基于重测序的伽师瓜高密度遗传图谱构建及主要果实性状QTL定位

Research objective: The research aimed to construct a high-density genetic linkage map of Jiashi melon and map the quantitative trait locus (QTL) of main fruit traits of the melon. The project was carried out based on the theoretical basis of chromosome interchange and recombination in classical genetics. At first, the recombinant inbred line (RIL) population of the cross of kalakesai (a variety of Jiashi melon) and PI511890 was re-sequenced to obtain the most widely used molecular marker in the complete genome. Then, the high-density genetic linkage map was drawn after determining the relative positions of and the distance between genes at the same chromosome by calculating the cross-over value. Moreover, the morphology, color, firmnesses, quality, yield, and maturity of fruit of Jiashi melon harvested after being cultivated for two years at three locations were subjected to the quantitative trait locus (QTL). Afterwards, the transcriptome sequencing was conducted for two parents and offsprings with different fruit traits. In addition, the molecular mechanism of the excellent fruit trait of Jiashi melon was explained through the annotation and analysis of differentially expressed genes in terms of mRNA levels of fruit traits and functional gene enrichment. Finally, the selected two most relevant candidate genes were subjected to gene cloning, establishment of the over-expression vector, and genetic transformation in melon. The research lays a foundation for speeding up the variety improvement, innovation, and molecular breeding of melon planted in Xinjiang Uygur Autonomous Region, China. In addition, it presents important guiding significance to illustrating the molecular genetics of main fruit traits of Jiashi melon.

研究目的：构建伽师瓜高密度遗传图谱，定位主要果实性状QTL及基因。本项目基于经典遗传学的染色体交换与重组的理论基础。首先，对伽师瓜“卡拉克赛”×PI511890重组自交系群体进行重测序，获得全基因组范围内最广泛的分子标记，通过计算交换值，确定位于同一染色体基因的相对位置和距离，绘成高密度连锁遗传图。然后，对经过两年三点种植获得的果实形态、果实颜色、果实硬度、果实品质、产量及熟性进行QTL定位。其次，对两个亲本、差异果实性状子代进行转录组测序，通过对果实性状mRNA水平的表达差异基因、功能基因富集注释分析，鉴定果实差异性状候选基因，解析伽师瓜优异果实性状分子机理。最后，对相关性最强的2个候选基因进行基因克隆、表达载体构建及甜瓜的遗传转化。这一研究为加快新疆厚皮甜瓜品种改良及分子育种奠定基础，同时对阐明伽师瓜主要果实性状的分子遗传规律有重要意义。

甜瓜是世界上极具多态性的果实性蔬菜作物。我们构建了由3626个 bins、平均图距83kb 高密度的哈密瓜遗传图谱和9个主要QTL其物理区间在43.47 kb 到 1.89 Mb之间。在两种环境条件下重复检测到两个种子性状QTLs，连锁分析显示定位区间在522 kb。扫描非同义变异区间总计注释到40个基因，其中转录组测序显示 EVM0009818细胞分裂素激活信号基因在亲本幼果中差异表达。选择性清除分析鉴定种子大小的152个清除性号，包括两个种子相关QTLs和9个已经在拟南芥和水稻中鉴定功能的调控种子大小的同源基因。这项工作说明了结合基于重测序的遗传图谱进行QTL定位和结合KASP基因分型和RNA-seq分析联合分析促进QTL精细定位的能力。这一研究为加快新疆厚皮甜瓜品种改良及分子育种奠定基础，同时对阐明伽师瓜主要果实性状的分子遗传规律有重要意义。