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Oryza brachyantha A. Chev. et Roehr

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The Wild Oryza Genomes

Abstract

The growing interest in the Oryza genus comes from the feasibility of studying genome evolution of these closely related species, as well as the direct impact of identifying desirable phenotypes that could be transferred to Oryza sativa, one of the world’s most important cereals. Among the Oryza species, Oryza brachyantha is unique: it is highly divergent, has the smallest genome in the genus and is the only FF species, and has several traits that could be useful to improve Oryza sativa. However, our understanding of the basic biology of O. brachyantha and conservation of its diversity in germplasm are still preliminary. In this chapter, we summarize the current knowledge on O. brachyantha, especially on its recently published genomes (nuclear and chloroplastidic), basic genetics, and sequence comparisons with other Oryza species. The information gathered here should be useful to guide efforts to conserve and explore O. brachyantha diversity, a necessary step in order to achieve both basic and applied science goals in the future.

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References

  • Abbasi FM, Shah AH, Perveen F, Afzal M, Sajid M, Masood R, Nawaz F (2010) Genomic affinity between Oryza sativa and Oryza brachyantha as revealed by in situ hybridization and chromosome pairing. Afr J Biotech 9:3068–3072

    Google Scholar 

  • Aggarwal RK, Brar DS, Huang N, Khush GS (1996) Molecular analysis of introgression in Oryza sativa/O. brachyantha and O. sativa/O. granulata derivatives. Int Rice Res. Notes 21:14

    Google Scholar 

  • Ammiraju JS, Luo M, Goicoechea JL, Wang W, Kudrna D, Mueller C, Talag J, Kim H, Sisneros NB, Blackmon B, Fang E, Tomkins JB, Brar D, MacKill D, McCouch S, Kurata N, Lambert G, Galbraith DW, Arumuganathan K, Rao K, Walling JG, Gill N, Yu Y, SanMiguel P, Soderlund C, Jackson S, Wing RA (2006) The Oryza bacterial artificial chromosome library resource: construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza. Genome Res 16:140–147

    Article  PubMed  PubMed Central  Google Scholar 

  • Ammiraju JS, Lu F, Sanyal A, Yu Y, Song X, Jiang N, Pontaroli AC, Rambo T, Currie J, Collura K, Talag J, Fan C, Goicoechea JL, Zuccolo A, Chen J, Bennetzen JL, Chen M, Jackson S, Wing RA (2008) Dynamic evolution of Oryza genomes is revealed by comparative genomic analysis of a genus-wide vertical data set. Plant Cell 20:3191–3209

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Atwell BJ, Wang H, Scafaro AP (2014) Could abiotic stress tolerance in wild relatives of rice be used to improve Oryza sativa? Plant Sci 215–216:48–58

    Article  PubMed  Google Scholar 

  • Brar DS, Dalmacio R, Elloran R, Aggarwal R, Angeles R, Khush GS (1996) Gene transfer and molecular characterization of introgression from wild Oryza species into rice. In: Khush GS (ed) Rice Genetics III. International Rice Research Institute, Manila, pp 477–485

    Google Scholar 

  • Brar DS, Khush GS (2002) Transferring genes from wild species into rice. In: Kang MS (ed) Quantitative genetics, genomics and plant breeding. CABI, Wallingford, pp 197–217

    Google Scholar 

  • Chang KD, Fang SA, Chang FC, Chung MC (2010) Chromosomal conservation and sequence diversity of ribosomal RNA genes of two distant Oryza species. Genomics 96:181–190

    Article  CAS  PubMed  Google Scholar 

  • Chen J, Huang Q, Gao D, Wang J, Lang Y, Liu T, Li B, Bai Z, Goicochea JL, Liang C, Chen C, Zhang W, Sun A, Liao Y, Zhang X, Yang L, Song C, Wang M, Shi J, Liu G, Liu J, Zhou H, Zhou W, Yu Q, An N, Chen Y, Cai Q, Wnag B, Liu B, Min J, Huang Y, Wu H, Li Z, Zhang Y, Yin Y, Song W, Jiang J, Jackson SA, Wing RA, Wang J, Chen M (2013) Whole genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution. Nat Commun 4:1595

