, Volume 210, Issue 2, pp 151–163 | Cite as

Development of chromosome segment substitution lines (CSSLs) of Oryza longistaminata A. Chev. & Röhr in the background of the elite japonica rice cultivar, Taichung 65 and their evaluation for yield traits

  • Joie M. Ramos
  • Tomoyuki Furuta
  • Kanako Uehara
  • Niwa Chihiro
  • Rosalyn B. Angeles-Shim
  • Junghyun Shim
  • Darshan S. Brar
  • Motoyuki Ashikari
  • Kshirod K. Jena


Oryza longistaminata (AA genome) is a wild rice species that is phenotypically inferior to cultivated rice but possesses useful alleles that can be used to improve agronomically important traits. Interspecific hybrids that are derived from cultivated rice and wild rice species with AA genome are important contributors of genetic diversity in rice. To illustrate the potential of wild rice relatives as a source of novel alleles for rice improvement, a total of 40 chromosome segment substitution lines (CSSLs) of O. longistaminata in the background of the elite japonica cultivar Taichung 65 were developed and evaluated for yield and various yield-related traits. A number of CSSLs carrying putative quantitative trait loci (QTLs) controlling different yield-related traits were identified during both dry and wet seasons. In particular, 10 major putative QTLs controlling early heading date, plant height, tiller number, panicle length, number of primary branches per panicle, grain number per panicle, grain width, and grain thickness were identified. Interestingly, one of the CSSL lines, LTSL26, with major putative QTLs on chromosomes 1 and 8 that increase grain number per panicle, showed pleiotropic effects on other traits such as plant height, days to flowering, tiller number, number of branches per panicle, and grain length. These results suggest that O. longistaminata is a good source of new alleles that can be used to improve yield-related traits in cultivated rice varieties.


Wild rice Chromosome segment substitution lines (CSSLs) O. longistaminata QTL mapping Taichung 65 



Our sincere thanks go to the members of the Novel Gene Resources Laboratory (previously Wide Hybridization Laboratory), particularly to Mr. Eleazar “Boyet” Manalaysay, who helped in the production of LTSLs and in the evaluation of the materials. This research is supported by the Japan Society for the Promotion of Science (JSPS) Ronpaku Program in collaboration with the International Rice Research Institute, Philippines; Nagoya University, Japan, and the Science and Technology Research Program for Agriculture, Forestry, Fisheries and Food Industry; and is partially supported by JST, CREST.


