Skip to main content
SpringerLink
Log in

Dissection of genetic overlap of salt tolerance QTLs at the seedling and tillering stages using backcross introgression lines in rice

  • Article
  • Published:
Science in China Series C: Life Sciences Aims and scope Submit manuscript

Abstract

QTLs for salt-tolerance (ST) related traits at the seedling and tillering stages were identified using 99 BC2F8 introgression lines (IL) derived from a cross between IR64 (indica) as a recurrent parent and Binam (japonica) from Iran as the donor parent. Thirteen QTLs affecting survival days of seedlings (SDS), score of salt toxicity of leaves (SST), shoot K+ concentration (SKC) and shoot Na+ concentration (SNC) at the seedling stage and 22 QTLs underlying fresh weight of shoots (FW), tiller number per plant (TN) and plant height (PH) at the tillering stage were identified. Most QTLs detected at the tillering stage showed obvious differential expression to salt stress and were classified into three types based on their differential behaviors. Type I included 11 QTLs which were expressed only under the non-stress condition. Type II included five QTLs expressed in the control and the salt stress conditions, and three of them (QPh5, QPh8 and QTn9) had similar quantity and the same direction of gene effect, suggesting their expression was less influenced by salt stress. Type III included six QTLs which were detectable only under salt stress, suggesting that these QTLs were apparently induced by the stress. Thirteen QTLs affecting trait difference or trait stability of ILs between the stress and non-stress conditions were identified and the Binam alleles at all loci except QPh4, QTn2 and QFw2a decreased trait difference. The three QTLs less influenced by the stress and 13 QTLs affecting trait stability were considered as ST QTLs which contributed to ST. Comparing the distribution of QTLs detected at the seedling and tillering stages, most (69%) of them were genetically independent. Only four were the same or adjacent regions on chromosomes 1, 2, 8 and 11 harboring ST QTLs detected at the two stages, suggesting that partial genetic overlap of ST across the two stages occurs. It is likely, therefore, to develop ST rice variety for both stages by pyramiding of ST QTLs of different stages or selection against the overlapping QTLs between the two stages via marker-assisted selection (MAS).

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. Yeo A R, Flowers T J. Salinity resistance in rice (Oryza sativa L.) and a pyramiding approach to breeding varieties for saline soils. Aust J Plant Physiol, 1986, 13: 161–173, 10.1071/PP9860161

    Article  Google Scholar 

  2. Greenway H, Munns R. Mechanism of salt tolerance in nonhalophytes. Annu Rev Plant Physiol, 1980, 31: 149–190, 10.1146/annurev.pp.31.060180.001053, 1:CAS:528:DyaL3cXksVWntb4%3D

    Article  CAS  Google Scholar 

  3. Shannon M C. Principles and strategies in breeding for higher salttolerance. Plant Soil, 1985, 89: 227–241, 10.1007/BF02182244

    Article  Google Scholar 

  4. Lauchli A, Epstein E. Plant responses to saline and sodic conditions. In: Tanji K K, ed. Agricultural Salinity Assessment and Management. New York: Am Soc Civil Engrs, 1990. 113–137

    Google Scholar 

  5. Johnson D W, Smith S E, Dobrenz A K. Genetic and phenotypic relationships in response to NaCl at different developmental stages in alfalfa. Theor Appl Genet, 1992, 83: 833–838, 10.1007/BF00226705

    CAS  Google Scholar 

  6. Foolad M R, Lin G Y. Absence of a relationship between salt tolerance during germination and vegetative growth in tomato. Plant Breed, 1997, 116: 363–367, 10.1111/j.1439-0523.1997.tb01013.x, 1:CAS:528:DyaK2sXmvVagu7Y%3D

    Article  CAS  Google Scholar 

  7. Foolad M R, Chen F Q. RFLP mapping of QTLs conferring salt tolerance during the vegetative stage in tomato. Theor Appl Genet, 1999, 99: 235–243, 10.1007/s001220051229, 1:CAS:528:DyaK1MXlvFGltb4%3D

    Article  CAS  Google Scholar 

  8. Akbar M, Yabuno T. Breeding for saline-resistant varieties of rice: II. Comparative performance of some rice varieties to salinity during early development stage. Jap J Breed, 1974, 25: 176–181

    Google Scholar 

  9. Pearson G A. The salt tolerance of rice. Int Rice Commun Newsletter, 1961, 10: 1–4

    Google Scholar 

  10. Pearson G A, Ayers A D, Eberhard D L. Relative salt tolerance of rice during germination and early seedling development. Soil Sci, 1966, 102: 151–156, 10.1097/00010694-196609000-00003, 1:CAS:528:DyaF28XkvVGgsbs%3D

    Article  CAS  Google Scholar 

  11. Flowers T J, Yeo A R. Variability in the resistance of sodium chloride salinity within rice (Oryza sativa L.) varieties. New Phytol, 1981, 88: 363–373, 10.1111/j.1469-8137.1981.tb01731.x, 1:CAS:528:DyaL3MXlt12ksL8%3D