    Article  PubMed  PubMed Central  Google Scholar 

  • Chung MC, Lee YI, Cheng YY, Chou YJ, Lu CF (2008) Chromosomal polymorphism of ribosomal genes in the genus Oryza. Theor Appl Genet 116:745–753

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Coffman WR, Juliano BO (1987) Rice. Nutritional quality of cereal grains: genetic and agronomic improvement. ASACSSA-SSSA, Madison, WI, pp 101–131

    Google Scholar 

  • De Rop V, Padeganeh A, Maddox PS (2012) CENP-A: the key player behind centromere identity, propagation, and kinetochore assembly. Chromosoma 121:527–538

    Article  PubMed  PubMed Central  Google Scholar 

  • Dong Z, Wang H, Dong Y, Wang Y, Liu W, Miao G, Xiuyun L, Daqing W, Liu B (2013) Extensive microsatellite variation in rice induced by introgression from wild rice (Zizania latifolia Griseb.). PLoS ONE 8:e62317

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • dos Santos RS, Farias DR, Pegoraro C, Rombaldi CV, Fukao T, Wing RA, de Oliveira AC (2017) Evolutionary analysis of the SUB1 locus across the Oryza genomes. Rice 10:4

    Article  PubMed  PubMed Central  Google Scholar 

  • Duistermaat H (1987) A revision of Oryza (Gramineae) in Malesia and Australia. Blumea 32:157–193

    Google Scholar 

  • Fan C, Walling JG, Zhang J, Hirsch CD, Jiang J, Wing RA (2011) Conservation and purifying selection of transcribed genes located in a rice centromere. Plant Cell 23:2821–2830

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gao D, Gill N, Kim HR, Walling JG, Zhang W, Fan C, Yu Y, Ma J, SanMiguel P, Jiang N, Cheng Z, Wing RA, Jiang J, Jackson SA (2009) A lineage-specific centromere retrotransposon in Oryza brachyantha. Plant J 60:820–831

    Article  CAS  PubMed  Google Scholar 

  • International Rice Genome Sequencing P (2005) The map-based sequence of the rice genome. Nature 436:793–800

    Article  Google Scholar 

  • Jacquemin J, Bhatia D, Singh K, Wing RA (2013) The International Oryza Map Alignment Project: development of a genus-wide comparative genomics platform to help solve the 9 billion-people question. Curr Opin Plant Biol 16:147–156

    Article  CAS  PubMed  Google Scholar 

  • Jacquemin J, Ammiraju JS, Haberer G, Billheimer DD, Yu Y, Liu LC, Rivera LF, Mayer K, Chen M, Wing RA (2014) Fifteen million years of evolution in the Oryza genus shows extensive gene family expansion. Mol Plant 7:642–656

    Article  CAS  PubMed  Google Scholar 

  • Jones JD, Dangl JL (2006) The plant immune system. Nature 444:323–329

    Article  CAS  PubMed  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 

  • Kawahara Y, de la Bastide M, Hamilton JP, Kanamori H, McCombie WR, Ouyang S, Schwartz DC, Tanaka T, Wu J, Zhou S, Childs KL, Davidson RM, Lin H, Quesada-Ocampo L, Vaillancourt B, Sakai H, Lee SS, Kim J, Numa H, Itoh T, Buell CR, Matsumoto T (2013) Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice 6:4

    Article  PubMed  PubMed Central  Google Scholar 

  • Lee HR, Zhang W, Langdon T, Jin W, Yan H, Cheng Z, Jiang J (2005) Chromatin immunoprecipitation cloning reveals rapid evolutionary patterns of centromeric DNA in Oryza species. Proc Natl Acad Sci U S A 102:11793–11798

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li Y, Yuan F, Wen Z, Li Y, Wang F, Zhu T, Zhuo W, Jin X, Wang Y, Zhao H, Pei ZM, Han S (2015) Genome-wide survey and expression analysis of the OSCA gene family in rice. BMC Plant Biol 15:261

