The development of a high-density genetic map significantly improves the quality of reference genome assemblies for rose

Publication Overview
TitleThe development of a high-density genetic map significantly improves the quality of reference genome assemblies for rose
AuthorsLi S, Yang G, Yang S, Just J, Yan H, Zhou N, Jian H, Wang Q, Chen M, Qiu X, Zhang H, Dong X, Jiang X, Sun Y, Zhong M, Bendahmane M, Ning G, Ge H, Hu JY, Tang K
TypeJournal Article
Journal NameScientific reports
Volume9
Issue1
Year2019
Page(s)5985
CitationLi S, Yang G, Yang S, Just J, Yan H, Zhou N, Jian H, Wang Q, Chen M, Qiu X, Zhang H, Dong X, Jiang X, Sun Y, Zhong M, Bendahmane M, Ning G, Ge H, Hu JY, Tang K. The development of a high-density genetic map significantly improves the quality of reference genome assemblies for rose. Scientific reports. 2019 Apr 12; 9(1):5985.

Abstract

Roses are important woody plants featuring a set of important traits that cannot be investigated in traditional model plants. Here, we used the restriction-site associated DNA sequencing (RAD-seq) technology to develop a high-density linkage map of the backcross progeny (BC1F1) between Rosa chinensis 'Old Blush' (OB) and R. wichuraiana 'Basyes' Thornless' (BT). We obtained 643.63 million pair-end reads and identified 139,834 polymorphic tags that were distributed uniformly in the rose genome. 2,213 reliable markers were assigned to seven linkage groups (LGs). The length of the genetic map was 1,027.425 cM in total with a mean distance of 0.96 cM per marker locus. This new linkage map allowed anchoring an extra of 1.21/23.14 Mb (12.18/44.52%) of the unassembled OB scaffolds to the seven reference pseudo-chromosomes, thus significantly improved the quality of assembly of OB reference genome. We demonstrate that, while this new linkage map shares high collinearity level with strawberry genome, it also features two chromosomal rearrangements, indicating its usefulness as a resource for understanding the evolutionary scenario among Rosaceae genomes. Together with the newly released genome sequences for OB, this linkage map will facilitate the identification of genetic components underpinning key agricultural and biological traits, hence should greatly advance the studies and breeding efforts of rose.

Features
This publication contains information about 2,213 features:
Feature NameUniquenameType
Rosa_SNP.198273Rosa_SNP.198273genetic_marker
Rosa_SNP.205956Rosa_SNP.205956genetic_marker
Rosa_SNP.72205Rosa_SNP.72205genetic_marker
Rosa_SNP.205971Rosa_SNP.205971genetic_marker
Rosa_SNP.167367Rosa_SNP.167367genetic_marker
Rosa_SNP.227785Rosa_SNP.227785genetic_marker
Rosa_SNP.53977Rosa_SNP.53977genetic_marker
Rosa_SNP.165759Rosa_SNP.165759genetic_marker
Rosa_SNP.156874Rosa_SNP.156874genetic_marker
Rosa_SNP.123948Rosa_SNP.123948genetic_marker
Rosa_SNP.38483Rosa_SNP.38483genetic_marker
Rosa_SNP.205958Rosa_SNP.205958genetic_marker
Rosa_SNP.3278Rosa_SNP.3278genetic_marker
Rosa_SNP.126564Rosa_SNP.126564genetic_marker
Rosa_SNP.123290Rosa_SNP.123290genetic_marker
Rosa_SNP.278223Rosa_SNP.278223genetic_marker
Rosa_SNP.109523Rosa_SNP.109523genetic_marker
Rosa_SNP.124982Rosa_SNP.124982genetic_marker
Rosa_SNP.227308Rosa_SNP.227308genetic_marker
Rosa_SNP.102704Rosa_SNP.102704genetic_marker
Rosa_SNP.102705Rosa_SNP.102705genetic_marker
Rosa_SNP.15518Rosa_SNP.15518genetic_marker
Rosa_SNP.101382Rosa_SNP.101382genetic_marker
Rosa_SNP.39292Rosa_SNP.39292genetic_marker
Rosa_SNP.262069Rosa_SNP.262069genetic_marker

Pages

Featuremaps
This publication contains information about 1 maps:
Map Name
Rose-Old_Blush_x_Basyes_Thornless-BC1F1
Stocks
This publication contains information about 2 stocks:
Stock NameUniquenameType
Basyes' ThornlessBasyes' Thornlesscultivar
Old_Blush_x_Basyes_Thornless-BC1F1Old_Blush_x_Basyes_Thornless-BC1F1population
Cross References
This publication is also available in the following databases:
DatabaseAccession
PMID: PubMedPMID:30979937