With their high economic value and cultural significance, modern roses are one of the most important ornamental plants. Because of their complicated genetic background and tetraploid nature, the creation of high-density genetic maps of roses has been a challenge that has slowed the pace of molecular breeding for modern roses. The current construction of tetraploid genetic maps based on existing diploid rose genomes could lead to inaccurate marker information and genotyping results. Therefore, we generated the first high-quality tetraploid genome of Rosa chinensis ‘Yunzheng Xiawei.’ Utilizing Illumina, PacBio, and Hi-C sequencing technologies, we assembled a genome of 858.59 Mb with 14 pseudo-chromosomes. Mode of inheritance analysis using PolyOrigin indicated that modern roses show both quadrivalent and bivalent pairing. Based on this reference genome, high-density genetic maps were constructed using MSTmap with nearly saturated markers. Quantitative trait locus (QTL) analysis was conducted using WinQTLCart and R/qtl for flavonoids and carotenoids, and 11 QTL clusters were identified. By combining the genome annotation, phylogenetic analyses, and gene expression analyses, we were able to identify several key genes related to flavonoid and carotenoid biosynthesis. This study provides the basis for further genetic analyses of highly heterozygous tetraploid roses and could facilitate the progress of marker-assisted selection in modern roses.

中文翻译：

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将来自四倍体玫瑰基因组的分子证据汇编成近乎饱和的图谱，用于鉴定色素相关基因


现代玫瑰具有很高的经济价值和文化意义，是最重要的观赏植物之一。由于玫瑰复杂的遗传背景和四倍体性质，创建高密度玫瑰遗传图谱一直是一个挑战，它减缓了现代玫瑰分子育种的步伐。目前基于现有二倍体玫瑰基因组构建的四倍体遗传图谱可能导致标记信息和基因分型结果不准确。因此，我们生成了第一个高质量的五倍体蔷薇 'Yunzheng Xiawei' 四倍体基因组。利用 Illumina、PacBio 和 Hi-C 测序技术，我们组装了一个 858.59 Mb 的基因组和 14 条伪染色体。使用 PolyOrigin 的遗传分析模式表明，现代玫瑰同时表现出四价和二价配对。基于该参考基因组，使用具有近乎饱和标记的 MSTmap 构建了高密度遗传图谱。使用 WinQTLCart 和 R/qtl 对类黄酮和类胡萝卜素进行数量性状位点 （QTL） 分析，鉴定出 11 个 QTL 簇。通过结合基因组注释、系统发育分析和基因表达分析，我们能够鉴定出与类黄酮和类胡萝卜素生物合成相关的几个关键基因。本研究为高度杂合四倍体玫瑰的进一步遗传分析提供了基础，并可能促进现代玫瑰中标记辅助选择的进展。