College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China.
Sci Rep. 2017 Apr 26;7(1):1184. doi: 10.1038/s41598-017-01338-7.
Grass carp (Ctenopharyngodon idella) is an important economic species in freshwater aquaculture and its industry has been confined due to variety degeneration and frequent diseases. Marker-assisted selection is a feasible method for selective breeding of new varieties. Transcriptome data have greatly facilitated high-throughput single nucleotide polymorphism (SNP) marker discovery and phenotype association study. In this study, we gained a total of 25,981 and 5,775 high quality SNPs in two transcriptomes from individuals and cell lines, respectively. Comparative transcriptome analysis identified 413 and 832 grass carp reovirus (GCRV)-resistant-association SNPs as well as 1,381 and 1,606 GCRV-susceptible-association SNPs in individuals and cell lines, respectively. Integrated analysis indicated 22 genes with single SNP share common resistant/susceptible traits in two transcriptomes. Furthermore, we infected grass carp with GCRV, genotyping and association analyses were performed, and 9 in 22 SNPs were confirmed by PCR-RFLP. Meanwhile, mRNA expression profiles of 6 genes containing confirmed SNPs were examined by qRT-PCR. The results demonstrated that mRNA expressions were significant differences in resistant/susceptible individuals and cell lines. The present study develops an important strategy for high throughput screening of phenotype association genetic markers and the results will serve in grass carp breeding for GCRV resistance.
草鱼（Ctenopharyngodon idella）是淡水养殖业中的一种重要经济鱼类，但由于品种退化和频繁发生疾病，其产业受到了限制。标记辅助选择是培育新品种的可行方法。转录组数据极大地促进了高通量单核苷酸多态性（SNP）标记的发现和表型关联研究。在这项研究中，我们分别从个体和细胞系中获得了总共 25981 个和 5775 个高质量的 SNP。比较转录组分析鉴定了 413 个和 832 个草鱼呼肠孤病毒（GCRV）抗性关联 SNP，以及个体和细胞系中分别为 1381 个和 1606 个 GCRV 易感关联 SNP。综合分析表明，在两个转录组中，有 22 个基因具有单个 SNP 共享的共同抗性/易感特征。此外，我们用 GCRV 感染草鱼，进行基因分型和关联分析，在 22 个 SNP 中有 9 个通过 PCR-RFLP 得到确认。同时，通过 qRT-PCR 检查了包含确认 SNP 的 6 个基因的 mRNA 表达谱。结果表明，抗性/易感个体和细胞系中的 mRNA 表达存在显著差异。本研究为高通量筛选表型关联遗传标记提供了一种重要策略，研究结果将用于草鱼对 GCRV 抗性的选育。
