Whole genome resequencing data enables a targeted SNP panel for conservation and aquaculture of Oreochromis cichlid fishes.
Whole genome resequencing data enables a targeted SNP panel for conservation and aquaculture of Oreochromis cichlid fishes.
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DOI：
10.1016/j.aquaculture.2021.737637
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发表时间：
2022-02-15
期刊：
影响因子：
--
通讯作者：
Turner GF
中科院分区：
文献类型：
--
作者：
Ciezarek A;Ford AGP;Etherington GJ;Kasozi N;Malinsky M;Mehta TK;Penso-Dolfin L;Ngatunga BP;Shechonge A;Tamatamah R;Haerty W;Di Palma F;Genner MJ;Turner GF
Oreochromis属的慈鲷鱼是全球罗非鱼养殖和渔业的基础。用于水产养殖的亲鱼通常从野生种群中采集，在非洲，野生种群可能来自包含多个Oreochromis物种的地点。然而，许多物种很难在形态上区分，这阻碍了保持高质量养殖品种的努力。此外，已知非本地养殖罗非鱼种群广泛分布于非洲各地，并与本地Oreochromis物种杂交，而本地Oreochromis物种本身对捕捞渔业很重要。这些杂交种的形态鉴定特别不可靠。在这里，我们描述了一个单核苷酸多态性（SNP）基因分型面板从全基因组重测序数据，使目标物种识别在坦桑尼亚的发展。我们证明了一个优化的面板的96个全基因组SNP的基础上FST离群值进行重复全基因组重测序区分物种和识别杂交种。我们还表明，该面板优于基于微卫星和基于表型的分类方法。案例研究表明，几个地方引进的水产养殖物种已成为建立在野外，威胁本地Oreochromis物种。这里确定的新的SNP标记代表了一个重要的资源，用于评估亲鱼的纯度在孵化场，并帮助保护独特的地方性生物多样性。我们提出了一个新的面板的96个SNPs，它可以用来准确地区分物种和杂交罗非鱼。该SNP面板执行对全基因组数据的比对，并且比微卫星或形态学分配更可靠。这将有助于评估水产养殖的亲鱼，以及入侵罗非鱼和本地罗非鱼之间的杂交。
Cichlid fish of the genus Oreochromis form the basis of the global tilapia aquaculture and fisheries industries. Broodstocks for aquaculture are often collected from wild populations, which in Africa may be from locations containing multiple Oreochromis species. However, many species are difficult to distinguish morphologically, hampering efforts to maintain good quality farmed strains. Additionally, non-native farmed tilapia populations are known to be widely distributed across Africa and to hybridize with native Oreochromis species, which themselves are important for capture fisheries. The morphological identification of these hybrids is particularly unreliable. Here, we describe the development of a single nucleotide polymorphism (SNP) genotyping panel from whole-genome resequencing data that enables targeted species identification in Tanzania. We demonstrate that an optimized panel of 96 genome-wide SNPs based on FST outliers performs comparably to whole genome resequencing in distinguishing species and identifying hybrids. We also show this panel outperforms microsatellite-based and phenotype-based classification methods. Case studies indicate several locations where introduced aquaculture species have become established in the wild, threatening native Oreochromis species. The novel SNP markers identified here represent an important resource for assessing broodstock purity in hatcheries and helping to conserve unique endemic biodiversity. We present a novel panel of 96 SNPs, which can be used to accurately distinguish species and hybrids of Oreochromis tilapias. This SNP panel performs comparably to full-genome data, and is more reliable than microsatellite or morphological assignment. This will enable assessment of broodstock for aquaculture, as well as hybridisation between invasive and native tilapia.
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影响因子：
9.2
作者：
Conte, Matthew A.;Joshi, Rajesh;Kocher, Thomas D.
通讯作者：
Kocher, Thomas D.
影响因子：
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通讯作者：
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