    Article  PubMed  PubMed Central  Google Scholar 

  • Liu F, Tembrock LR, Sun C, Han G, Guo C, Wu Z (2016) The complete plastid genome of the wild rice species Oryza brachyantha (Poaceae). Mitochondrial DNA 1:218–219

    Article  Google Scholar 

  • Lu F, Ammiraju JS, Sanyal A, Zhang S, Song R, Chen J, Liu G, Sui Y, Song J, Cheng Z, De Oliveira AC, Bennetzen JL, Jackson AS, Wing RA, Chen M (2009) Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes. Proc Natl Acad Sci U S A 106:2071–2076

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • McAinsh MR, Pittman JK (2009) Shaping the calcium signature. New Phytol 181:275–294

    Article  CAS  PubMed  Google Scholar 

  • Menguer PK, Sperotto RA, Ricachenevsky FK (2017) A walk on the wild side: Oryza species as source for rice abiotic stress tolerance. Genet Mol Biol 40:238–252 https://doi.org/10.1590/1678-4685-GMB-2016-0093

    Google Scholar 

  • Miyamoto K, Fujita M, Shenton MR, Akashi S, Sugawara C, Sakai A, Horie K, Hasegawa M, Kawaide H, Mitsuhashi W, Nojiri H, Yamane H, Kurata N, Okada K, Toyomasu T (2016) Evolutionary trajectory of phytoalexin biosynthetic gene clusters in rice. Plant J 87:293–304

    Article  CAS  PubMed  Google Scholar 

  • Mullins IM, Hilu KW (2002) Sequence variation in the gene encoding the 10-kDa prolamin in Oryza (Poaceae). I. Phylogenetic implications. Theor Appl Genet 105:841–846

    Article  CAS  PubMed  Google Scholar 

  • Mullins IM, Hilu KW (2004) Amino acid variation in the 10 kDa Oryza prolamin seed storage protein. J Agric Food Chem 52:2242–2246

    Article  CAS  PubMed  Google Scholar 

  • Narain A, Kar MK, Kaliaperumal V, Sen P (2016) Development of monosomic alien addition lines from the wild rice (Oryza brachyantha A. Chev. et Roehr.) for introgression of yellow stem borer (Scirpophaga incertulas Walker.) resistance into cultivated rice (Oryza sativa L.). Euphytica 209:603–613

    Article  CAS  Google Scholar 

  • Ohmido N, Ohtsubo H, Ohtsubo E, Fukui K (1996) Physical mapping of several genes in rice using fluorescent in situ hybridization. In: Khush GS (ed) Rice Genetics III, Manila, pp 467–470

    Google Scholar 

  • Okada K (2011) The biosynthesis of isoprenoids and the mechanisms regulating it in plants. Biosci Biotechnol Biochem 75:1219–1225

    Article  CAS  PubMed  Google Scholar 

  • Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, Schmutz J, Spannagl M, Tang H, Wang X, Wicker T, Bharti AK, Chapman J, Feltus FA, Gowik U, Grigoriev IV, Lyons E, Maher CA, Martis M, Narechania A, Otillar RP, Penning BW, Salamov AA, Wang Y, Zhang L, Carpita NC, Freeling M, Gingle AR, Hash CT, Keller B, Klein P, Kresovich S, McCann MC, Ming R, Peterson DG, Mehboob-ur-Rahman, Ware D, Westhoff P, Mayer KF, Messing J, Rokhsar DS (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457:551–556

    Google Scholar 

  • Ram T, Laha GS, Gautam SK, Deen R, Madhav MS, Brar DS, Viraktamath BC (2010) Identification of a new gene introgressed from Oryza brachyantha with broad-spectrum resistance to bacterial blight of rice in India. RGN 25:57–58

    Google Scholar 

  • Ramachandran R, Khan ZR (1991) Mechanisms of resistance in wild rice Oryza brachyantha to rice leaffolder Cnaphalocrocis medinalis (Guenée) (Lepidoptera: Pyralidae). J Chem Ecol 17:41–65

