, 213:96 | Cite as

Linkage map construction and QTL identification of P-deficiency tolerance in Oryza rufipogon Griff. at early seedling stage

  • Xiang-Dong LuoEmail author
  • Jian Liu
  • Liang-Fang Dai
  • Fan-Tao Zhang
  • Yong Wan
  • Jian-Kun XieEmail author


Low phosphorus availability is a major factor limiting rice productivity. In this study, a population of backcross recombinant inbred lines (BILs) derived from an inter-specific cross (Oryza sativa L. × O. rufipogon Griff.) was used for genetic linkage map construction and quantitative trait locus (QTL) mapping. The results showed that a linkage map consisting of 153 markers was constructed. Twenty-one out of 231 BILs were tolerant of low-phosphorus according to the index to P-deficiency tolerance. Twenty-three QTLs on chromosomes 1, 2, 3, 7, 8, 9 and 11 were detected, of which eight QTLs showed high (22.93–37.32%) contribution to phenotypic variation. In addition, most of QTLs in this study (18 out of 23 QTLs) were located and overlapped on the chromosome 1, 3 and 11, which individually explained 6.07–34.70% phenotypic variation, indicating that there might be multiple main effect QTLs related to P-deficiency tolerance in O. rufipogon, and these QTLs might cluster in the same region. These results would provide helpful information for cloning and utilizing the P-deficiency tolerance-responsive genes from O. rufipogon.


Common wild rice P-deficiency tolerance Linkage map QTL Backcross recombinant inbred lines 



This research was partially supported by the National Natural Science Foundation of China (31260255, 31360147 and 31660384), the Development Program for Young Scientists of Jiangxi Province, China (20112BCB23007) and the Scientific Planning Project of Jiangxi Provincial Education Department (GJJ12184 and KJLD12059).