  1. Ali ML, Sanchez PL, Yu SB, Lorieux M, Eizenga GC (2010) Chromosome segment substitution lines: a powerful tool for the introgression of valuable genes from Oryza wild species into cultivated rice (O. sativa). Rice 3:218–234CrossRefGoogle Scholar
  2. Ando T, Yamamoto T, Shimizu T, Ma XF, Shomura A, Takeuchi Y, Lin SY, Yano M (2008) Genetic dissection and pyramiding of quantitative traits for panicle architecture by using chromosomal segment substitution lines in rice. Theor Appl Genet 116:881–890CrossRefPubMedGoogle Scholar
  3. Brar DS, Khush GS (1997) Alien introgression in rice. Plant Mol Biol 35:35–47CrossRefPubMedGoogle Scholar
  4. Brar DS, Khush GS (2002) Transferring of genes from wild species into rice. In: Kang MS (ed) Quantitative genetics, genomics and plant breeding. CAB International, Wallingford, pp 197–217Google Scholar
  5. Brar DS, Khush GS (2003) Utilization of wild species in rice. In: Nanda JS, Sharma SD (eds) Monograph on genus Oryza. Science Pub. Inc., Enfield, pp 283–309Google Scholar
  6. Brar DS, Khush GS (2006) Cytogenetic manipulation and germplasm enhancement of rice (Oryza sativa L.). In: Singh RJ, Jauhar PP (eds) Genetic resources, chromosome engineering and crop improvement. CRC Press, Boca Raton, pp 115–158CrossRefGoogle Scholar
  7. Brar DS, Singh K (2011) Oryza. In: Kole C (ed) Wild crop relatives: genomics and breeding resources: cereals. Springer, Heidelberg, pp 321–366CrossRefGoogle Scholar
  8. Chen Z, Hu F, Xu P, Li J, Deng X, Zhou J (2009) QTL analysis for hybrid sterility and plant height in interspecific populations derived from a wild rice relative, Oryza longistaminata. Breed Sci 59:441–445CrossRefGoogle Scholar
  9. Chu YE, Oka HI (1970) Introgression across isolating barriers in wild and cultivated Oryza species. Evolution 24:344–355CrossRefGoogle Scholar
  10. Doi K, Iwata N, Yosimura A (1997) The construction of chromosome substitution lines of African rice (Oryza glaberrima Steud.) in the background of Japonica rice (O. sativa L.). Rice Genet Newsl 14:39–41Google Scholar
  11. Ebitani T, Takeuchi Y, Nonoue Y, Yamamoto T, Takeuchi K, Yano M (2005) Construction and evaluation of chromosome segment substitution lines carrying overlapping chromosome segments of indica rice cultivar “Kasalath” in a genetic background of japonica elite cultivar ‘Koshihikari’. Breed Sci 55:65–73CrossRefGoogle Scholar
  12. Furuta T, Uehara K, Angeles-Shim RB, Shim J, Ashikari M, Takashi T (2014) Development and evaluation of chromosome segment substitution lines (CSSLs) carrying chromosome segments derived from Oryza rufipogon in the genetic background of Oryza sativa L. Breed Sci 63:468–475CrossRefPubMedPubMedCentralGoogle Scholar
  13. Gichuhi E, Himi E, Takahashi H, Maekawa M (2012) Oryza longistaminata’s chromosome segments are responsible for agronomically important traits for environmentally smart rice. In: Proceedings of the 2012 JKUAT scientific, technological and industrialization conference-science, technology and innovation for sustainable development. Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya, pp 723–726Google Scholar
  14. Gutierrez AG, Carabali SJ, Giraldo OX, Martinez CP, Correa F, Prado G, Tohme J, Lorieux M (2010) Identification of a Rice stripe necrosis virus resistance locus and yield component QTLs using Oryza sativa × O. glaberrima introgression lines. BMC Plant Biol 10(1):6CrossRefPubMedPubMedCentralGoogle Scholar
  15. Jena KK (2010) The species of the genus Oryza and transfer of useful genes from wild species into cultivated rice, O. sativa. Breed Sci 60:518–523CrossRefGoogle Scholar
  16. Kanya JI, Hauser TP, Kinyamario JI, Amugune NO (2012) Hybridization potential between cultivated rice, Oryza sativa and African rice Oryza longistaminata. Int J Agric Res 7(6):291–302CrossRefGoogle Scholar
  17. Khush GS, Bacalangco E, Ogawa T (1990) A new gene for resistance to bacterial blight from O. longistaminata. Rice Genet Newsl 7:121–122Google Scholar
