Du Xuedi, Song Kai, Wang Jinpeng, Cong Rihao, Li Li, Zhang Guofan
Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, 266071, China.
Department of Aquaculture, Yangzhou University, Yangzhou, Jiangsu, 101300, China.
J Genomics. 2017 Jul 18;5:83-90. doi: 10.7150/jgen.19146. eCollection 2017.
Carotenoids are commonly deposited in the gonads of marine bivalves but rarely in their adductor muscles. An orange-adductor variant was identified in our breeding program for the bay scallop . In the present study, bay scallop genome survey sequencing was conducted, followed by genotyping by sequencing (GBS)-based case-control association analysis in a selfing family that exhibited segregation in adductor color. K-mer analysis (K=17) revealed that the bay scallop genome is about 990 Mb in length. assembly produced 217,310 scaffold sequences, which provided 72.1% coverage of the whole genome and covered 72,187 transcripts, thereby yielding the most informative sequence resource for bay scallop to date. The average carotenoid content of the orange-adductor progenies was significantly higher than that of the white-adductor progenies. Thus, 20 individuals of each subgroup were sampled for case-control analysis. As many as 15,224 heterozygous loci were identified in the parent, among which 9280 were genotyped in at least 10 individuals of each of the two sub-groups. Association analysis indicated that 126 SNPs were associated with carotenoid accumulation in the adductor muscle and that 88 of these were significantly enriched on 28 scaffolds (FDR controlled < 0.05). The SNPs and genes located on these scaffolds can serve as valuable candidates for further research into the mechanisms by which marine bivalves accumulate carotenoids in their adductor muscles.
类胡萝卜素通常沉积在海洋双壳贝类的性腺中，但很少沉积在其闭壳肌中。在我们的海湾扇贝育种计划中鉴定出了一种橙色闭壳肌变体。在本研究中，进行了海湾扇贝基因组调查测序，随后在一个闭壳肌颜色出现分离的自交家系中，通过基于测序的基因分型（GBS）进行病例对照关联分析。K-mer分析（K=17）表明，海湾扇贝基因组长度约为990 Mb。组装产生了217,310个支架序列，覆盖了全基因组的72.1%，涵盖了72,187个转录本，从而产生了迄今为止海湾扇贝最丰富的序列资源。橙色闭壳肌后代的类胡萝卜素平均含量显著高于白色闭壳肌后代。因此，每个亚组抽取20个个体进行病例对照分析。在亲本中鉴定出多达15,224个杂合位点，其中9280个在两个亚组的至少10个个体中进行了基因分型。关联分析表明，有126个单核苷酸多态性（SNP）与闭壳肌中的类胡萝卜素积累相关，其中88个在28个支架上显著富集（错误发现率控制<0.05）。位于这些支架上的SNP和基因可作为有价值的候选对象，用于进一步研究海洋双壳贝类在其闭壳肌中积累类胡萝卜素的机制。
