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Tan Q, Liu X, Gao H, et al. Comparison Between Flat and Round Peaches, Genomic Evidences of Heterozygosity Events. Front Plant Sci. 2019;10:592doi: 10.3389/fpls.2019.00592.
Tan, Q., Liu, X., Gao, H., Xiao, W., Chen, X., Fu, X., Li, L., Li, D., & Gao, D. (2019). Comparison Between Flat and Round Peaches, Genomic Evidences of Heterozygosity Events. Frontiers in plant science, 10592. https://doi.org/10.3389/fpls.2019.00592
Tan, Qiuping, et al. "Comparison Between Flat and Round Peaches, Genomic Evidences of Heterozygosity Events." Frontiers in plant science vol. 10 (2019): 592. doi: https://doi.org/10.3389/fpls.2019.00592
Tan Q, Liu X, Gao H, Xiao W, Chen X, Fu X, Li L, Li D, Gao D. Comparison Between Flat and Round Peaches, Genomic Evidences of Heterozygosity Events. Front Plant Sci. 2019 May 14;10:592. doi: 10.3389/fpls.2019.00592. eCollection 2019. PMID: 31164893; PMCID: PMC6535965.
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Front Plant Sci. 2019 May 14;10:592. doi: 10.3389/fpls.2019.00592. eCollection 2019.

Comparison Between Flat and Round Peaches, Genomic Evidences of Heterozygosity Events.

Frontiers in plant science

Qiuping Tan, Xiao Liu, Hongru Gao, Wei Xiao, Xiude Chen, Xiling Fu, Ling Li, Dongmei Li, Dongsheng Gao

Affiliations

  1. College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China.
  2. State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China.
  3. Fruit Innovation of Modern Agricultural Industry Technology System in Shandong Province, Shandong Agricultural University, Tai'an, China.
  4. College of Horticulture, Nanjing Agricultural University, Nanjing, China.

PMID: 31164893 PMCID: PMC6535965 DOI: 10.3389/fpls.2019.00592

Abstract

Bud sports occur in many plant species, including fruit trees. Although they are correlated with genetic variance in somatic cells, the mechanisms responsible for bud sports are mostly unknown. In this study, a peach bud sport whose fruit shape was transformed to round from flat was identified by next generation sequencing (NGS), and we provide evidence that a long loss of heterozygosity (LOH) event may be responsible for this alteration in fruit shape. Moreover, compared to the reference genome, we identified 237,476 high quality single nucleotide polymorphisms (SNPs) in the wild-type and bud sport genomes. Using this SNP set, a long LOH event was identified at the distal end of scaffold Pp06 of the bud sport genome. Haplotypes from 155 additional peach accessions were phased, suggesting that the homozygous distal end of scaffold Pp06 of the bud sport was likely derived from only one haplotype of the wild-type flat peach. A genome-wide association study (GWAS) of 127 peach accessions was conducted to associate a SNP found at 26,924,482 bp of scaffold Pp06 to differences in fruit shape. All accessions with round-shaped fruit were found to have an A/A genotype, while those with A/T, or T/T genotypes had flat-shaped fruits. Finally, we also found that 236 peach accessions and 141 Prunus species with round-type fruit were found to have an A/A genotype at this SNP, while 22 flat peach accessions had an A/T genotype. Taken together, our results suggest that genes flanking this A/T polymorphism, and haplotyped carrying the T allele may determine flat fruit shape in this population. Furthermore, the LOH event resulting in the loss of the haplotype carrying the T allele may therefore be responsible for fruit shape alteration in wild-type flat peach.

Keywords: Prunus persica; bud sport; fruit shape; genome-wide association study; next generation sequencing

References

  1. Nat Biotechnol. 2000 Sep;18(9):1001-5 - PubMed
  2. Plant J. 2002 Nov;32(3):277-84 - PubMed
  3. Cancer Res. 1992 Oct 1;52(19):5368-72 - PubMed
  4. Nat Genet. 2006 Aug;38(8):904-9 - PubMed
  5. Genome. 2007 Mar;50(3):297-302 - PubMed
  6. Am J Hum Genet. 2007 Sep;81(3):559-75 - PubMed
  7. Am J Hum Genet. 2007 Nov;81(5):1084-97 - PubMed
  8. Plant Physiol. 2008 Jul;147(3):985-1003 - PubMed
  9. Bioinformatics. 2009 Aug 15;25(16):2078-9 - PubMed
  10. Genome Res. 2009 Sep;19(9):1639-45 - PubMed
  11. Science. 2009 Nov 20;326(5956):1115-7 - PubMed
  12. Nat Rev Genet. 2010 Jan;11(1):31-46 - PubMed
  13. Nature. 2010 Mar 25;464(7288):587-91 - PubMed
  14. Nature. 2010 Jun 3;465(7298):627-31 - PubMed
  15. Genome Res. 2010 Sep;20(9):1297-303 - PubMed
  16. Nat Genet. 2010 Nov;42(11):961-7 - PubMed
  17. Bioinformatics. 2011 Aug 1;27(15):2156-8 - PubMed
  18. Nat Biotechnol. 2011 Dec 11;30(1):105-11 - PubMed
  19. Genome Res. 2012 Mar;22(3):568-76 - PubMed
  20. Nat Genet. 2012 Jun 17;44(7):821-4 - PubMed
  21. Nature. 2012 Oct 25;490(7421):497-501 - PubMed
  22. J Exp Bot. 2012 Nov;63(18):6359-69 - PubMed
  23. Nat Genet. 2013 May;45(5):487-94 - PubMed
  24. Proc Natl Acad Sci U S A. 2014 Mar 4;111(9):E866-75 - PubMed
  25. Genome Biol. 2014 Jul 31;15(7):415 - PubMed
  26. PLoS Genet. 2015 Apr 02;11(4):e1005081 - PubMed
  27. PLoS One. 2015 Sep 09;10(9):e0136803 - PubMed
  28. Development. 2016 May 1;143(9):1612-22 - PubMed
  29. Nat Commun. 2016 Sep 02;7:12685 - PubMed
  30. Nat Commun. 2016 Nov 08;7:13246 - PubMed
  31. Nature. 1987 Oct 1-7;329(6138):451-4 - PubMed
  32. Sci Rep. 2017 Jul 27;7(1):6714 - PubMed
  33. Plant Physiol. 2017 Oct;175(2):786-801 - PubMed
  34. Proc Natl Acad Sci U S A. 1987 Dec;84(24):9252-6 - PubMed
  35. Nature. 1985 Jul 25-31;316(6026):330-4 - PubMed
  36. Hortic Res. 2018 Jul 15;5:44 - PubMed
  37. Science. 1996 Dec 20;274(5295):2057-9 - PubMed

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