    Article  CAS  Google Scholar 

  12. Gong J M, He P, Qian Q, et al. Identification of salt-tolerance QTL in rice (Oryza sativa L.). Chin Sci Bull, 1999, 44(1): 68–71, 10.1007/BF03182889

    Article  Google Scholar 

  13. Gu X Y, Mei M T, Yan X L, et al. Preliminary detection of quantitative trait loci for salt tolerance in rice. Chin J Rice Sci (in Chinese), 2000, 14(2): 65–70

    Google Scholar 

  14. Prasad S R, Bagali P G, Hittalmani S, et al. Molecular mapping of quantitative trait loci associated with seedling tolerance to salt stress in rice (Oryza sativa L). Curr Sci, 2000, 78: 162–164, 1:CAS:528:DC%2BD3cXhtV2gs7k%3D

    CAS  Google Scholar 

  15. Lin H X, Zhu M Z, Yano M, et al. QTLs for Na+ and K+ uptake of the shoots and roots controlling rice salt tolerance. Theor Appl Genet, 2004, 108: 253–260, 14513218, 10.1007/s00122-003-1421-y, 1:CAS:528:DC%2BD2cXjtFCntg%3D%3D

    Article  CAS  Google Scholar 

  16. Koyama M L, Levesley A, Koebner R M et al. Quantitative trait loci for component physiological traits determining salt tolerance in rice. Plant Physiol, 2001, 125: 406–422, 11154348, 10.1104/pp.125.1.406, 1:CAS:528:DC%2BD3MXjslyls70%3D

    Article  CAS  Google Scholar 

  17. Zhang G Y, Guo Y, Chen S L, et al. RFLP tagging of a salt tolerance gene. Plant Sci, 1995, 110(2):227–234, 10.1016/0168-9452(95)04219-K, 1:CAS:528:DyaK2MXotFCqtro%3D

    Article  CAS  Google Scholar 

  18. Lee S Y, Ahn J H, Cha Y S, et al. Mapping of quantitative trait loci for salt tolerance at the seedling stage in rice. Mol Cells, 2006, 21(2): 192–196, 16682812, 1:CAS:528:DC%2BD28Xlt1Wjsro%3D

    CAS  Google Scholar 

  19. Sun Y, Zang J P, Wang Y, et al. Mining favorable salt-tolerant QTL from rice germplasm using a backcrossing introgression line population. Acta Agron Sin (in Chinese), 2007, 33(10): 1611–1617, 1:CAS:528:DC%2BD1cXht1aktrvI

    CAS  Google Scholar 

  20. Takehisa H, Shimodate T, Fukuta Y, et al. Identification of quantitative trait loci for plant growth of rice in paddy field flooded with salt water. Field Crops Res, 2004, 89: 85–95, 10.1016/j.fcr.2004.01.026

    Article  Google Scholar 

  21. Yoshida S, Forno D A, Cock J H, et al. Laboratory Manual for Physiological Studies of Rice. 3rd ed. Manila: IRRI, 1976. 1–83

    Google Scholar 

  22. International Rice Research Institute. Standard Evaluation System for Rice. 4th ed. Manila: IRRI, 1996. 52

    Google Scholar 

  23. Temnykh S, Declerck G, Lukashova A, et al. Computationaland experimental analysis of microsatellites in rice (Oryza sativa L.): Frequency, length variation, transposon associations, and genetic marker potential. Genome Res, 2001, 11: 1441–1452, 11483586, 10.1101/gr.184001, 1:CAS:528:DC%2BD3MXlvVGgu70%3D

    Article  CAS  Google Scholar 

  24. SAS Institute. SAS/STAT User’s Guide. NC: SAS Institute Cary, 1996

    Google Scholar 

  25. Li Z K, Yu S B, Lafitte H R, et al. QTL×environment interactions in rice. I. Heading date and plant height. Theor Appl Genet, 2003, 108: 141–153, 12961067, 10.1007/s00122-003-1401-2, 1:STN:280:DC%2BD3srnt1Skug%3D%3D

    Article  CAS  Google Scholar 

  26. Xu J L, Lafitte H R, Gao Y M, et al. QTLs for drought avoidance and tolerance identified in a set of random introgression lines of rice. Theor Appl Genet, 2005, 111: 1642–1650, 16200414, 10.1007/s00122-005-0099-8, 1:STN:280:DC%2BD2MngtlOktA%3D%3D

    Article  CAS  Google Scholar 

  27. Huang Y, Li L H, Chen Y, et al. Comparative analysis of gene expression at early seedling stage between a rice hybrid and its parents using a cDNA microarray of 9198 uni-sequences. Sci China Ser C-Life Sci, 2006, 49(6): 519–529, 10.1007/s11427-006-2031-0, 1:CAS:528:DC%2BD2sXitlOltQ%3D%3D

    Article  CAS  Google Scholar 

  28. Gao H J, Yang R Q. Composite interval mapping of QTL for dynamic traits. Chin Sci Bull, 2006, 51(15): 1857–1862, 10.1007/s11434-006-2050-z

