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

世界上大部分的渔业都被过度开发，似乎不可避免的是，养鱼业将在很大程度上取代渔业，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，需要以鱼粉为食。罗非鱼是一种热带淡水鱼，主要可以在蔬菜和农业废料上种植，因此对未来的可持续生产大有希望。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。大多数罗非鱼的生产都是基于少数品种，但非洲有50多种野生物种，它们可能含有生长、抗病、耐温、耐盐等有价值的基因。许多罗非鱼将很容易杂交，因此自然遗传性状可以很容易地培育成养殖品系，而不需要转基因技术。然而，这一特点也使它们容易受到外来养殖菌株在自然水体中的遗传淹没，这种做法现在在非洲很普遍。目前，人们对野生罗非鱼品种的状况所知甚少，国际机构似乎基本上没有意识到正在进行广泛放养，对其可能产生的后果也几乎没有认识。我们建议调查坦桑尼亚的自然罗非鱼多样性，这是一个特别的野生罗非鱼品种的热点。我们将通过对本地和放养形式的基因组进行测序，在分子遗传水平上评估放养的影响。我们将找到纯本地品种的种群，并提出就地和移地保护的建议（例如在池塘养殖或精子库中）。我们将利用鳞片环估计纯种和杂交形式在其自然栖息地的生长速度，并将其与特定的遗传性状联系起来，预测放养可能产生的遗传后果。我们还将从稳定同位素比值的角度研究纯种菌株和杂交菌株的生态位。有可能来自本地菌株的遗传物质实际上帮助杂交形式建立自己，或者实际上，如果没有定期放养计划的补充，可能在某些栖息地，放养的形式可能无法建立起来。我们将开发杂交的快速分子诊断测试，以使其他地方的渔业管理人员受益，并使用这些来校准简单的视觉方法，以识别现场的杂交品种。所有这些罗非鱼品系的基因组序列信息将被存入在线公共数据库，为今后罗非鱼品系发育和保护研究提供重要资源。我们还将向坦桑尼亚政府和世界鱼类协会（WorldFish）等国际机构提供建议，建议它们保留纯的本地种群，以便优先保护它们。这可以通过将组织/精子样本长期冷冻保存来支持，这样这些独特的濒危遗传资源就可以为将来寻求改善罗非鱼品系的育种者提供。

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.