Molecular Genetics and Genomics

, Volume 293, Issue 4, pp 967–981 | Cite as

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

  • Chao Liu
  • Di Wu
  • Lingli Wang
  • Jiangbo Dang
  • Qiao He
  • Qigao Guo
  • Guolu Liang
Original Article


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.


Triploid 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.


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).

Compliance with ethical standards

Conflict of interest

All authors declare that they have no conflict of interest.

Ethical standards

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

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  1. Adams KL, Wendel JF (2005) Polyploidy and genome evolution in plants. Curr Opin Plant Biol 8:135–141CrossRefPubMedGoogle Scholar
  2. Adams KL, Percifield R, Wendel JF (2004) Organ-specific silencing or duplicated genes in a newly synthesized cotton allotetraploid. Genetics 168:2217–2226CrossRefPubMedPubMedCentralGoogle Scholar
  3. Auger DL, Gray AD, Ream TS, Kato A, Coe EH, Birchler JA (2005) Nonadditive gene expression in diploid and triploid hybrids of maize. Genetics 169:389–97CrossRefPubMedPubMedCentralGoogle Scholar
  4. Bell GDM, Kane NC, Rieseberg LH, Adams KL (2013) RNA-Seq analysis of allele-specific expression, hybrid effects, and regulatory divergence in hybrids compared with their parents from natural populations. Genom Biol Evol 5(7):1309–1323CrossRefGoogle Scholar
  5. 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
  6. Birchler JA, Auger DL, Riddle NC (2003) In search of the molecular basis of heterosis. Plant Cell 15:2236–2239CrossRefPubMedPubMedCentralGoogle Scholar
  7. Bruce AB (1910) The mendelian theory of heredity and the augmentation of vigor. Science 32:627–628CrossRefPubMedGoogle Scholar
  8. Chen ZJ (2007) Genetic and epigenetic mechanisms for gene expression and phenotypic variation in plant polyploids. Annu Rev Plant Biol 58:377–406CrossRefPubMedPubMedCentralGoogle Scholar
  9. Chen ZJ (2010) Molecular mechanisms of polyploidy and hybrid vigor. Trends Plant Sci 15(2):57–71CrossRefPubMedPubMedCentralGoogle Scholar
  10. Chen ZJ (2013) Genomic and epigenetic insights into the molecular bases of heterosis. Nat Rev Genet 14:471–482CrossRefPubMedGoogle Scholar
  11. 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
  12. 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
  13. Cubillos FA, Stegle O, Grondin C, Canut M, Tisné S, Gy I, Loudet O (2014) Extensive cis-regulatory variation robust to environmental perturbation in Arabidopsis. Plant Cell 26:4298–310CrossRefPubMedPubMedCentralGoogle Scholar
  14. East EM (1909) The distinction between development and heredity in inbreeding. Am Nat 43:173–181CrossRefGoogle Scholar
  15. Feng SQ, Chen XL, Wu SJ, Chen XS (2015) Recent advances in understanding plant heterosis. Agric Sci 6:1033–1038Google Scholar
  16. Fujimoto R, Taylor JM, Shirasawa S, Peacock WJ, Dennis ES (2012) Heterosis of Arabidopsis hybrids between C24 and Col is associated with increased photosynthesis capacity. Proc Natl Acad Sci USA 109:7109–7114CrossRefPubMedGoogle Scholar
  17. Ge X, Chen W, Song S, Wang W, Hu S, Yu J (2008) Transcriptomic profiling of mature embryo from an elite super-hybrid rice LYP9 and its parental lines. BMC Plant Biol 8:114CrossRefPubMedPubMedCentralGoogle Scholar
  18. Gibney ER, Nolan CM (2010) Epigenetics and gene expression. Heredity 105:4–13CrossRefPubMedGoogle Scholar
  19. Groszmann M, Greaves IK, Albertyn ZI, Scofield GN, Peacock WJ, Dennis ES (2011) Changes in 24-nt siRNA levels in Arabidopsis hybrids suggest an epigenetic contribution to hybrid vigor. Proc Natl Acad Sci USA 108:2617–2622CrossRefPubMedGoogle Scholar
  20. Guo M, Rafalski JA (2013) Gene expression and heterosis in maize hybrids. In: Chen ZJ, Birchler JA (eds) Polyploid and hybrid genomics. Wiley, New York, pp 59–84CrossRefGoogle Scholar
