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Identification of QTLs with main, epistatic and QTL × environment interaction effects for salt tolerance in rice seedlings under different salinity conditions

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Abstract

Salt tolerance of rice (Oryza sativa L.) at the seedling stage is one of the major determinants of its stable establishment in saline soil. One population of recombinant inbred lines (RILs, F 2:9) derived from a cross between the salt-tolerant variety Jiucaiqing and the salt-sensitive variety IR26 was used to determine the genetic mechanism of four salt tolerance indices, seedling height (SH), dry shoot weight (DSW), dry root weight (DRW) and Na/K ratios (Na/K) in roots after 10 days in three salt concentrations (0.0, 0.5 and 0.7 % NaCl). The main effect QTLs (M-QTLs) and epistatic QTLs (E-QTLs) were detected by QTL IciMapping program using single environment phenotypic values. Eleven M-QTLs and 11 E-QTLs were identified for the salt tolerance indices. There were six M-QTLs and two E-QTLs identified for SH, three M-QTLs and five E-QTLs identified for DSW, two M-QTLs and one E-QTL identified for DRW, and three E-QTLs identified for Na/K. The phenotypic variation explained by each M-QTL and E-QTL ranged from 7.8 to 23.9 % and 13.3 to 73.7 %, respectively. The QTL-by-environment interactions were detected by QTLNetwork program in the joint analyses of multi-environment phenotypic values. Six M-QTLs and five E-QTLs were identified. The phenotypic variation explained by each QTL and QTL × environment interaction ranged from 0.95 to 6.90 % and 0.02 to 0.50 %, respectively. By comparing chromosomal positions of these M-QTLs with those previously identified, five M-QTLs qSH1.3, qSH12.1, qSH12.2, qDSW12.1 and qDRW11 might represent novel salt tolerance genes. Five selected RILs with high salt tolerance had six to eight positive alleles of the M-QTLs, indicating that pyramiding by marker-assisted selection (MAS) of M-QTLs can be applied in rice salt tolerance breeding programs.

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Acknowledgments

This work was supported by the National Natural Science Foundation of China (Grant No. 31000748), the Natural Science Foundation of Jiangsu Province (Grant No. BK2010452). We thank reviewers for the careful reading of the manuscript and constructive comments.

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Authors and Affiliations

  1. The Laboratory of Seed Science and Technology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, People’s Republic of China

    Zhoufei Wang, Jinping Cheng, Zhiwei Chen, Ji Huang, Yongmei Bao, Jianfei Wang & Hongsheng Zhang

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  1. Zhoufei Wang
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  2. Jinping Cheng
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  3. Zhiwei Chen
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  4. Ji Huang
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  6. Jianfei Wang
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  7. Hongsheng Zhang
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Correspondence to Jianfei Wang or Hongsheng Zhang.

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Communicated by J. Wang.

Zhoufei Wang and Jinping Cheng contributed equally to this work.

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Wang, Z., Cheng, J., Chen, Z. et al. Identification of QTLs with main, epistatic and QTL × environment interaction effects for salt tolerance in rice seedlings under different salinity conditions. Theor Appl Genet 125, 807–815 (2012). https://doi.org/10.1007/s00122-012-1873-z

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