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Genomewide mapping reveals a combination of different genetic effects causing the genetic basis of heterosis in two elite rice hybrids

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Abstract

North Carolina design III (NCIII) is one of the most powerful and widely used mating designs for understanding the genetic basis of heterosis. However, the quantitative trait mapping (QTL) conducted in previous studies with this design was mainly based on analysis of variance (ANOVA), composite interval or multiple interval mapping methods. These methodologies could not investigate all kinds of genetic effects, especially epistatic effects, simultaneously on the whole genome. In this study, with a statistical method for mapping epistatic QTL associated with heterosis using the recombinant inbred line (RIL)-based NCIII design, we conducted QTL mapping for nine agronomic traits of two elite hybrids to characterize the mode of gene action contributing to heterosis on a whole genomewide scale. In total, 23 main-effect QTL (M-QTL) and 23 digenic interactions in IJ (indica ×japonica) hybrids, 11 M-QTL and 82 digenic interactions in II (indica ×indica) hybrid QTLs were identified in the present study. The variation explained by individual M-QTL or interactions ranged from 2.3 to 11.0%. The number of digenic interactions and the total variation explained by interactions of each trait were larger than those of M-QTL. The augmented genetic effect ratio of most M-QTL and digenic interactions in (L 1–L 2) data of two backcross populations (L 1 and L 2) showed complete dominance or overdominance, and in (L 1+L 2) data showed an additive effect. Our results indicated that the dominance, overdominance and epistatic effect were important in conditioning the genetic basis of heterosis of the two elite hybrids. The relative contributions of the genetic components varied with traits and the genetic basis of the two hybrids was different.

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Acknowledgements

This work was financially supported by the 973 Programme (no. 2011CB100102), the National Natural Science Foundation of China (no. 31000666), the China Postdoctoral Science Foundation (no. 2012M511722, no. 2014T70769), Hunan Province Postdoctoral Science Foundation (no. 2012RS4039) and Hunan Province Natural Science Foundation (13JJ4065).

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    Authors and Affiliations

    1. Hunan Provincial Key Laboratory for Biology and Control of Plant Disease and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha, 410128, People’s Republic of China

      LANZHI LI, HONGYAN ZHANG, ZHIMING WANG & CONGWEI SUN

    2. State Key Laboratory of Hybrid Rice, College of Life Science, Wuhan University, Wuhan, 430072, People’s Republic of China

      LANZHI LI & ZHONGLI HU

    3. Section on Statistical Genomics, State Key Laboratory of Crop Genetics and Germplasm Enhancement/Chinese National Center for Soybean Improvement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, People’s Republic of China

      XIAOHONG HE & YUANMING ZHANG

    4. National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People’s Republic of China

      TONGMIN MOU

    5. Department of Breeding, China National Hybrid Rice Research and Development Center, Changsha, 410125, People’s Republic of China

      XINQI LI

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    1. LANZHI LI
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    Correspondence to ZHONGLI HU.

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    [Li L., He X., Zhang H., Wang Z., Sun C., Mou T., Li X., Zhang Y. and Hu Z. 2015 Genomewide mapping reveals a combination of different genetic effects causing the genetic basis of heterosis in two elite rice hybrids. J. Genet. 94, xx–xx]

    Lanzhi Li and Xiaohong He contributed equally to this work.

    HZ, ZW and CS participated in programme compile and data analysis. TM and XL conducted the field design and material collection. YZ and ZH conceived of the study, and participated in its design and coordination and helped to draft the manuscript. All authors read and approved the final manuscript.

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    LI, L., HE, X., ZHANG, H. et al. Genomewide mapping reveals a combination of different genetic effects causing the genetic basis of heterosis in two elite rice hybrids. J Genet 94, 261–270 (2015). https://doi.org/10.1007/s12041-015-0527-8

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    • DOI: https://doi.org/10.1007/s12041-015-0527-8

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