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Cis-regulated additively expressed genes play a fundamental role in the formation of triploid loquat (Eriobotrya japonica (Thunb.) Lindl.) Heterosis

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Abstract

Triploid loquat (Eriobotrya japonica (Thunb.) Lindl.) has greater vigor than their respective diploid and tetraploid parents, but the molecular basis of this triploid heterosis remains unclear. Recent studies have suggested that DNA methylation is involved in heterosis, which is a recognized method of suppressing gene expression. However, our previous studies revealed a trend of increased DNA methylation in triploid loquat hybrids compared to their parents. To elucidate the mechanism of triploid loquat heterosis, we investigated the levels and regulation of relative gene expression between hybrid and parental lines using RNA-Seq technology. We found that gene expression in the hybrid lines was down-regulated and gene expression analysis revealed that approximately 94.56 and 86.97% were expressed additively in triploid-A and triploid-B, respectively. Analyses of the allele-specific gene expression in the hybrids revealed significantly more Longquan-1 alleles were preferentially expressed in the two hybrid lines. Further analysis of cis- and trans-regulatory effects showed that gene expression variation between parental alleles is largely attributable to cis-regulatory variation in triploid loquat and analyses of genes belonging to cis-regulatory variation showed that 88–90% of cis genes contributed to an additive expression pattern. Taken together, our results suggest that gene expression variation in triploid loquat fundamentally cis-regulated may play a dominant role in triploid loquat heterosis.

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Acknowledgements

We are grateful to Biomarker Technologies, Beijing, China for providing technical support.

Funding

This work was supported by National Science and Technology Support Projects (2013BAD02B02-1), State Spark-Program (2015GA811003), Central Fiscal for Forestry Science and Technology Extension and Demonstration Project (Chongqing forest research extension 2016-03) and the program of Chongqing forestry key scientific and technological projects (Chongqing forest research 2016-10), Basic and frontier research project of Chongqing (cstc2014jcyjA80006).

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  1. College of Horticulture and Landscape Architecture, Southwest University, Tiansheng Road 2, Chongqing, 400715, People’s Republic of China

    Chao Liu, Di Wu, Jiangbo Dang, Qiao He, Qigao Guo & Guolu Liang

  2. Technical Advice Station of Economic Crop, Yubei District, Chongqing, People’s Republic of China

    Lingli Wang

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  1. Chao Liu
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  2. Di Wu
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  3. Lingli Wang
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Correspondence to Qigao Guo or Guolu Liang.

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Liu, C., Wu, D., Wang, L. et al. Cis-regulated additively expressed genes play a fundamental role in the formation of triploid loquat (Eriobotrya japonica (Thunb.) Lindl.) Heterosis. Mol Genet Genomics 293, 967–981 (2018). https://doi.org/10.1007/s00438-018-1433-6

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