  21. Guo M, Rupe MA, Zinselmeier C, Habben J, Bowen BA, Smith OS (2004) Allelic variation of gene expression in maize hybrids. Plant cell 16:1707–1716CrossRefPubMedPubMedCentralGoogle Scholar
  22. Guo M, Rupe MA, Yang X, Crasta O, Zinselmeier C, Smith OS, Bowen B (2006) Genome-wide transcript analysis of maize hybrids: allelic additive gene expression and yield heterosis. Theor Appl Genet 113:831–845CrossRefPubMedGoogle Scholar
  23. Guo H, Mendrikahy JN, Xie L, Deng J, Lu Z, Wu J, Li X, Shahid MQ, Liu X (2017) Transcriptome analysis of neo-tetraploid rice reveals specific differential gene expressions associated with fertility and heterosis. Sci Rep 7:40139CrossRefPubMedPubMedCentralGoogle Scholar
  24. Hochholdinger F, Hoecker N (2007) Towards the molecular basis of heterosis. Trends Plant Sci 12:427–432CrossRefPubMedGoogle Scholar
  25. Hofmann NR (2012) A global view of hybrid vigor: DNA methylation, small RNAs, and gene expression. Plant Cell 24:841CrossRefPubMedPubMedCentralGoogle Scholar
  26. Hu X, Wang H, Diao X, Liu Z, Li K, Wu Y, Liang Q, Wang H, Huang C (2016) Transcriptome profiling and comparison of maize ear heterosis during the spikelet and floret differentiation stages. BMC Genom 17:959CrossRefGoogle Scholar
  27. Huang Y, Zhang L, Zhang J, Yuan D, Xu C, Li X, Zhou D, Wang S, Zhang Q (2006) Heterosis and polymorphisms of gene expression in an elite rice hybrid as revealed by a microarray analysis of 9198 unique ESTs. Plant Mol Biol 62:579–591CrossRefPubMedGoogle Scholar
  28. Huang W, Ye J, Zhang J, Lin Y, He M, Huang J (2016) Transcriptome analysis of Chlorella zofingiensis to identify genes and their expressions involved in astaxanthin and triacylglycerol biosynthesis. Algal Res 17:236–243CrossRefGoogle Scholar
  29. Jackson S, Chen ZJ (2010) Genomic and expression plasticity of polyploidy. Curr Opin Plant Biol 13(2):153–159CrossRefPubMedGoogle Scholar
  30. Khatib H (2007) Is it genomic imprinting or preferential expression? Bioessays 29(10):1022–1028CrossRefPubMedGoogle Scholar
  31. Kyndt T, Denil S, Haegeman A, Trooskens G, De Meyer T, Van Criekinge W, Gheysen G (2012) Transcriptome analysis of rice mature root tissue and root tips in early development by massive parallel sequencing. J Exp Bot 63:2141–2157CrossRefPubMedGoogle Scholar
  32. Leitch IJ, Bennett MD (1997) Polyploidy in angiosperms. Trends Plant Sci 2:470–476CrossRefGoogle Scholar
  33. Lemos B, Araripe LO, Fontanillas P, Hartl DL (2008) Dominance and the evolutionary accumulation of cis- and trans-effects on gene expression. Proc Natl Acad Sci USA 105:14471–14476CrossRefPubMedGoogle Scholar
  34. Li W, Zhu H, Challa GS, Zhang Z (2013) A non-additive interaction in a single locus causes a very short root phenotype in wheat. Theor Appl Genet 126:1189–1200CrossRefPubMedGoogle Scholar
  35. Li X, Shahid MQ, Wu J, Wang L, Liu X, Lu Y (2016) Comparative small RNA analysis of pollen development in autotetraploid and diploid rice. Int J Mol Sci 17:499CrossRefPubMedPubMedCentralGoogle Scholar
  36. Li X, Shahid MQ, Xia J, Lu Z, Fang N, Wang L, Wu J, Chen Z, Liu X (2017) Analysis of small RNAs revealed differential expressions during pollen and embryo sac development in autotetraploid rice. BMC Genom 18:129CrossRefGoogle Scholar
  37. Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2−∆∆Ct method. Methods 25:402–408CrossRefPubMedPubMedCentralGoogle Scholar
  38. Madlung A (2013) Polyploidy and its effect on evolutionary success: old questions revisited with new tools. Heredity 110:99–104CrossRefPubMedGoogle Scholar
  39. McManus CJ, Coolon JD, Duff MO, Eipper-Mains J, Graveley BR, Wittkopp PJ (2010) Regulatory divergence in Drosophila revealed by mRNA-sEq. Genom Res 20:816–25CrossRefGoogle Scholar