  1. Abel S, Ticconi CA, Delatorre CA (2002) Phosphate sensing in higher plants. Physiol Plant 115:1–8CrossRefPubMedGoogle Scholar
  2. Chen XR, Chen M, He HH, Zhu CL, Peng XS, He XP, Fu JR, Ouyang LJ (2011) Low-phosphorus tolerance and related physiological mechanism of Xieqingzao B//Xieqingzao B/Dongxiang wild rice BC1F9 populations. Chin J Appl Ecol 22:1169–1174Google Scholar
  3. Churchill GA, Doerge RW (1994) Empirical threshold value for quantitative trait mapping. Genetics 138:963–971PubMedPubMedCentralGoogle Scholar
  4. Cordell D, Drangert JO, White S (2009) The story of phosphorus: global food security and food for thought. Glob Environ Change 19:292–305CrossRefGoogle Scholar
  5. Deng XJ, Luo XD, Chen YL, Hu BL, Xie JK (2012) Genetic diversity and genetic changes in the introgression lines derived from Oryza sativa L. mating with O. rufipogon Griff. J Integr Agric 11(7):1059–1066CrossRefGoogle Scholar
  6. Gamuyao R, Chin JH, Pariasca-Tanaka J, Pesaresi P, Catausan S, Dalid C, Slamet-Loedin I, Tecson-Mendoza EM, Wissuwa M, Heuer S (2012) The protein kinase Pstol1 from traditional rice confers tolerance of phosphorus deficiency. Nature 488(7412):535–539CrossRefPubMedGoogle Scholar
  7. Hermans C, Hammond JP, White PJ, Verbruggen N (2006) How do plants respond to nutrient shortage by biomass allocation? Trends Plant Sci 11:610–617CrossRefPubMedGoogle Scholar
  8. Heuer S, Lu XC, Joonghyoun C, Tanaka JP, Kanamori H, Matsumoto T, Leon TD, Ulat VJ, Ismail AM, Yano M, Wissuwa M (2009) Comparative sequence analyses of the major quantitative trait locus phosphorus uptake 1 (pup1) reveal a complex genetic structure. Plant Biotechnol J 7(5):456–471CrossRefPubMedGoogle Scholar
  9. Hu B, Wu P, Liao CY, Zhang WP, Ni JJ (2001) QTLs and epistasis underlying activity of acid phosphatase under phosphorus sufficient and deficient condition in rice (Oryza sativa L.). Plant Soil 230:99–105CrossRefGoogle Scholar
  10. Huang C (2005) Screening for tolerance to low-phosphorus Stress of Chinese japonica rice core collection (Oyrza sativa L.) and detection of QTL for tolerance to low-phosphorus of rice. Dissertation, China Agricultural University, pp 18–25Google Scholar
  11. Koide Y, Pariasca-Tanaka J, Rose T, Fukuo A, Konisho K, Yanagihara S, Fukuta Y, Wissuwa M (2013) QTLs for phosphorus-deficiency tolerance detected in upland NERICA varieties. Plant Breed 132:259–265CrossRefGoogle Scholar
  12. Kosambi DD (1944) The estimation of map distance from recombination values. Ann Eugen 12:172–175CrossRefGoogle Scholar
  13. Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE, Newburg L (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181CrossRefPubMedGoogle Scholar
  14. Lebreton C, Lazic-Jancic V, Steed A, Pekic S, Quarrie SA (1995) Identification of QTL for drought responses in maize and their use in testing causal relationships between traits. J Exp Bot 46:853–865CrossRefGoogle Scholar
  15. Li JZ, Xie Y, Dai AY, Liu LF, Li ZC (2009) Root and shoot traits responses to phosphorus deficiency and QTL analysis at seedling stage using introgression lines of rice. J Genet Genom 36:173–183CrossRefGoogle Scholar
  16. Li YT, Gu M, Zhang X, Zhang J, Fan HM, Li PP, Li ZF, Xu GH (2014) Engineering a sensitive visual-tracking reporter system for real-time monitoring phosphorus deficiency in tobacco. Plant Biotechnol J 12:674–684CrossRefPubMedGoogle Scholar
  17. Luo XD, Dai LF, Cao JF, Jian SR, Chen YL, Hu BL, Xie JK (2012) Identification and molecular cytology analysis of cold tolerance introgression lines derived from Oryza sativa L. mating with O. rufipogon Griff. Euphytica 187:461–469CrossRefGoogle Scholar
  18. McCouch SR, CGSNL (Committee on Gene Symbolization, Nomenclature and Linkage, Rice Genetics Cooperative) (2008) Gene nomenclature system for rice. Rice 1:72–84CrossRefGoogle Scholar
  19. Mu P, Huang C, Li JX, Liu LF, Liu UJ, Li ZC (2008) Yield trait variation and QTL mapping in a DH population of rice under phosphorus deficiency. Acta Agron Sin 34:1137–1142Google Scholar
  20. Mukherjee A, Sarkar S, Chakraborty AS, Yelne R, Kavishetty V, Biswas T, Mandal N, Bhattacharyya S (2014) Phosphate acquisition efficiency and phosphate starvation tolerance locus (PSTOL1) in rice. J Genet 93:683–688CrossRefPubMedGoogle Scholar
