Cis-regulated additively expressed genes play a fundamental role in the formation of triploid loquat (Eriobotrya japonica (Thunb.) Lindl.) Heterosis
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.
KeywordsTriploid loquat RNA-Seq Additive gene expression Allele-specific gene expression Cis regulation Heterosis
We are grateful to Biomarker Technologies, Beijing, China for providing technical support.
Compliance with ethical standards
Conflict of interest
All authors declare that they have no conflict of interest.
This article does not contain any studies with human participants or animals performed by any of the authors.
- Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B 57(1):289–300Google Scholar
- Coors JG, Pandey S (1999) The genetics and exploitation of heterosis in crops. American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, MadisonGoogle Scholar
- Crow JF (1999) Dominance and overdominance. In: Coors JG, Pandey S (eds) The genetics and exploitation of heterosis in crops. American Society of Agronomy, Madison, pp 49–58Google Scholar
- Feng SQ, Chen XL, Wu SJ, Chen XS (2015) Recent advances in understanding plant heterosis. Agric Sci 6:1033–1038Google Scholar
- Meyer RC, Witucka-Wall H, Becher M, Blacha A, Boudichevskaia A, Dörmann P, Fiehn O, Friedel S, von Korff M, Lisec J, Melzer M, Repsilber D, Schmidt R, Scholz M, Selbig J, Willmitzer L, Altmann T (2012) Heterosis manifestation during early Arabidopsis seedling development is characterized by intermediate gene expression and enhanced metabolic activity in the hybrids. Plant J 71:669–683CrossRefPubMedGoogle Scholar
- Shull GH (1908) The composition of a field of maize. Am Breeders Assoc Rep 4:296–301Google Scholar
- Song GS, Zhai HL, Peng YG, Zhang L, Wei G, Chen XY, Xiao YG, Wang L, Chen YJ, Wu B, Chen B, Zhang Y, Chen H, Feng XJ, Gong WK, Liu Y, Yin ZJ, Wang F, Liu GZ, Xu HL, Wei XL, Zhao XL, Ouwerkerk PBF, Hankemeier T, Reijmers T, Heijden RH, Lu CM, Wang M, Greef J, Zhu Z (2010) Comparative transcriptional profiling and preliminary study on heterosis mechanism of super-hybrid rice. Mol Plant 3:1012–1025CrossRefPubMedPubMedCentralGoogle Scholar
- Wang WX (2008) Genome variation and DNA methylation analysis of natural and artificial triploid loquats. Southwest University, ChongqingGoogle Scholar
- Wei G, Tao Y, Liu G, Chen C, Luo R, Xia H, Gan Q, Zeng H, Lu Z, Han Y, Li X, Song G, Zhai H, Peng Y, Li D, Xu H, Wei X, Cao M, Deng H, Xin Y, Yuan L, Yu J, Zhu Z, Zhu L (2009) A transcriptomic analysis of superhybrid rice LYP9 and its parents. Proc Natl Acad Sci 106:7695–7701CrossRefPubMedPubMedCentralGoogle Scholar