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Identification of QTLs with Additive, Epistatic, and QTL × Seed Maturity Interaction Effects for Seed Vigor in Rice

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Abstract

Seed maturity is a critical process of seed vigor establishment. In this study, one rice population of recombinant inbred lines (RILs) was used to determine the genetic characteristics of seed vigor, including the germination potential (GP), germination rate (GR), germination index (GI), and time for 50 % of germination (T50), at 4, 5, and 6 weeks after heading in 2 years. Significant differences of seed vigor were observed among two parents and RIL population; the heritability of four traits was more than 90 % at three maturity stages. A total of 19 additive and 2 epistatic quantitative trait loci (QTL) for seed vigor were identified using QTL Cartographer and QTLNetwork program, respectively, in 2012, while 16 simple sequence repeat (SSR) markers associated with seed vigor were detected using bulked segregant analysis (BSA) in 2013. The phenotypic variation explained by each additive, epistatic QTL, and QTL × seed maturity interaction ranged from 9.19 to 22.94 %, 7.23 to 7.75 %, and 0.05 to 0.63 %, respectively. Ten additive QTLs were stably expressed in 2 years which might play important roles in establishment of seed vigor in different environments. By comparing chromosomal positions of ten stably expressed additive QTLs with those previously identified, they might be true QTLs for seed vigor; the regions of QTLs for seed vigor are likely to coincide with QTLs for seed dormancy, seed reserve mobilization, low-temperature germinability, and seedling growth. Using four selected RILs, three cross-combinations were predicted to improve seed vigor; 9 to 10 elite alleles could be pyramided by each combination. The selected RILs and the identified QTLs might be applicable for the improvement of seed vigor by marker-assisted selection (MAS) in rice.

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Acknowledgment

This work was supported by the National Natural Science Foundation of China (Grant Nos. 31271806 and 31000748), the Fundamental Research Funds for the Central Universities (Grant No. KYZ201402 and KYZ201505), and the Special Fund for Agro-scientific Research in the Public Interest (Grant No. 201203052).

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    Authors and Affiliations

    1. The Laboratory of Seed Science and Technology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, People’s Republic of China

      Yanyan Lai, Jinping Cheng, Yongqi He, Bin Yang, Zhoufei Wang & Hongsheng Zhang

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    1. Yanyan Lai
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    2. Jinping Cheng
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    3. Yongqi He
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    4. Bin Yang
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    5. Zhoufei Wang
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    6. Hongsheng Zhang
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    Correspondence to Zhoufei Wang or Hongsheng Zhang.

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    Yanyan Lai and Jinping Cheng contributed equally to this work.

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    Lai, Y., Cheng, J., He, Y. et al. Identification of QTLs with Additive, Epistatic, and QTL × Seed Maturity Interaction Effects for Seed Vigor in Rice. Plant Mol Biol Rep 34, 160–171 (2016). https://doi.org/10.1007/s11105-015-0913-7

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