  21. Murray HG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8:4321–4326CrossRefPubMedPubMedCentralGoogle Scholar
  22. Ni JJ, Wu P, Senadhira D, Senadhira D, Huang N (1998) Mapping QTLs for phosphorus deficiency tolerance in rice (Oryza sativa L.). Theor Appl Genet 97:1361–1369CrossRefGoogle Scholar
  23. Pariasca-Tanaka J, Chin JH, DraméK N, Dalid C, Heuer S, Wissuwa M (2014) A novel allele of the P-starvation tolerance gene OsPSTOL1 from African rice (Oryza glaberrima Steud) and its distribution in the genus Oryza. Theor Appl Genet 127:1387–1398CrossRefPubMedPubMedCentralGoogle Scholar
  24. Qiu HB, Mei XP, Liu CX, Wang JG, Wang GQ, Wang X, Liu Z, Cai YL (2013) Fine mapping of quantitative trait loci for acid phosphatase activity in maize leaf under low phosphorus stress. Mol Breed 32:629–639CrossRefGoogle Scholar
  25. Shimizu A, Yanagihara S, Kawasaki S, Ikehashi H (2004) Phosphorus deficiency-induced root elongation and its QTL in rice (Oryza sativa L.). Theor Appl Genet 109:1361–1368CrossRefPubMedGoogle Scholar
  26. Shimizu A, Kat K, Komatsu A, Motomura K, Ikehashi H (2008) Genetic analysis of root elongation induced by phosphorus deficiency in rice (Oryza sativa L.): fine QTL mapping and multivariate analysis of related traits. Theor Appl Genet 117:987–996CrossRefPubMedGoogle Scholar
  27. Sun CQ, Wang XK, Yoshimura A, Iwata N (2001) Comparison of the genetic diversity of common wild rice (Oryza rufipogon Griff.) and cultivated rice (O. sativa L.) using RFLP markers. Theor Appl Genet 102:157–162CrossRefGoogle Scholar
  28. Tan LB, Liu FX, Xue W, Wang GJ, Ye S, Zhu ZF, Fu YC, Wang XK, Sun CQ (2007) Development of Oryza rufipogon and O. sativa introgression lines and assessment for yield-related quantitative trait loci. J Integr Plant Biol 49:871–884CrossRefGoogle Scholar
  29. Vejchasarn P, Lynch JP, Brown KM (2016) Genetic variability in phosphorus responses of rice root phenotypes. Rice 9:29CrossRefPubMedPubMedCentralGoogle Scholar
  30. Wang S, Basten CJ, Zeng ZB (2005) Windows QTL Cartographer 2.5. Department of Statistics, North Carolina State University, RaleighGoogle Scholar
  31. Wasaki J, Yonetani R, Shinano T, Kai M, Osaki M (2003) Expression of the OsPI1 gene, cloned from rice roots using cDNA microarray, rapidly responds to phosphorus status. New Phytol 158(2):239–248CrossRefGoogle Scholar
  32. Wissuwa M, Wegner J, Ae N (2002) Substitutionmapping of Pup1: a major QTL increasing phosphorus uptake of rice from a phosphorus-deficient soil. Theor Appl Genet 105:890–897CrossRefPubMedGoogle Scholar
  33. Xie J, Agrama HA, Kong D, Zhuang J, Hu B, Wan Y, Yan W (2010) Genetic diversity associated with conservation of endangered Dongxiang wild rice (Oryza rufipogon). Genet Resour Crop Evol 57:597–609CrossRefGoogle Scholar
  34. Yi K, Wu Z, Zhou J, Du L, Guo L, Wu Y, Wu P (2005) OsPTF1, a novel transcription factor involved in tolerance to phosphate starvation in rice. Plant Physiol 138:2087–2096CrossRefPubMedPubMedCentralGoogle Scholar
  35. York LM, Nord EA, Lynch JP (2013) Integration of root phenes for soil resource acquisition. Front Plant Sci 4:1–15CrossRefGoogle Scholar
  36. Yoshida S, Forno DA, Cock JH, Gomez KA (1976) Laboratory manual for physiological studies of rice, 3rd edn. International Rice Research Institute, ManilaGoogle Scholar
  37. Zhang FT, Cui FL, Zhang LX, Wen XF, Luo XD, Zhou Y, Li X, Wan Y, Zhang J, Xie JK (2014) Development and identification of a introgression line with strong drought resistance at seedling stage derived from Oryza sativa L. mating with Oryza rufipogon Griff. Euphytica 200:1–7CrossRefGoogle Scholar
  38. Zhu J, Lynch JP (2004) The contribution of lateral rooting to phosphorus acquisition efficiency in maize (Zea mays) seedlings. Funct Plant Biol 31:949–958CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2017

Authors and Affiliations

  1. 1.College of Life ScienceJiangxi Normal UniversityNanchangChina
  2. 2.Rice Research InstituteJiangxi Academy of Agricultural ScienceNanchangChina

Personalised recommendations