  40. Meyer S, Pospisil H, Scholten S (2007) Heterosis associated gene expression in maize embryos 6 days after fertilization exhibits additive, dominant and overdominant pattern. Plant Mol Biol 63:381–391CrossRefPubMedGoogle Scholar
  41. 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
  42. Mori A, Romero-Severson J, Severson DW (2007) Genetic basis for reproductive diapause is correlated with life history traits within the Culex pipiens complex. Insect Mol Biol 16(5):515–524PubMedGoogle Scholar
  43. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-SEq. Nat Method 5:621–628CrossRefGoogle Scholar
  44. Ni Z, Kim ED, Ha M, Lackey E, Liu J, Zhang Y, Sun Q, Chen ZJ (2009) Altered circadian rhythms regulate growth vigour in hybrids and allopolyploids. Nature 457:327–331CrossRefPubMedGoogle Scholar
  45. Otto SP, Whitton J (2000) Polyploid incidence and evolution. Annu Rev Genet 34:401–37CrossRefPubMedGoogle Scholar
  46. Paschold A, Jia Y, Marcon C, Lund S, Larson NB, Yeh CT, Ossowski S, Lanz C, Nettleton D, Schnable PS, Hochholdinger F (2012) Complementation contributes to transcriptome complexity in maize (Zea mays L.) hybrids relative to their inbred parents. Genom Res 22(12):2445–2454CrossRefGoogle Scholar
  47. Paun O, Fay MF, Soltis DE, Chase MW (2007) Genetic and epigenetic alterations after hybridization and genome doubling. Taxon 56:649–656CrossRefPubMedPubMedCentralGoogle Scholar
  48. Ronald J, Akey JM, Whittle J, Smith EN, Yvert G, Kruglyak L (2005) Simultaneous genotyping, gene-expression measurement, and detection of allele-specific expression with oligonucleotide arrays. Genom Res 15:284–291CrossRefGoogle Scholar
  49. Shi X, Ng DWK, Zhang C, Comai L, Ye W, Chen ZJ (2012) Cis- and trans-regulatory divergence between progenitor species determines gene-expression novelty in Arabidopsis allopolyploids. Nat Commun 3:950CrossRefPubMedGoogle Scholar
  50. Shull GH (1908) The composition of a field of maize. Am Breeders Assoc Rep 4:296–301Google Scholar
  51. Soltis DE, Soltis PS (1999) Polyploidy: recurrent formation and genome evolution. Trends Ecol Evol 14(9):348–352CrossRefPubMedGoogle Scholar
  52. Song R, Messing J (2003) Gene expression of a gene family in maize based on noncollinear haplotypes. Proc Natl Acad Sci USA 100:9055–9060CrossRefPubMedGoogle Scholar
  53. 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
  54. Springer NM. Stupar RM (2007) Allelic variation and heterosis in maize: how do two halves make more than a whole? Genom Res 17:264–275CrossRefGoogle Scholar
  55. Stupar RM, Springer NM (2006) Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression patterns in the F1 hybrid. Genetics 173:2199–2210CrossRefPubMedPubMedCentralGoogle Scholar
  56. Stupar RM, Gardiner JM, Oldre AG, Haun WJ, Chandler VL, Springer NM (2008) Gene expression analyses in maize in breeds and hybrids with varying levels of heterosis. BMC Plant Biol 8:33CrossRefPubMedPubMedCentralGoogle Scholar
  57. Swanson-Wagner RA, Jia Y, DeCook R, Borsuk LA, Nettleton D, Schnable PS (2006) All possible modes of gene action are observed in a global comparison of gene expression in a maize F1 hybrid and its inbred parents. Proc Natl Acad Sci USA 103:6805–6810CrossRefPubMedGoogle Scholar
  58. Thiemann A, Fu J, Schrag TA, Melchinger AE, Frisch M, Scholten S (2010) Correlation between parental transcriptome and field data for the characterization of heterosis in Zea mays L. Theor Appl Genet 120(2):401–13CrossRefPubMedGoogle Scholar
  59. Thiemann A, Fu J, Seifert F, Grant-Dwonton RT, Schrag TA, Pospisil H, Frisch M, Melchinger AE, Scholten S (2014) Genome-wide meta-analysis of maize heterosis reveals the potential role of additive gene expression at pericentromeric loci. BMC Plant Biol 14:88CrossRefPubMedPubMedCentralGoogle Scholar
  60. Tirosh I, Reikhav S, Levy AA, Barkai N (2009) A yeast hybrid provides insight into the evolution of gene expression regulation. Science 324:659–662CrossRefPubMedGoogle Scholar
