org/10.7717/peerj.11752

    Article  PubMed  PubMed Central  Google Scholar 

  • Karasawa MM, Vencovsky R, Silva CM, Zucchi MI, Oliveira GC, Veasey EA (2007) Genetic structure of Brazilian wild rice (Oryza glumaepatula Steud.) populations analyzed using microsatellite markers. Genet Mol Biol 30:400–410

    Article  CAS  Google Scholar 

  • Khan A, Ahmad H, Shuaib M, Bahadur S, Hussain F (2020) Enumeration of genetic diversity of wild rice through phenotypic trait analysis. Gene Rep 21:100797. https://doi.org/10.1016/j.genrep.2020.100855

    Article  CAS  Google Scholar 

  • Khush GS (2005) What it will take to feed 5.0 billion rice consumers in 2030? Plant Mol Biol 59:1–6

    Article  CAS  PubMed  Google Scholar 

  • Khush GS (2013) Strategies for increasing the yield potential of cereals: case of rice as an example. Plant Breed 132:433–436. https://doi.org/10.1111/pbr.1991

    Article  CAS  Google Scholar 

  • Khush GS, Virk PS (2000) Rice breeding: achievements and future strategies. Crop Improv 27:115–144

    Google Scholar 

  • Kim H, Jung J, Singh N, Greenberg A, Doyle JJ, Tyagi W, Chung JW, Kimball J, Hamilton RS, McCouch SR (2016) Population dynamics among six major groups of the Oryza rufipogon species complex, wild relative of cultivated Asian rice. Rice 9:56. https://doi.org/10.1186/s12284-016-0119-0

    Article  PubMed  PubMed Central  Google Scholar 

  • Labarosa SJE, Sevilla NR, Tabanao DAA, Baldo NB, Ebuna HL, Jamago JM (2021) Genetic diversity and structure of Oryza rufipogon Griff. populations in the Philippines. Philipp J Sci 150 (S1):17–28. https://doi.org/10.56899/150.S1.03

  • Le S, Josse J, Husson F (2008) FactoMineR: an R package for multivariate analysis. J Stat Softw 25:1–18

    Article  Google Scholar 

  • Liu W, Shahid MQ, Bai L, Lu Z, Chen Y, Jiang L, Diao M, Liu X, Lu Y (2015) Evaluation of genetic diversity and development of a core collection of wild rice (Oryza rufipogon Griff.) populations in China. PLoS One 10:e0145990. https://doi.org/10.1371/journal.pone.0145990

  • Lu F, Ammiraju JSS, Sanyal A, Zhang S, Song R, Chen J, Li G, Sui Y, Song X, Cheng Z, de Oliveira AC, Bennetzen JL, Jackson SA, Wing RA, Chen M (2009) Comparative sequence analysis of Monoculm1-orthologous regions in 14 Oryza genomes. Proc Natl Acad Sci USA 106:2071–2076. https://doi.org/10.1073/pnas.0812798106

    Article  PubMed  PubMed Central  Google Scholar 

  • Lu BR, Sharma SD (2003) Exploration, collection and conservation of wild Oryza species. In: Nanda JS, Sharma SD (eds) Monograph on genus Oryza, Oxford & IBH Publishing, New Delhi, pp 263–282.

  • Luo J, Liu H, Zhou T, Gu B, Huang X, Shangguan Y, Zhu J, Li Y, Zhao Y, Wang Y, Zhao Q (2013) An-1 encodes a basic helix-loop-helix protein that regulates awn development, grain size, and grain number in rice. Plant Cell 25:360–3376. https://doi.org/10.1105/tpc.113.113589

    Article  CAS  Google Scholar 

  • Mangosongo H, Lyaruu H, Mneney E (2019) Agro-morphological characterization of the wild rice (Oryza longistaminata) populations from selected areas of Tanzania. Tanzan J Sci 45:9–17

    Google Scholar 

  • Mangosongo H, Mneney E, Harvey J, Kyallo M (2020) Assessment of genetic diversity of the wild rice (Oryza longistaminata) populations in Tanzania using microsatellite markers. Tanzan J Sci 46:828–839

    Google Scholar 

  • Mason AS (2015) SSR genotyping. In: Batley J (ed.) Plant genotyping: Methods and protocols, Methods in molecular biology, vol. 1245, Humana Press, New York, pp 77–89. https://doi.org/10.1007/978-1-4939-1966-6_6