    Article  CAS  PubMed  Google Scholar 

  • Ray S, Bose LK, Ray J, Ngangkham U, Katara JL, Samantaray S, Behera L, Anumalla M, Singh ON, Chen M, Wing RA, Mohapatra T (2016) Development and validation of cross-transferable and polymorphic DNA markers for detecting alien genome introgression in Oryza sativa from Oryza brachyantha. Mol Genet Genomics 291:1783–1794

    Article  CAS  PubMed  Google Scholar 

  • Ricachenevsky FK, Sperotto RA (2016) Into the wild: Oryza species as sources for enhanced nutrient accumulation and metal tolerance in rice. Front Plant Sci 7:974

    Google Scholar 

  • Sanchez PL, 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. Springer, New York, pp 9–26

    Chapter  Google Scholar 

  • Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock SM, Belter E, Du F, Kim K, Abbott RM, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson SM, Gillam B, Chen W, Yan L, Higginbotham J, Cardenas M, Waligorski J, Applebaum E, Phelps L, Falcone J, Kanchi K, Thane T, Scimone A, Thane N, Henke J, Wang T, Ruppert J, Shah N, Rotter K, Hodges J, Ingenthron E, Cordes M, Kohlberg S, Sgro J, Delgado B, Mead K, Chinwalla A, Leonard S, Crouse K, Collura K, Kudrna D, Currie J, He R, Angelova A, Rajasekar S, Mueller T, Lomeli R, Scara G, Ko A, Delaney K, Wissotski M, Lopez G, Campos D, Braidotti M, Ashley E, Golser W, Kim H, Lee S, Lin J, Dujmic Z, Kim W, Talag J, Zuccolo A, Fan C, Sebastian A, Kramer M, Spiegel L, Nascimento L, Zutavern T, Miller B, Ambroise C, Muller S, Spooner W, Narechania A, Ren L, Wei S, Kumari S, Faga B, Levy MJ, McMahan L, Van Buren P, Vaughn MW, Ying K, Yeh CT, Emrich SJ, Jia Y, Kalyanaraman A, Hsia AP, Barbazuk WB, Baucom RS, Brutnell TP, Carpita NC, Chaparro C, Chia JM, Deragon JM, Estill JC, Fu Y, Jeddeloh JA, Han Y, Lee H, Li P, Lisch DR, Liu S, Liu Z, Nagel DH, McCann MC, SanMiguel P, Myers AM, Nettleton D, Nguyen J, Penning BW, Ponnala L, Schneider KL, Schwartz DC, Sharma A, Soderlund C, Springer NM, Sun Q, Wang H, Waterman M, Westerman R, Wolfgruber TK, Yang L, Yu Y, Zhang L, Zhou S, Zhu Q, Bennetzen JL, Dawe RK, Jiang J, Jiang N, Presting GG, Wessler SR, Aluru S, Martienssen RA, Clifton SW, McCombie WR, Wing RA, Wilson RK (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326:1112–1115

    Google Scholar 

  • Sengupta S, Majumder AL (2010) Porteresia coarctata (Roxb.) Tateoka, a wild rice: a potential model for studying salt-stress biology in rice. Plant Cell Environ 33:526–542

    Article  CAS  PubMed  Google Scholar 

  • Shavrukov Y (2013) Salt stress or salt shock: which genes are we studying? J Exp Bot 64:119–127

    CAS  Google Scholar 

  • Shi J, Wolf SE, Burke JM, Presting GG, Ross-Ibarra J, Dawe RK (2010) Widespread gene conversion in centromere cores. PLoS Biol 8:e1000327

    Article  PubMed  PubMed Central  Google Scholar 

  • Singh S, Chand S, Singh NK, Sharma TR (2015) Genome-wide distribution, organisation and functional characterization of disease resistance and defence response genes across rice species. PLoS ONE 10:e0125964

