IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France.
ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium.
Nat Plants. 2018 Jul;4(7):473-484. doi: 10.1038/s41477-018-0166-1. Epub 2018 Jun 11.
Rose is the world's most important ornamental plant, with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers and potted plants. 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 hallmark chromosomal features, including the pericentromeric regions, 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 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 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.
玫瑰是世界上最重要的观赏植物，具有经济、文化和象征意义。玫瑰在世界各地被种植，并作为花园玫瑰、切花和盆栽植物出售。玫瑰是异花授粉的，可以有不同的倍性水平。我们的目标是通过测序一个加倍单倍体，结合长读长和短读长，并锚定到高密度遗传图谱，为蔷薇属开发一个高质量的参考基因组序列，并研究主要观赏性状的基因组结构和遗传基础。我们从 Rosa chinensis 'Old Blush' 中产生了一个加倍单倍体玫瑰品系（'HapOB'），并生成了一个锚定到七个拟染色体的玫瑰基因组组装（512Mb，N50 为 3.4Mb，564 个 contigs）。组装体的 512Mb 长度代表了玫瑰估计的单倍体基因组大小的 90.1-96.1%。组装体的 95%仅包含在 196 个 contigs 中。通过使用高密度二倍体和四倍体遗传图谱验证了锚定。我们通过转座元件家族的注释和使用荧光原位杂交定位着丝粒重复序列，描绘了标志性的染色体特征，包括着丝粒周围区域。蔷薇属基因组与 Fragaria vesca 基因组显示出广泛的同线性，我们仅确定了两个主要的重排。使用从属的不同部分选择的七个二倍体和一个四倍体 Rosa 物种的重测序数据分析了遗传多样性。通过结合遗传和基因组方法，我们鉴定了关键观赏性状的潜在遗传调控因子，包括刺密度和花瓣数量。提出了一个蔷薇属 APETALA2/TOE 同源物是蔷薇属花瓣数量的主要调控因子。这个参考序列是研究多倍体化、减数分裂和发育过程的重要资源，正如我们在花和刺发育方面所展示的那样。它还将通过开发与性状相关的分子标记、鉴定它们的基因以及利用蔷薇科的同线性来加速育种。