  18. Kobayashi N, Ikeda R, Domingo IT, Vaughan DA (1993) Resistance to infection of rice tungro viruses and vector resistance in wild species of rice (Oryza spp.). Jpn J Breed 43:377–378CrossRefGoogle Scholar
  19. Kobayashi N, Ikeda R, Vaughan DA (1994) Screening wild species of rice (Oryza spp.) for resistance to rice tungro disease. JARQ-Jpn Agric Res Q 28(4):230–236Google Scholar
  20. Li J, Xiao J, Grandillo S, Jiang L, Wan Y, Deng Q, Yuan L, McCouch SR (2004) QTL detection for rice grain quality traits using an interspecific backcross population derived from cultivated Asian rice (O. sativa L.) and African rice (O. glaberrima S.). Genome 47:697–704CrossRefPubMedGoogle Scholar
  21. Marathi B, Jena KK (2015) Floral traits to enhance outcrossing for higher hybrid seed production in rice: present status and future prospects. Euphytica 201:1–14CrossRefGoogle Scholar
  22. Marathi B, Ramos J, Hechanova SL, Oane RH, Jena KK (2015) SNP genotyping and characterization of pistil traits revealing a distinct phylogenetic relationship among the species of Oryza. Euphytica 201:131–148CrossRefGoogle Scholar
  23. McCouch SR, Sweeney M, Li J, Jiang H, Thomson M, Septiningsih E (2007) Through the genetic bottleneck: O. rufipogon as a source of trait-enhancing alleles for O. sativa. Euphytica 154:317–339CrossRefGoogle Scholar
  24. Moncada P, Martinez CP, Borrero J, Chatel M, Gauch H, Guimaraes E, Tohme J, McCouch SR (2001) Quantitative trait loci for yield and yield components in an Oryza sativa × Oryza rufipogon BC2F2 population evaluated in an upland environment. Theor Appl Genet 102:41–52CrossRefGoogle Scholar
  25. Neff MM, Neff JD, Chory J, Pepper AE (1998) dCAPs, a simple technique for the genetic analysis of single nucleotide polymorphisms: experimental applications in Arabidopsis thaliana genetics. Plant J 14(3):387–392CrossRefPubMedGoogle Scholar
  26. Reintar RIS (2007) Molecular characterization of introgression from O. longistaminata A. Chev. et Roehr. into rice (Oryza sativa L.). Dissertation, University of the Philippines, Los Baños (UPLB)Google Scholar
  27. Ronald PC, Albano B, Tabien R, Abenes L, Wu KS, McCouch SR, Tanksley SD (1992) Genetic and physical analysis of the rice bacterial blight disease resistance locus, Xa21. Mol Gen Genet 236(1):113–120PubMedGoogle Scholar
  28. Sanchez PL, Sobrizal Ikeda K, Yasui H, Yoshimura A (2003) Identifying late heading genes in rice using Oryza glumaepatula introgression lines. In: Khush GS, Brar DS, Hardy B (eds) Advances in rice genetics, proceedings of the fourth international rice genetics symposium. International Rice Research Institute, Los Baños, pp 153–154Google Scholar
  29. 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: crops and models 5. Springer, New York, pp 9–25CrossRefGoogle Scholar
  30. Schneider CA, Rasband WS, Eliceiri KW (2012) NIH Image to ImageJ: 25 years of image analysis. Nat Methods 9:671–675CrossRefPubMedGoogle Scholar
  31. Septiningsih EM, Prasetyono J, Lubis E, Thai TH, Tjubaryat T, Moeljopawiro S, McCouch SR (2003) Identification of quantitative trait loci for yield and yield components in an advanced backcross population derived from the Oryza sativa variety IR64 and the wild relative O. rufipogon. Theor Appl Genet 107:1419–1432CrossRefPubMedGoogle Scholar
  32. Shan X, Lui Z, Dong Z, Wang Y, Chen Y, Lin X, Long L, Han F, Dong Y, Lui B (2005) Mobilization of the Active MITE transposons mPing and Pong in rice by introgression from wild rice (Zizania latifolia Griseb.). Mol Biol Evol 22:976–990CrossRefPubMedGoogle Scholar
  33. Shim RA, Angeles ER, Ashikari M, Takashi T (2010) Development and evaluation of Oryza glaberrima Steud. chromosome segment substitution lines (CSSLs) in the background of O. sativa L. cv. Koshihikari. Breed Sci 60:613–619CrossRefGoogle Scholar