  61. Wang WX (2008) Genome variation and DNA methylation analysis of natural and artificial triploid loquats. Southwest University, ChongqingGoogle Scholar
  62. Wang J, Tian L, Madlung A, Lee HS, Chen M, Lee JJ, Watson B, Kagochi T, Comai L, Chen ZJ (2004) Stochastic and epigenetic changes of gene expression in Arabidopsis polyploids. Genetics 167:1961–1973CrossRefPubMedPubMedCentralGoogle Scholar
  63. Wang J, Tian L, Lee HS, Wei NE, Jiang H, Watson B, Madlung A, Osborn TC, Doerge RW, Comai L, Chen ZJ (2006) Genomewide nonadditive gene regulation in Arabidopsis allotetraploids. Genetics 172:507–517CrossRefPubMedPubMedCentralGoogle Scholar
  64. Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57–63CrossRefPubMedPubMedCentralGoogle Scholar
  65. Wang H, Fang Y, Wang L, Zhu W, Ji H, Wang H, Xu S, Sima Y (2015) Heterosis and differential gene expression in hybrids and parents in Bombyx mori by digital gene expression profiling. Sci Rep 5:8750CrossRefPubMedPubMedCentralGoogle Scholar
  66. Wang Y, Shahid MQ, Lin S, Chen C, Hu C (2017) Footprints of domestication revealed by RAD-tag resequencing in loquat: SNP data reveals a non-significant domestication bottleneck and a single domestication event. BMC Genom 18:354CrossRefGoogle Scholar
  67. 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 106:7695–7701CrossRefPubMedGoogle Scholar
  68. Wittkopp PJ, Kalay G (2012) Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence. Nat Rev Genet 13:59–69CrossRefGoogle Scholar
  69. Wittkopp PJ, Haerum BK, Clark AG (2004) Evolutionary changes in cis and trans gene regulation. Nature 430:85–88CrossRefPubMedGoogle Scholar
  70. Wu D, Fan W, He Q, Guo Q, Spano AJ, Wang Y, Timko MP, Liang G (2015) Genetic diversity of loquat (Eriobotrya japonica (Thunb.) Lindl.) native to Guizhou Province (China) and its potential in the genetic improvement of domesticated cultivars. Plant Mol Biol Rep 33:952–961CrossRefGoogle Scholar
  71. Yoo M, Szadkowski E, Wendel J (2013) Homoeolog expression bias and expression level dominance in allopolyploid cotton. Heredity 110:171–80CrossRefPubMedGoogle Scholar
  72. Yu SB, Li JX, Xu CG, Tan YF, Gao YJ, Li XH, Zhang Q, Saghai Maroof MA (1997) Importance of epistasis as the genetic basis of heterosis in an elite rice hybrid. Proc Natl Acad Sci USA 94:9226–9231CrossRefPubMedGoogle Scholar
  73. Zhai R, Feng Y, Wang H, Zhan X, Shen X, Wu W, Zhang Y, Chen D, Dai G, Yang Z, Cao L, Cheng S (2013a) Transcriptome analysis of rice root heterosis by RNA-SEq. BMC Genom 14:19CrossRefGoogle Scholar
  74. Zhai R, Feng Y, Zhan X, Shen X, Wu W, Yu P, Zhang Y, Chen D, Wang H, Lin Z, Cao L, Cheng S (2013b) Identification of transcriptome SNPs for assessing allele-specific gene expression in a superhybrid rice Xieyou9308. PLoS One 8:e60668CrossRefPubMedPubMedCentralGoogle Scholar
  75. Zhang X, Borevitz JO (2009) Global analysis of allele-specific expression in Arabidopsis thaliana. Genetics 182:943–954CrossRefPubMedPubMedCentralGoogle Scholar
  76. Zhang HY, He H, Chen LB, Li L, Liang MZ, Wang XF, Liu XG, He GM, Chen RS, Ma LG, Deng XW (2008) A genome-wide transcription analysis reveals a close correlation of promoter INDEL polymorphism and heterotic gene expression in rice hybrids. Mol Plant 1(5):720–731CrossRefPubMedGoogle Scholar
  77. Zhang J, Liu Y, Xia EH, Yao QY, Liu XD, Gao LZ (2015) Autotetraploid rice methylome analysis reveals methylation variation of transposable elements and their effects on gene expression. Proc Natl Acad Sci USA 112:E7022–9CrossRefPubMedGoogle Scholar

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Authors and Affiliations

  1. 1.College of Horticulture and Landscape ArchitectureSouthwest UniversityChongqingPeople’s Republic of China
  2. 2.Technical Advice Station of Economic CropChongqingPeople’s Republic of China

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