  • McCouch SR, McNally KL, Wang W, Hamilton RS (2012) Genomics of gene banks: A case study in rice. Am J Bot 99:407–423. https://doi.org/10.3732/ajb.1100385

    Article  PubMed  Google Scholar 

  • Melaku G, Haileselassie T, Feyissa T, Kiboi S (2013) Genetic diversity of the African wild rice (Oryza longistaminata Chev. et Roehr) from Ethiopia as revealed by SSR markers. Genet Resour Crop Evol 60:1047–1056. https://doi.org/10.1007/s10722-012-9900-0

    Article  CAS  Google Scholar 

  • Melaku G, Labroo M, Liyu H, Shilai Z, Guangfu H, Jing Z, Tesfaye K, Haileselassie T, Hu F (2019) Genetic diversity and differentiation of the African wild rice (Oryza longistaminata) in Ethiopia. Sci Afr 6:e00138. https://doi.org/10.1016/j.sciaf.2019.e00138

    Article  Google Scholar 

  • Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucl Acids Res 8:4321–4325

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nagaraju J, Kathirvel M, Kumar RR, Siddiq EA, Hasnain SE (2002) Genetic analysis of traditional and evolved Basmati and non-Basmati rice varieties by using fluorescence-based ISSR-PCR and SSR markers. Proc Natl Acad of Sci USA 99:5836–5841. https://doi.org/10.1073/pnas.042099099

    Article  CAS  Google Scholar 

  • Orn C, Shishido R, Akimoto M, Ishikawa R, Htun TM, Nonomura KI, Koide Y, Sarom M, Vang S, Sophany S, Makara O (2015) Evaluation of genetic variation among wild rice populations in Cambodia. Breed Sci 65:430–437. https://doi.org/10.1270/jsbbs.65.430

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Parker PG, Snow AA, Schug MD, Booton GC, Fuerst PA (1998) What molecules can tell us about populations: choosing and using a molecular marker. Ecology 79:361–382

    Google Scholar 

  • Patel H, Gauraha D, Nair SK, Sao A (2022) Principal component analysis for yield and its attributing traits in indigenous germplasm accessions of rice (Oryza sativa L.). Pharma Innov J 11:337–340

    Google Scholar 

  • Peakall R, Smouse P (2012) GenAlEx 6.5: genetic analysis in Excel Population genetic software for teaching and research–an update. Bioinformatics 28:2537–2539

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Perrier X, Flori A, Bonnot F (2003) Data analysis methods. In: Hamon P, Seguin M, Perrier X, Glaszmann JC (eds) Genetic diversity of cultivated tropical plants. Enfield, Montpellier, pp 43–76

    Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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. https://doi.org/10.1007/s10722-012-9839-1

    Article  Google Scholar 

  • Ram SG, Thiruvengadam V, Vinod KK (2007) Genetic diversity among cultivars, landraces and wild relatives of rice as revealed by microsatellite markers. J Appl Genet 48:337–345

    Article  PubMed  Google Scholar 

  • Ren F, Lu BR, Li S, Huang J, Zhu Y (2003) A comparative study of genetic relationships among the AA-genome Oryza species using RAPD and SSR markers. Theor Appl Genet 108:113–120. https://doi.org/10.1007/s00122-003-1414-x

    Article  CAS  PubMed  Google Scholar 

  • Rohlf FJ (1998) NTSYSpc: Numerical taxonomy and multivariate analysis system version 2.02h, Exeter Software, Applied Biostatistics, New York.

  • Roy SC, Shil P (2020) Assessment of genetic heritability in rice breeding lines based on morphological traits and caryopsis ultrastructure. Sci Rep 10:7830. https://doi.org/10.1038/s41598-020-63976-8

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Samal R, Roy PS, Sahoo A, Kar MK, Patra BC, Marndi BC, Gundimeda JNR (2018) Morphological and molecular dissection of wild rices from eastern India suggests distinct speciation between O. rufipogon and O. nivara populations. Sci Rep 8:2773. https://doi.org/10.1038/s41598-018-20693-7

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sanchez PA, Wing RA, Brar DS (2013) The wild relatives of rice: genomes and genomics. In: Zhang Q, Wing RA (eds) Genetics and genomics of rice, Plant genetics and genomics: Crops and models 5, Springer Science-Business Media, New York, pp 9–25. https://doi.org/10.1007/978-1-4614-7903-1_2

