A high-quality genome sequence of Rosa chinensisto elucidate ornamental traits

First author: L. Hibrand Saint-Oyant; Affiliations: Université d’Angers (昂热大学): Beaucouzé, France

Corresponding author: F. Foucher

Rose is the world’s most important ornamental plant (观赏植物), with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers (切花) and potted plants (盆栽). Roses are outbred and can have various ploidy levels. Our objectives were to develop a high-quality reference genome sequence for the genus Rosa by sequencing a doubled haploid, combining long and short reads, and anchoring to a high-density genetic map, and to study the genome structure and genetic basis of major ornamental traits. We produced a doubled haploid rose line (‘HapOB’) from Rosa chinensis ‘Old Blush’ and generated a rose genome assembly anchored to seven pseudo-chromosomes (512 Mb with N50 of 3.4 Mb and 564 contigs). The length of 512 Mb represents 90.1–96.1% of the estimated haploid genome size of rose. Of the assembly, 95% is contained in only 196 contigs. The anchoring was validated using high-density diploid and tetraploid genetic maps. We delineated (描述) hallmark chromosomal features, including the pericentromeric regions (近着丝粒区域), through annotation of transposable element families and positioned centromeric repeats using fluorescent in situ hybridization. The rose genome displays extensive synteny with the Fragaria vesca (野草莓) genome, and we delineated only two major rearrangements. Genetic diversity was analysed using resequencing data of seven diploid and one tetraploid Rosa species selected from various sections of the genus. Combining genetic and genomic approaches, we identified potential genetic regulators of key ornamental traits, including prickle (棘) density and the number of flower petals. A rose APETALA2/TOE homologue is proposed to be the major regulator of petal number in rose. This reference sequence is an important resource for studying polyploidization, meiosis and developmental processes, as we demonstrated for flower and prickle development. It will also accelerate breeding through the development of molecular markers linked to traits, the identification of the genes underlying them and the exploitation of synteny across Rosaceae.

月季是世界范围内最为成功的观赏植物，具有很高的经济、文化和象征性价值。月季在全球都有栽培，主要售为园庭玫瑰、切花及盆栽。月季为异交植物，具有不同的倍性水平，本文主要通过对加倍单倍体进行了二代和三代测序，组装了一个高质量的参考基因组，并获得了一个高密度的遗传图谱，用以研究月季的基因组结构和主要园艺性状的遗传机制。作者通过月季品种‘Old Blush’构建了一个加倍单倍体的株系’HapOB’，并将月季基因组锚定到七条假染色体，大小为512Mb，contig N50长度3.4Mb。512Mb的月季基因组组装代表了90.1-96.1%的预测基因组大小。95%的月季基因组组装包含在196个contig中。作者还通过一个高密度的二倍体和六倍体遗传图谱来验证月季基因组的组装。作者通过对TE家族的注释以及荧光原位杂交定位着丝粒特异的重复序列描述了月季基因组的染色体特色近着丝粒区域。月季的基因组与野草莓的基因组存在广泛的共线性，这两个基因组仅存在两个主要的重排。作者通过对七个二倍体和一个六倍体的蔷薇属物种重测序分析了蔷薇属的遗传多样性。结合遗传学和基因组学的方法，作者鉴定了关键园艺性状的潜在遗传调控子，包括棘密度和花瓣数量。蔷薇APETALA2/TOE同源基因被认为是花瓣数量的主要调控基因。本文所提供的参考基因组是研究多倍化、减数分裂和发育的重要资源，同时通过性状相关的分子标记开发促进蔷薇科物种的育种，鉴定关键性状的调控基因等。

doi: https://doi.org/10.1038/s41477-018-0166-1

Journal: Nature Plants

Published date: 11 June, 2018

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