    Article  Google Scholar 

  29. Kurata N, Nagamura Y, Yamamoto K, et al. A 300 kilobase interval genetic map of rice including 883 expressed sequences. Nat Genet, 1994, 8: 365–372, 7894488, 10.1038/ng1294-365, 1:CAS:528:DyaK2MXitl2hsLY%3D

    Article  CAS  Google Scholar 

  30. Ware D, Jaiswal P, Ni J, et al. Gramene: A resource for comparative grass genomics. Nucleic Acid Res, 2002, 30: 103–105, 11752266, 10.1093/nar/30.1.103, 1:CAS:528:DC%2BD38Xht12kt7g%3D

    Article  CAS  Google Scholar 

  31. Qian Q, Yanagihara S, Teng S, et al. Isolation, expression characteristics and chromosomal locations of three cDNA fragments under salt stress in rice. Acta Bot Sin, 2003, 45(9): 1090–1095, 1:CAS:528:DC%2BD2cXhtFGgurrP

    CAS  Google Scholar 

  32. Lang N T, Masood S, Yanagihara S, et al. Mapping QTLs for salt tolerance in rice. In: Khush G S, Brar D S, Hardy B. Advances in Rice Genetics. Supplement to Rice Genetics IV. Proceedings of the Fourth International Rice Genetics Symposium, 22∼27 October 2000. Los Banos: IRRI, 2003. 294–298

    Google Scholar 

  33. Badawi A T. Rice-based production systems for food security and poverty alleviation in the Near East and North Africa. Int Rice Comm Newsl, 2004, 53: 123–128

    Google Scholar 

  34. Xiao J, Yuan L P, Tanksley S D. Identification of QTLs affecting traits of agronomic important in a recombinant inbred population derived from a subspecific rice cross. Theor Appl Genet, 1996, 92: 230–244, 10.1007/BF00223380, 1:CAS:528:DyaK28XltFOjsLg%3D

    Article  CAS  Google Scholar 

  35. He G M, Luo X J, Tian F, et al. Haplotype variation in structure and expression of a gene cluster associated with a quantitative trait locus for improved yield in rice. Genome Res, 2006, 16: 618–626, 16606701, 10.1101/gr.4814006, 1:CAS:528:DC%2BD28XkslCgsrY%3D

    Article  CAS  Google Scholar 

  36. Lee S Y, Ahn J H, Cha Y S, et al. Mapping of quantitative trait loci for salt tolerance at the seedling stage in rice. Mol Cells, 2006, 21(2): 192–196, 16682812, 1:CAS:528:DC%2BD28Xlt1Wjsro%3D

    CAS  Google Scholar 

  37. Li Z K, Fu B Y, Gao Y M, et al. Genome-wide introgression lines and a forward genetics strategy for functional genomic research of complex phenotypes in rice. Plant Mol Biol, 2005, 59: 33–52, 16217600, 10.1007/s11103-005-8519-3, 1:CAS:528:DC%2BD2MXhtV2ksbbE

    Article  CAS  Google Scholar 

  38. Xu J L, Gao Y M, Fu B Y, Li Z K. Indentification and screening of favorable genes from rice germplasm in backcross introgression populations. Mol Plant Breed (in Chinese), 2005, 3(5): 619–628, 1:CAS:528:DC%2BD28XpvVOjt7Y%3D

    CAS  Google Scholar 

  39. Ali A J, Xu J L, Ismail A M, et al. Hidden diversity for abiotic and biotic stress tolerances in the primary gene pool of rice revealed by a large backcross breeding program. Field Crops Res, 2006, 97: 66–76, 10.1016/j.fcr.2005.08.016

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Institute of Crop Sciences/National Key Facility for Crop Gene Resources & Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China

    JinPing Zang, Yong Sun, Yun Wang, Jing Yang, Fang Li, YongLi Zhou, LingHua Zhu, JianLong Xu & ZhiKang Li

  2. International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines

    Reys Jessica, Fotokian Mohammadhosein & ZhiKang Li

Authors
  1. JinPing Zang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yong Sun
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yun Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Jing Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Fang Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. YongLi Zhou
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. LingHua Zhu
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Reys Jessica
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Fotokian Mohammadhosein
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. JianLong Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. ZhiKang Li
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to JianLong Xu.

Additional information

Contributed equally to this work

Supported by State “973” Programs from the Ministry of Science and Technology of China (Grant No. 2006CB100100), National High Technology Research and Development Program of China (“863” Program) (Grant No. 2007AA10Z191), and National Natural Science Foundation of China (Grant No. 30570996)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Zang, J., Sun, Y., Wang, Y. et al. Dissection of genetic overlap of salt tolerance QTLs at the seedling and tillering stages using backcross introgression lines in rice. SCI CHINA SER C 51, 583–591 (2008). https://doi.org/10.1007/s11427-008-0081-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11427-008-0081-1

Keywords

Search

Navigation