The gilthead seabream (Sparus aurata) is an important cultivated species in the Mediterranean area. A major problem for the gilthead seabream aquaculture sector derives from the high frequency of phenotypic abnormalities, including discolorations. In this study, we applied a whole‐genome resequencing approach to identify a genomic region affecting a pigmentation defect that occurred in a cultivated S. aurata population. Two equimolar DNA pools were constructed using DNA extracted from 30 normally coloured and 21 non‐pigmented fish collected among the offspring of the same broodstock nucleus. Whole‐genome resequencing reads from the two DNA pools were aligned to the S. aurata draft genome and variant calling was performed. A whole‐genome heterozygosity scan from single pool sequencing data highlighted a peak of reduced heterozygosity of approximately 5 Mbp on chromosome 6 in the non‐pigmented pool that was not present in the normally coloured pool. The comparison of the non‐pigmented with the normally coloured fish using a whole‐genome F_ST analysis detected three main regions within the coordinates previously detected with the heterozygosity analysis. The results support the presence of a major locus affecting this discoloration defect in this fish population. The results of this study have practical applications, including the possibility of eliminating this defect from the breeding stock, with direct economic advantages derived from the reduction of discarded fry. Other studies are needed to identify the candidate gene and the causative mutation, which could add information to understand the complex biology of fish pigmentation.

中文翻译：

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鉴定确定养殖金头鲷（Sparus aurata）色素沉着缺陷的主要基因座

银头鲷（Sparus aurata）是地中海地区重要的养殖品种。对于金头鲷养殖而言，一个主要问题来自表型异常的频繁发生，包括变色。在这项研究中，我们应用了全基因组重测序方法，以鉴定影响在养殖的金黄色葡萄球菌中发生的色素沉着缺陷的基因组区域。使用从亲虾核后代中收集的30条正常着色的鱼和21条无色素的鱼中提取的DNA构造了两个等摩尔的DNA库。将来自两个DNA库的全基因组重测序读数与金黄色葡萄球菌对齐完成了基因组和变异调用草案。从单池测序数据进行的全基因组杂合性扫描突出显示了正常色素池中不存在的无色素池中6号染色体上约5 Mbp的杂合度降低峰。使用全基因组F _ST将无色素的鱼与正常着色的鱼进行比较分析检测到先前通过杂合性分析检测到的坐标内的三个主要区域。结果支持在该鱼类种群中存在影响该变色缺陷的主要基因座。这项研究的结果具有实际应用价值，包括有可能从种畜中消除这一缺陷，并具有减少丢弃鱼苗的直接经济优势。还需要其他研究来鉴定候选基因和致病突变，这可能会增加信息以了解鱼类色素沉着的复杂生物学。