基于转录组和简化基因组测序构建栀子高密度遗传图谱并定位产量相关性状QTL

Gardenia jasminoides Ellis., whose fruits are heavily used in traditional Chinese medicine and natural pigment industry at home and abroad, is an evergreen flowering plant cultivated in large scale in south China. It is prized for the strong sweet scent of its flowers, therefore is also used popularly in landscape gardening and fragrance industry. No modern breeding program has ever been applied to gardenia. In cultivation bases in China, gardenia plants now are suffering from serious germplasm degeneration and frequent disease occurrence. Improving gardenia cultivars by MAS (marker assistant selection) breeding will lead to an accumulation of valuable traits over time, thereby increase yield and quality to meet the demand from domestic and overseas market. In our preliminary tests, two good varieties with quite different morphological characteristics were identified from a large number of gardenia breeding materials. Then artificial pollination after emasculation (before the anthers burst) was carried out, and 436 F1 offspring were harvested. In this project, we propose high-density genetic mapping and locating QTLs controlling fruit yield in the established F1 hybrid population, using SSR and SNP markers that developed from transcriptome sequences and ddRAD-seq respectively. Constructing fine genetic linkage groups and mapping yield QTLs will provide a framework for map-based cloning and QTL pyramiding in MAS, and in the end help to increase gardenia quality and fruit production.

栀子用途广泛，是中药和色素产业的重要原料，国内外需求量大，我国多省份大面积栽培种植，但种源混乱，未经系统选育和驯化，多年种植后种质退化严重，病虫害较多，产量逐年递减，资源供不应求。选育良种是提高产量、促进栀子相关产业可持续发展的有效途径。本研究前期筛选了两个优良栀子类型作为亲本，建立了F1代杂交作图群体。拟利用已报道的转录组数据，开发SSR分子标记；利用ddRAD-seq技术，开发SNP分子标记；构建基于SSR和SNP分子标记的高密度遗传图谱，进行产量相关性状的QTL定位；为全面解析数量性状位点，挖掘有自主知识产权的功能基因，进行高产相关分子设计和组装育种提供科学依据。

栀子用途广泛，是中药和色素产业的重要原料，选育良种是提高产量、促进栀子相关产业可持续发展的有效途径。本项目以“高枝大果中叶宽冠型”栀子（编号为GD1）为母本，“短枝小果细叶矮冠型”栀子（编号为AX5）为父本，进行人工去雄授粉，杂交后获得了1303株实生苗。利用已发表文章中的SSR引物鉴定杂交种，从而构建了F1代作图群体（CP群体）。.以AX5的茎、叶片、果实、种子和萼片为材料，利用单分子实时DNA测序（Single Molecule Real Time DNA Sequencing，SMRTTM）技术，进行转录组测序。根据测序结果，设计了447对SSR引物。利用亲本和少量杂交种进行多态性初步筛选，然后在作图群体中扩增，最终获得25对符合孟德尔遗传规律的SSR引物。.从杂交种中随机筛选200个单株，在测序平台 Illumina Nova6000上进行简化基因组测序。采用“拟测交”策略，将多态性SNP标记进行过滤筛选后，保留符合群体特征的有效多态性标签。通过与已发表栀子参考基因组的联合分析，将SNP标记和25个SSR标记分为11个连锁群，构建了栀子高密度遗传图谱，最终获得上图标记4249个。初步定位了产量相关性状（冠幅和主干倾斜角度）的QTL区域，并获得了与目标性状连锁的分子标记。