, Volume 156, Issue 1–2, pp 237–246 | Cite as

Construction and characterization of 3-S Lines, an alternative population for mapping studies in rice (Oryza sativa L.)



Most traits of agronomic importance in rice are quantitative in nature and are controlled by polygenes, called quantitative trait loci (QTL). Understanding the nature and effect of QTLs are important for rice breeding to achieve higher yield and stability. Single segment substitution lines (SSSLs or 3-S Lines) were developed through simple sequence repeats (SSR) marker-facilitated backcrossing methods for Hua-Jing-Xian 74 (HJX74) with the donor segment from six elite germplasm and was characterized. Complete genome survey was carried out with 258 polymorphic SSR markers. Polymorphism of the donors with the recurrent parent varied between 32.98 and 60.73% with an average of 47.81%. Japonica donors were more polymorphic than indica donors. Number of substitution segments per plant decreased with the advancement of backcross generations. In BC2F1, BC3F1, BC3F2 and BC3F3 the average number of substitution segment per plant were 12.5, 5.98, 1.69 and 1.46, respectively. Average size of substitution segments also decreased with the number of times plants were backcrossed and selfed. In BC2F1, BC3F1, BC3F2 and BC3F3, average size of the segments was 25.43, 22.38, 20.78 and 18.15 cM, respectively. The rate of reduction of segment size was more in backcross (11.99%) than selfing (7.15%) generations. Percent recovery of recurrent parent genome in BC2F1, BC3F1, BC3F2 and BC3F3 was 82.24, 92.55, 98.04 and 98.52%, respectively. A total of 111 SSSLs comprising of 43 unique types were developed in BC3F2 and BC3F3. The estimated length of the segments in SSSLs ranged from 2.00 to 64.80 cM with an average of 21.75 cM, and 6.05 to 48.90 cM with an average of 20.95 cM in BC3F2 and BC3F3, respectively. Total length of all substitution segments was 2367.5 cM that covered 704.50 cM (39.25%) of the entire rice genome. Effective development and successful utilization of 3-S Lines for analysis of QTLs and mapping of genes established the suitability of the SSR marker facilitated backcross breeding approach for 3-S Lines development and its utilization.


Mapping population Molecular backcross breeding Rice 3-S Lines SSR markers QTL 


  1. Aida Y, Tsunimatsu H, Doi K, Yoshimura A (1997) Development of a series of introgression lines of japonica rice in the background of indica rice. RGN 14:41–43Google Scholar
  2. Anonymous (2000) Integrated international molecular breeding program. Progress report (1998–1999). IRRI, PhilippinesGoogle Scholar
  3. Cermakova L, Sharpe A, Trick M, Bechyne M, Lydiate, D (1999) Genetic analysis of quantitative traits in Brassica napus using substitution lines. In: Proceeding of the 10th international rapeseed congress, Canberra, AustraliaGoogle Scholar
  4. Doi K, Yoshimura A, Iwata N (1998) RFLP mapping and QTL analysis of heading date and pollen sterility using backcross population between Oryza sativa L and Oryza glaberrima Steud. Breed Sci 48:395–399Google Scholar
  5. Eshed Y, Zamir D 1995 An introgression line population of Lycopersicon pennellii in the cultivate tomato enables the identification and fine mapping of yield-associated QTLs. Genetics 141:1147–1162PubMedGoogle Scholar
  6. He FH, Xi ZY, Zeng RZ, Talukdar A, Zhang GQ (2005) Mapping of Heading date QTL in rice (Oryza sativa L.) using Single Segment Substitution Lines (SSSLs). Scientia Agricultura Sinica 38(8):1505–1513Google Scholar
  7. Kubo T, Nakemua K, Yoshimura A (1999) Development of a series of indica chromosome substitution lines in japonica background or rice. RGN 16:104–106Google Scholar
  8. Li W, Zeng R, Zhang Z, Zhang G (2003) Analysis of introgression segments in near isogenic line for F1 pollen sterility in rice (Oryza sativa L.). Chin J Rice Sci 17(2):95–99Google Scholar
  9. McCouch SR, Teytelman L, Xu Y, Lobos KB, Clare K, Walton M, Fu B, Maghirang R, Li Z, Xing Y, Zhang Q, Kono I, Yano M, Fjellstrom R, DeClerck G, Schneider D, Cartinhour S, Ware D, Stein L (2002) Development and mapping of 2240 new SSR markers for rice (Oryza sativa L). DNA Res 9:199–207PubMedCrossRefGoogle Scholar
  10. Monforte A, Tanksley S (2000) Development of a set of near isogenic and backcross recombinant inbred lines containing most of the Lycopersicon hirsutum genome in a L esculentum genetic background: a tool for gene mapping and gene discovery. Genome 43:808–813CrossRefGoogle Scholar
  11. Muehlbauer GJ, Specht JE, Thomas-Compton MA, Staswick PE, Bernard RL (1988) Near-Isogenic Lines- A potential resource in the integration of conventional and molecular linkage map. Crop Sci 28:729–735CrossRefGoogle Scholar
  12. Panaud O, Chen X, McCouch SR (1996) Development of microsatellite markers and characterization of simple sequence length polymorphism (SSLP) in rice (Oryza sativa L). Mol Gen Genet 252:597–607PubMedGoogle Scholar
  13. Sobrizal, Ikeda K, Sanchez PL, Doi K, Angeles ER, Khush GS, Yoshimura A (1999) Development of Oryza glumaepatula introgression lines in rice O sativa. RGN 16:107–108Google Scholar
  14. Talukdar A, Zhang GQ (2006). 3-S Lines and mapping of gene for purple apiculus in rice. Indian J Genet 66(4):271–274Google Scholar
  15. Tanksley S, Nelson J (1996) Advanced backcross QTL analysis: a method for the simultaneous discovery and transfer of valuable QTLs from unadapted germplasm into elite breeding lines. Theor Appl Genet 92:191–203CrossRefGoogle Scholar
  16. Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch SR (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativa L): frequency, length variation, transposon associations and genetic marker potential. Genome Res 11:1441–1452PubMedCrossRefGoogle Scholar
  17. Zhang GQ, Zeng RZ, Zhang ZM, Ding XH, Li WT, Liu GM, He FH, Talukdar A, Xi ZY, Qin LJ, Shi JQ, Feng MJ, Chen L, Chen ZL, Zhu HT (2004) The construction of a library of Single Segment Substitution Lines in rice (Oryza sativa L.). Rice Genet Newsl 21:85–87Google Scholar
  18. Zheng K, Huang N, Bennett J, Khush G (1995) PCR-based marker-assisted selection in rice breeding. IRRI discussion paper series. No. 12. IRRI, Manila, PhilippinesGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2007

Authors and Affiliations

  1. 1.Division of GeneticsIndian Agricultural Research InstituteNew DelhiIndia
  2. 2.South China Agricultural UniversityGuangzhouP. R. China

Personalised recommendations