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.48062Rosa_SNP.48062genetic_marker
Rosa_SNP.12058Rosa_SNP.12058genetic_marker
Rosa_SNP.27686Rosa_SNP.27686genetic_marker
Rosa_SNP.289197Rosa_SNP.289197genetic_marker
Rosa_SNP.207966Rosa_SNP.207966genetic_marker
Rosa_SNP.118060Rosa_SNP.118060genetic_marker
Rosa_SNP.95691Rosa_SNP.95691genetic_marker
Rosa_SNP.281080Rosa_SNP.281080genetic_marker
Rosa_SNP.167014Rosa_SNP.167014genetic_marker
Rosa_SNP.224173Rosa_SNP.224173genetic_marker
Rosa_SNP.21278Rosa_SNP.21278genetic_marker
Rosa_SNP.292075Rosa_SNP.292075genetic_marker
Rosa_SNP.64272Rosa_SNP.64272genetic_marker
Rosa_SNP.289198Rosa_SNP.289198genetic_marker
Rosa_SNP.239611Rosa_SNP.239611genetic_marker
Rosa_SNP.239608Rosa_SNP.239608genetic_marker
Rosa_SNP.40847Rosa_SNP.40847genetic_marker
Rosa_SNP.293425Rosa_SNP.293425genetic_marker
Rosa_SNP.27685Rosa_SNP.27685genetic_marker
Rosa_SNP.276890Rosa_SNP.276890genetic_marker
Rosa_SNP.278398Rosa_SNP.278398genetic_marker
Rosa_SNP.89050Rosa_SNP.89050genetic_marker
Rosa_SNP.79378Rosa_SNP.79378genetic_marker
Rosa_SNP.196722Rosa_SNP.196722genetic_marker
Rosa_SNP.229434Rosa_SNP.229434genetic_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' Thornlessaccession
Old_Blush_x_Basyes_Thornless-BC1F1Old_Blush_x_Basyes_Thornless-BC1F1population