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Identification of QTLs with additive, epistatic and QTL × development interaction effects for seed dormancy in rice

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Abstract

Seed dormancy (SD) is an important agronomic trait affecting crop yield and quality. In this study, one rice population of recombinant inbred lines (RILs) was used to determine the genetic characteristics of SD at the early (4 weeks after heading), middle (5 weeks after heading) and late (6 weeks after heading) development stages. The level of SD decreased with the process of seed development, and the SD was significantly affected by the heading date (HD) and temperature at the early and middle development stages. A total of eight additive quantitative trait loci (QTLs) for SD were identified at three development stages, and more QTLs were expressed at the early and late development stages. Among them, four, one and three additive QTLs were identified at the early, middle and late development stages, respectively. Epistatic QTLs and QTL-by-development interactions were detected by the joint analysis of multi-development phenotypic values, and one additive and two epistatic QTLs were identified. The phenotypic variation of SD explained by each additive, epistatic QTL and QTL × development interaction ranged from 8.0 to 13.5 %, 0.7 to 3.9 % and 1.3 to 2.8 %, respectively. One major QTL qSD7.1 for SD was tightly linked to the major QTL qHD7.4 for HD, which might be applied to reveal the relationship of SD and HD. By comparing chromosomal positions of these additive QTLs with those previously identified, five additive QTLs qSD1.1, qSD2.1, qSD2.2, qSD4.1 and qSD4.2 might represent novel genes. The best three cross combinations for the development of RIL populations were predicted to improve SD. The selected RILs and the identified QTLs might be applicable to improve the rice pre-harvest sprouting tolerance by the marker-assisted selection approach.

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Abbreviations

GP:

Germination percentage

HD:

Heading date

MAS:

Marker-assisted selection

PHS:

Pre-harvest sprouting

QTLs:

Quantitative trait loci

RILs:

Recombinant inbred lines

SD:

Seed dormancy

SSR:

Simple sequence repeats

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Acknowledgments

This work was supported by the National Natural Science Foundation of China (Grant No. 31271806; 31000748), the Special Fund for Agro-scientific Research in the Public Interest (Grant No. 201203052), the Fundamental Research Funds for the Central Universities (Grant No. KYZ201202-9) and the 111 Project.

Conflict of interest

The authors have declared that no competing interests exist.

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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

    Ling Wang, Jinping Cheng, Yanyan Lai, Wenli Du, Xi Huang, Zhoufei Wang & Hongsheng Zhang

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  1. Ling Wang
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  2. Jinping Cheng
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  3. Yanyan Lai
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  4. Wenli Du
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  5. Xi Huang
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  6. Zhoufei Wang
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  7. Hongsheng Zhang
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Correspondence to Zhoufei Wang or Hongsheng Zhang.

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L. Wang and J. Cheng contributed equally to this work.

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Wang, L., Cheng, J., Lai, Y. et al. Identification of QTLs with additive, epistatic and QTL × development interaction effects for seed dormancy in rice. Planta 239, 411–420 (2014). https://doi.org/10.1007/s00425-013-1991-0

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  • DOI: https://doi.org/10.1007/s00425-013-1991-0

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