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

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.

A genomic link in China roses: and they all lived prickly but water deficient ever after?

“…The collinearity between the assembled BT chromosome sequences and the K5 genetic map (Bourke et al, 2018) was very high with most of the association efficiency above 95% (Supplementary Table S8; Supplementary Figure S3). Except chromosome in the OBxBT genetic map, on which the distribution of molecular markers was obviously skewed (Li et al, 2019c), all the other 6 chromosomes showed a very good collinearity with correlation rate around 90% (Supplementary Figure S4; Supplementary Table S8). We next aligned our BT assembly to the recently reported haploOB genome sequences (Hibrand Saint-Oyant et al, 2018;Raymond et al, 2018) and identified a very high collinearity of BT assembly to both Raymond's (Figure 2A,2B) and Hibrand Saint-Oyant's (Supplementary Figure S3) genomes, revealing a high synteny level and gene order between these two genotypes.…”

“…To understand the genetic pattern of stem prickle density, we scored stem prickle density in the 99-individual F1 and the 148-individual BC1F1 populations generated via crossing the prickleless BT and prickly OB ( Figure 3A; supplementary Figure S17-S19) (Li et al, 2019c;Li et al, 2015). In the F1 population, the number of prickleless vs. prickly individuals is 13:86, a ratio not deviating from 1:7 (three loci hypothesis, Chi-square test, p=0.96) or 1:15 (four loci hypothesis, Chi-square test, p=0.43).…”

“…We conducted a QTL analysis using the 2,160 SNP markers for the BC1F1 population (Li et al, 2019c). Three QTL were identified using interval mapping To further understand the genetic pattern of QTL regions in other rose genotypes, we obtained the genomic sequencing data (minimum 15x) for three available prickleless (including one wild species R. banksiae and two cultivated genotypes; the only prickleless genotypes in our ~200 rose collection) and eight prickly roses (all wild genotypes), and estimated their weighted-Fst values per 100 Kb window (Supplementary Table S27).…”

“…The quality of this assembly was next assessed using two independent genetic maps: the integrated K5 map based on 172 tetraploid individuals (Bourke et al, 2018), and a recently developed genetic map for 150 diploid individuals for a BC1F1 population between R. chinensis 'Old Blush' (OB) and BT (OBxBT map) (Li et al, 2019c). Genetic markers were aligned against the assembled BT genome with blastn (e-value<=1e-5) and association rates were evaluated with…”

“…BT grows in a relatively moisture environment and has at least six pairs of contrasting traits like once flowering behavior, prickleless on stem, prostrate growth during vegetative growth season, white-colored single flowers, high resistance to black spots in comparison to OB genotype (Byrne et al, 2007;Li et al, 2015). These have allowed this species frequently used as parental materials for constructing a set of genetic populations aiming at dissecting the genetic bases of these important traits (Crespel et al, 2002;Hibrand Saint-Oyant et al, 2018;Li et al, 2019c;Li et al, 2015;Shupert et al, 2007;Spiller et al, 2011). Despite of the importance in rose genetics and culture, molecular information of BT is limited with only transcriptomic and molecular markers information available (Crespel et al, 2002;Cui et al, 2020;Hibrand Saint-Oyant et al, 2018;Li et al, 2019c;Li et al, 2018;Li et al, 2015;Shupert et al, 2007;Spiller et al, 2011).…”