    Article  PubMed  PubMed Central  Google Scholar 

  • Smith CW, Dilday RH (2003) Rice: Origin, history, technology, andproduction, 1st edn. Wiley, Hoboken, NewJersey, p 656

    Google Scholar 

  • Sui Y, Li B, Shi J, Chen M (2014) Genomic, regulatory and epigenetic mechanisms underlying duplicated gene evolution in the natural allotetraploid Oryza minuta. BMC Genom 15:11

    Article  Google Scholar 

  • Suzuki A, Tanifuji S, Komeda Y, Kato A (1996) Structural and functional characterization of the intergenic spacer region of the rDNA in Daucus carota. Plant Cell Physiol 37:233–238

    Article  CAS  PubMed  Google Scholar 

  • Tang L, Zou X, Zhang L, Ge S (2015) Multilocus species tree analyses resolve the ancient radiation of the subtribe Zizaniinae (Poaceae). Mol Phylogenet Evol 84:232–239

    Article  PubMed  Google Scholar 

  • Toyomasu T (2008) Recent advances regarding diterpene cyclase genes in higher plants and fungi. Biosci Biotechnol Biochem 72:1168–1175

    Article  CAS  PubMed  Google Scholar 

  • Tzvelev N (1989) The system of grasses (Poaceae) and their evolution. Bot Rev 55:141–203

    Article  Google Scholar 

  • Uozu S, Ikehashi H, Ohmido N, Ohtsubo H, Ohtsubo E, Fukui K (1997) Repetitive sequences: cause for variation in genome size and chromosome morphology in the genus Oryza. Plant Mol Biol 35:791–799

    Article  CAS  PubMed  Google Scholar 

  • Vaughan D (1989) The genus Oryza L. current status of taxonomy. IRRI research paper series number 138

    Google Scholar 

  • Wambugu PW, Furtado A, Waters DL, Nyamongo DO, Henry RJ (2013) Conservation and utilization of African Oryza genetic resources. Rice 6:29

    Article  PubMed  PubMed Central  Google Scholar 

  • Watson L, Clifford HT, Dallwitz MJ (1985) The classification of Poaceae: subfamilies and supertribes. Austral J Bot 33:433–484

    Article  Google Scholar 

  • Xu K, Xu X, Fukao T, Canlas P, Maghirang-Rodriguez R, Heuer S, Ismail AM, Bailey-Serres J, Ronald PC, Mackill DJ (2006) Sub1A is an ethylene-response-factor like gene that confers submergence tolerance to rice. Nature 442:705–708

    Article  CAS  PubMed  Google Scholar 

  • Yamakawa H, Ebitani T, Terao T (2008) Comparison between locations of QTLs for grain chalkiness and genes responsive to high temperature during grain filling on the rice chromosome map. Breed Sci 58:337–343

    Article  Google Scholar 

  • Yi C, Zhang W, Dai X, Li X, Gong Z, Zhou Y, Liang G, Gu M (2013) Identification and diversity of functional centromere satellites in the wild rice species Oryza brachyantha. Chromosome Res 21:725–737

    Article  CAS  PubMed  Google Scholar 

  • Zhang S, Gu YQ, Singh J, Coleman-Derr D, Brar DS, Jiang N, Lemaux PG (2007) New insights into Oryza genome evolution: high gene colinearity and differential retrotransposon amplification. Plant Mol Biol 64:589–600

    Article  CAS  PubMed  Google Scholar 

  • Zou XH, Zhang FM, Zhang JG, Zang LL, Tang L, Wang J, Sang T, Ge S (2008) Analysis of 142 genes resolves the rapid diversification of the rice genus. Genome Biol 9:R49

    Article  PubMed  PubMed Central  Google Scholar 

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Correspondence to Felipe Klein Ricachenevsky .

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Ricachenevsky, F.K., Buffon, G., Schwambach, J., Sperotto, R.A. (2018). Oryza brachyantha A. Chev. et Roehr. In: Mondal, T., Henry, R. (eds) The Wild Oryza Genomes. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-319-71997-9_7

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