Genomic approaches to identification and preservation of wild tilapia genetic resources for aquaculture

鉴定和保存水产养殖野生罗非鱼遗传资源的基因组方法

• 批准号: BB/M026736/1
• 负责人: George Turner
• 金额: $ 31.36万
• 依托单位: Bangor University
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2015
• 资助国家: 英国
• 起止时间: 2015 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FM026736%2F1
• 关键词: Genomic; approaches; identification; preservation; wild

Most of the world's fisheries are over-exploited and it seems inevitable that fish-farming will largely replace fishing, just as livestock arming has replaced hunting as the main source of food from land animals. Unfortunately, many farmed fish, such as salmon, are themselves predators and need to be fed on fish meal. Tilapia are tropical freshwater fish that can be grown largely on vegetable matter and agricultural waste and so promise much for future sustainable production. Global tilapia production grew 280 percent over the 10 years to 2012, with a harvest of ~4.5 million tonnes, more than 5 times greater than the entire UK fishery and aquaculture industry. Tilapia is now a $7.6 billion dollar industry. Most tilapia production is based on a handful of strains, but there are more than 50 wild species throughout Africa which could harbour valuable genes for growth, disease resistance, temperature & salt tolerance etc. Many tilapia will hybridize readily, so that the natural genetic traits could easily be bred into farmed strains without the need for GM technology. However, this feature also renders them vulnerable to genetic swamping by stocking with alien farmed strains into natural water bodies, a practice now widespread in Africa. At present, little is known of the status of wild tilapia strains, and international agencies seem to be largely unaware that widespread stocking is in progress, and there is little appreciation of its possible consequences. We propose to survey the natural tilapia diversity of Tanzania, a particular hotspot for wild tilapia strains. We will assess the effects of stocking at the molecular genetic level through sequencing the genomes of native and stocked forms. We will locate pure stocks of native forms and make recommendations for their conservation in-situ and ex-situ (e.g. in pond culture or sperm banks). We will estimate the growth rates of pure and hybrid forms in their natural habitats using scale rings and relate these to particular genetic traits, making predictions of the likely genetic consequences of stocking. We will also investigate the ecological niches of pure and hybrid strains from stable isotope ratios. It is possible that genetic material from native strains is actually helping hybrid forms to establish themselves, or indeed that the stocked forms may be failing to get established, perhaps in some habitats, if not supplemented by regular stocking programmes. We will develop quick molecular diagnostic tests of hybridization for the benefit of fishery managers in other locations, and use these to calibrate simple visual methods to identify hybrids in the field. The genome sequence information of all of these tilapia strains will be deposited in online public databases, where it will provide a major resource for future studies in tilapia strain development and conservation. We will also advise the government of Tanzanian and international agencies such as WorldFish about remaining pure populations of native strains to prioritise their conservation. This be backed up by depositing tissue/sperm samples for long-term deep-freeze storage, so that these unique and endangered genetic resources might be available to breeders seeking to improve tilapia strains in the future.

世界上大多数渔业都被过度开发，似乎不可避免的是，养鱼将在很大程度上取代捕鱼，就像畜牧业取代狩猎成为陆地动物的主要食物来源一样。不幸的是，许多养殖鱼类，如鲑鱼，本身就是捕食者，需要以鱼粉喂养。罗非鱼是一种热带淡水鱼，主要可以用蔬菜和农业废料种植，因此对未来的可持续生产有很大希望。截至2012年的10年间，全球罗非鱼产量增长了280%，收获量约为450万吨，是整个英国渔业和水产养殖业的5倍多。罗非鱼现在是一个价值76亿美元的产业。大多数罗非鱼生产是基于少数几个菌株，但有超过50个野生品种在整个非洲可能窝藏有价值的基因的增长，抗病性，温度和耐盐性等许多罗非鱼将很容易杂交，使自然遗传性状可以很容易地培育成养殖品种，而不需要转基因技术。然而，这一特点也使它们容易受到基因沼泽的影响，因为它们将外来养殖的菌株放养到自然水体中，这种做法现在在非洲很普遍。目前，对野生罗非鱼品系的状况知之甚少，国际机构似乎基本上不知道正在进行大规模放养，对其可能产生的后果也知之甚少。我们建议调查自然罗非鱼的多样性坦桑尼亚，野生罗非鱼品系的一个特别热点。我们将评估放养的影响，在分子遗传水平上，通过测序的基因组的本地和放养形式。我们将找到原生形式的纯股票，并提出建议，为他们的保护原位和异地（例如，在池塘养殖或精子银行）。我们将估计纯和混合形式的增长率在其自然栖息地使用规模戒指，并与这些特定的遗传性状，作出预测的可能的遗传后果放养。我们也将从稳定同位素比率来探讨纯系和杂交系的生态位。有可能来自本地品种的遗传物质实际上正在帮助杂交品种建立自己，或者如果没有定期的放养计划的补充，放养的品种可能无法建立，也许在某些栖息地。我们将为其他地区的渔业管理人员开发杂交的快速分子诊断测试，并使用这些测试来校准简单的视觉方法，以在现场识别杂交种。所有这些罗非鱼品系的基因组序列信息将被保存在在线公共数据库中，在那里它将为罗非鱼品系开发和保护的未来研究提供主要资源。我们还将向坦桑尼亚政府和国际机构（如WorldFish）提供建议，以保留本地菌株的纯种群，并优先保护它们。这可以通过存放组织/精子样本进行长期深冻储存来支持，以便这些独特和濒危的遗传资源可以用于未来寻求改进罗非鱼品系的育种者。

项目成果

Whole genome resequencing data enables a targeted SNP panel for conservation and aquaculture of Oreochromis cichlid fishes.

• DOI: 10.1016/j.aquaculture.2021.737637
• 发表时间: 2022-02-15
• 期刊: Aquaculture (Amsterdam, Netherlands)
• 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
• 通讯作者: Turner GF

Newly discovered cichlid fish biodiversity threatened by hybridization with non-native species

新发现的丽鱼科鱼类生物多样性受到与非本地物种杂交的威胁

• DOI: 10.1101/2020.08.06.240002
• 发表时间: 2020
• 作者: Blackwell T

A survey of fishes of Hombolo Lake, Dodoma, Tanzania, with evidence for local extinction of a native tilapia as a consequence of stocking

对坦桑尼亚多多马洪博洛湖鱼类的调查，有证据表明当地本地罗非鱼因放养而灭绝

• DOI: 10.1101/452847
• 发表时间: 2018
• 作者: Turner G

Ancient and ongoing hybridization in the Oreochromis cichlid fishes

• DOI: 10.1101/2023.05.19.541459
• 发表时间: 2023-09
• 期刊: bioRxiv
• 作者: A. Ciezarek;Tarang K. Mehta;Angela Man;Antonia G P Ford;G. D. Kavembe;N. Kasozi;B. Ngatunga;A. Shec

Whole genome resequencing data enables a targeted SNP panel for conservation and aquaculture of Oreochromis cichlid fishes

全基因组重测序数据为 Oreochromis cichlid 鱼类的保护和水产养殖提供了有针对性的 SNP 组合

• DOI: 10.1101/2021.03.24.436760
• 发表时间: 2021
• 作者: Ciezarek A