  • Sandamal S, Tennakoon A, Amarasekera DABN, Marambe B, Ratnasekera D (2021) Functional trait diversity of wild rice species in Sri Lanka: implications for field identification and application. J Natn Sci Foundation 49:369–382. https://doi.org/10.4038/jnsfsr.v49i3.10223

    Article  CAS  Google Scholar 

  • Sarla N, Bobba S, Siddiq EA (2003) ISSR and SSR markers based on AG and GA repeats delineate geographically diverse Oryza nivara accessions and reveal rare alleles. Curr Sci 84:683–690

    Google Scholar 

  • Sathishkumar P, Kumar PR, Maddala SS, Rao SD, Sundaram RM, Gopala KS, Singh AK, Singh K, Rao SLV, Rani SN, Madhav SM (2021) Development of core set of aromatic rice (Oryza sativa L. indica) based on molecular and morphological diversity. Genet Resour Crop Evol 68:441–450. https://doi.org/10.1007/s10722-020-01074-4

    Article  CAS  Google Scholar 

  • Shannon CE, Weaver W (1949) The mathematical theory of communication. University of Illinois Press, pp 1–117.

  • Singh A, Singh B, Panda K, Rai VP, Singh AK, Singh SP, Chouhan SK, Rai V, Singh PK, Singh NK (2013) Wild rices of eastern Indo-Gangetic plains of India constitute two sub-populations harbouring rich genetic diversity. Plant Omics J 6:121–127

    CAS  Google Scholar 

  • Singh BP, Singh B, Mishra S, Kumar V, Singh NK (2016) Genetic diversity and population structure in Indian wild rice accessions. Aus J Crop Sci 10:144–151

    Google Scholar 

  • Singh B, Singh N, Mishra S, Tripathi K, Singh BP, Rai V, Singh AK, Singh NK (2018) Morphological and molecular data reveal three distinct populations of Indian wild rice Oryza rufipogon Griff. species complex. Front Plant Sci 9:123. https://doi.org/10.3389/fpls.2018.00123

    Article  PubMed  PubMed Central  Google Scholar 

  • Stein JC, Yu Y, Copetti D, Zwickl DJ, Zhang L, Zhang C et al (2018) Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza. Nat Genet 50:285–296. https://doi.org/10.1038/s41588-018-0040-0

    Article  CAS  PubMed  Google Scholar 

  • 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 9:239–252. https://doi.org/10.5539/jas.v9n6p239

    Article  Google Scholar 

  • Tiwari S, Yadav MC, Dikshit N, Yadav VK, Pani DR, Latha M (2020) Morphological characterization and genetic identity of crop wild relatives of rice (Oryza sativa L.) collected from different ecological niches of India. Genet Resour Crop Evol 67:2037–2055. https://doi.org/10.1007/s10722-020-00958-9

    Article  CAS  Google Scholar 

  • Vaughan DA (1989) The genus Oryza L. Current status of taxonomy. IRRI Res Pap Ser 138:1–21

    Google Scholar 

  • Vaughan DA, Morishima H, Kadowaki K (2003) Diversity in the Oryza genus. Curr Opin Plant Biol 6:139–146. https://doi.org/10.1016/S1369-5266(03)00009-8

    Article  CAS  PubMed  Google Scholar 

  • Vaughan DA, Kadowaki KL, Kaga A, Tomooka N (2005) On the phylogeny and biography of the genus Oryza. Breed Sci 55:113–122

    Article  CAS  Google Scholar 

  • Vaughan DA, Lu BR, Tomooka N (2008) The evolving story of rice evolution. Plant Sci 174:394–408. https://doi.org/10.1016/j.plantsci.2008.01.016

    Article  CAS  Google Scholar 

  • Volk GM, Khoury CK, Greene SL, Byrne P (2020) Introduction to crop wild relatives. In: Volk GM, Byrne P (eds) Crop wild relatives and their use in plant breeding. Fort Collins, Colorado.

