Construction of a highly saturated linkage map in Japanese plum (Prunus salicina L.) using GBS for SNP marker calling

PLoS One. 2018 Dec 3;13(12):e0208032. doi: 10.1371/journal.pone.0208032. eCollection 2018.

Abstract

This study reports the construction of high density linkage maps of Japanese plum (Prunus salicina Lindl.) using single nucleotide polymorphism markers (SNPs), obtained with a GBS strategy. The mapping population (An x Au) was obtained by crossing cv. "Angeleno" (An) as maternal line and cv. "Aurora" (Au) as the pollen donor. A total of 49,826 SNPs were identified using the peach genome V2.1 as a reference. Then a stringent filtering was carried out, which revealed 1,441 high quality SNPs in 137 An x Au offspring, which were mapped in eight linkage groups. Finally, the consensus map was built using 732 SNPs which spanned 617 cM with an average of 0.96 cM between adjacent markers. The majority of the SNPs were distributed in the intragenic region in all the linkage groups. Considering all linkage groups together, 85.6% of the SNPs were located in intragenic regions and only 14.4% were located in intergenic regions. The genetic linkage analysis was able to co-localize two to three SNPs over 37 putative orthologous genes in eight linkage groups in the Japanese plum map. These results indicate a high level of synteny and collinearity between Japanese plum and peach genomes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromosome Mapping*
  • DNA, Intergenic / genetics
  • DNA, Plant / genetics
  • Genetic Linkage
  • Genome, Plant / genetics*
  • Genotyping Techniques
  • Polymorphism, Single Nucleotide / genetics
  • Prunus domestica / genetics*
  • Prunus persica / genetics*
  • Sequence Analysis, DNA
  • Synteny*

Substances

  • DNA, Intergenic
  • DNA, Plant

Grants and funding

This research was supported by Fondo Nacional de Desarrollo Cientifico y Tecnologico (http://www.conicyt.cl/fondecyt/), FONDECYT/Regular no 1160600. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Author Rolando García-González is employed by Sociedad BioTECNOS Ltda. This affiliation commenced towards the end of this study. Sociedad BioTECNOS Ltda provided support in the form of salary for author RG-G, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific role of this author is articulated in the ‘author contributions’ section.