  34. Shim RA, Vinarao R, Marathi B, Jena K (2014) Molecular analysis of Oryza latifolia Desv. (CCDD Genome)-derived introgression lines and identification of value-added traits for rice (O. sativa L.) improvement. J Hered 105(5):676–689CrossRefGoogle Scholar
  35. Soriano IR, Schmit V, Brar DS, Prot JC, Reversat G (1999) Resistance to rice knot nematode Meloidogyne graminicola identified in Oryza longistaminata and O. glaberrima. Nematology 1(4):395–398CrossRefGoogle Scholar
  36. Statistical Tools for Agricultural Research (STAR), version 1.0 (2013) Biometrics and Breeding Informatics, PBGB Division, International Rice Research Institute, Los Baños, Laguna, PhilippinesGoogle Scholar
  37. Susanto U, Aswidinnoor H, Koswara J, Aetiawan A, Lopena V, Torrizo L, Virk PS (2008) QTL mapping of yield, yield components and morphological traits in rice (Oryza sativa L.) using SSR markers. Bull Agron 36(3):188–195Google Scholar
  38. Swamy BPM, Sarla N (2008) Yield enhancing quantitative trait loci (QTLs) from wild species. Biotechnol Adv 26(1):106–120CrossRefPubMedGoogle Scholar
  39. Swamy BPM, Kaladhar K, Ramesha MS, Viraktamath VC, Sarla N (2011) Molecular mapping of QTLs for yield and related traits in Oryza sativa cv Swarna × O. nivara (IRGC 81848) backcross population. Rice Sci 18(3):178–186CrossRefGoogle Scholar
  40. Takai T, Nonoue Y, Yamamoto S, Yamanouchi U, Matsubara K, Liang Z, Lin H, Ono N, Uga Y, Yano M (2007) Development of chromosome segment substitution lines derived from backcross between indica donor rice cultivar ‘Nona Bokra” and japonica recipient cultivar ‘Koshihikari’. Breed Sci 57:257–261CrossRefGoogle Scholar
  41. Varma CMK, Gouda PK, Saikumar S, Shenoy V, Shashidhar HE, Neelamraju S (2012) Transgressive segregation for yield traits in Oryza sativa IR58025B × Oryza meridionalis Ng. BC2F3 population under irrigated and aerobic conditions. J Crop Sci Biotechnol 15(3):231–238CrossRefGoogle Scholar
  42. Wang YM, Dong ZY, Zhang ZJ, Lin XY, Shen Y, Zhou D, Lui B (2005) Extensive de novo genomic variation in rice induced by introgression from wild rice (Zizania latifolia Griseb.). Genetics 170:1945–1956CrossRefPubMedPubMedCentralGoogle Scholar
  43. Xiao J, Li J, Grandillo S, Ahn SN, Yuan L, Tanksley S, McCouch SR (1998) Identification of trait-improving quantitative trait loci alleles from wild rice relative, O. rufipogon. Genetics 150:899–909PubMedPubMedCentralGoogle Scholar
  44. Yang H, Hu L, Hurek T, Reinhold-Hurek B (2010) Global characterization of the root transcriptome of a wild species of rice, Oryza longistaminata, by deep sequencing. BMC Genom 11:705–712CrossRefGoogle Scholar
  45. Zhang F, Li T, Shan Q, Guo Y, Xu P, Hui F, Tao D (2008) Weed suppression ability of Oryza longistaminata and Oryza sativa. Allelopathy J 22(2):345–352Google Scholar
  46. Zhang H, Zhao Q, Sun ZZ, Zhang CQ, Feng Q, Tang SZ, Liang GH, Gu MH, Han B, Liu QQ (2011) Development and high-throughput genotyping of substitution lines carrying the chromosome segments of indica 93-11 in the background of japonica Nipponbare. J Genet Genom 38(12):603–611CrossRefGoogle Scholar
  47. Zhao J, Li J, Xu P, Zhou J, Hu F, Deng X, Deng W, Tao D (2012) A new gene controlling hybrid sterility between Oryza sativa and Oryza longistaminata. Euphytica 187:339–344CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2016

Authors and Affiliations

  • Joie M. Ramos
    • 1
    • 2
  • Tomoyuki Furuta
    • 2
  • Kanako Uehara
    • 2
  • Niwa Chihiro
    • 2
  • Rosalyn B. Angeles-Shim
    • 1
    • 2
  • Junghyun Shim
    • 1
  • Darshan S. Brar
    • 3
  • Motoyuki Ashikari
    • 2
    • 4
  • Kshirod K. Jena
    • 1
  1. 1.Novel Gene Resources Laboratory, Plant Breeding, Genetics, and Biotechnology DivisionInternational Rice Research InstituteMetro ManilaPhilippines
  2. 2.Bioscience and Biotechnology CenterNagoya UniversityChikusa, NagoyaJapan
  3. 3.School of Agricultural BiotechnologyPunjab Agricultural UniversityLudhianaIndia
  4. 4.CRESTJapan Science and Technology AgencyTokyoJapan

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