  • Wang J, Shi J, Liu S, Sun X, Huang J, Qiao W, Cheng Y, Zhang L, Zheng X, Yang Q (2020) Conservation recommendations for Oryza rufipogon Griff. in China based on genetic diversity analysis. Sci Rep 10:14375. https://doi.org/10.1038/s41598-020-70989-w

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xu R, Sun C (2021) What happened during domestication of wild to cultivated rice. Crop J 9:564–576. https://doi.org/10.1016/j.cj.2021.02.005

    Article  Google Scholar 

  • Xu X, Liu X, Ge S, Jensen JD, Hu F, Li X et al (2012) Resequencing of 50 accessions of cultivated and wild rice yields markers for identifying agronomically important traits. Nat Biotech 30:105–111. https://doi.org/10.1038/nbt.2050

    Article  CAS  Google Scholar 

  • Yap I P, Nelson RJ (1996) WINBOOT: A program for performing bootstrap analysis of binary data to determine the confidence limits of UPGMA-based dendrograms. IRRI Discussion Paper Series 14, Manila, Philippines.

  • Yeh FC, Yang R, Boyle T (1999) POPGENE, version 1.31. Microsoft window-based freeware for population genetic analysis, University of Alberta. Edmonton, Canada.

  • Zhang J, Pan D, Fan Z, Yu H, Jiang L, Lv S, Sun B, Chen W, Mao X, Liu Q, Li C (2022) Genetic diversity of wild rice accessions (Oryza rufipogon Griff.) in Guangdong and Hainan Provinces, China, and construction of a wild rice core collection. Front Plant Sci 13:999454. https://doi.org/10.3389/fpls.2022.999454

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhou HF, Xie ZW, Ge S (2003) Microsatellite analysis of genetic diversity and population genetic structure of a wild rice (Oryza rufipogon Griff.) in China. Theor Appl Genet 107:332–339. https://doi.org/10.1007/s00122-003-1251-y

    Article  CAS  PubMed  Google Scholar 

  • Zhou H, Li S, Liu J, Hu J, Le S, Li M (2023) Identification and analysis of the genetic integrity of different types of rice resources through SSR markers. Sci Rep 13:2428. https://doi.org/10.1038/s41598-023-29514-y

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhu Q, Ge S (2005) Phylogenetic relationships among A-genome species of the genus Oryza revealed by intron sequences of four nuclear genes. New Phyto 167:249–265. https://doi.org/10.1111/j.1469-8137.2005.01406.x

    Article  CAS  Google Scholar 

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Acknowledgements

The first author is grateful to the Director, ICAR-IARI, New Delhi, for granting Senior Research Fellowship during Ph.D. study. The authors are thankful to the Director, ICAR-NBPGR, New Delhi, for providing research facilities and the Head, Division of Germplasm Conservation, and the Curator of National Gene Bank, ICAR-NBPGR, New Delhi, for providing the seeds of various accessions of Oryza species.

Funding

Network project on National Innovations in Climate Resilient Agriculture (NICRA) titled “Focused collection of climate-smart germplasm of rice and wheat, their valuation and genetic enhancement through pre-breeding for abiotic stress tolerance” with scheme code 13921 and project code 1006607.

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Authors and Affiliations

  1. Division of Genomic Resources, Indian Council of Agricultural Research (ICAR) - National Bureau of Plant Genetic Resources, New Delhi, 110012, India

    Aswin Mahendran, Mahesh C. Yadav, Shailesh Tiwari, Rakesh Kumar Bairwa, Mukesh Kumar Rana & Rakesh Singh

  2. The Graduate School, ICAR - Indian Agricultural Research Institute, New Delhi, 110012, India

    Aswin Mahendran

  3. Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India

    S. Gopala Krishnan

  4. ICAR-National Institute of Plant Biotechnology, New Delhi, 110012, India

    Tapan Kumar Mondal

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Contributions

MCY conceived the idea, planned DNA experiments, and edited and finalized the manuscript. AM performed experiments, data recording, and analysis, and prepared draft manuscript. ST and RKB performed DNA extraction and gel data acquisition. SGK planned field experiments and reviewed manuscript. MKR, RS, and TKM reviewed the manuscript. All authors read and approved the final manuscript.

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Correspondence to Mahesh C. Yadav.

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Mahendran, A., Yadav, M.C., Tiwari, S. et al. Population structure and genetic differentiation analyses reveal high level of diversity and allelic richness in crop wild relatives of AA genome species of rice (Oryza sativa L.) in India. J Appl Genetics 64, 645–666 (2023). https://doi.org/10.1007/s13353-023-00787-3

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