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

世界上大多数渔业都被过度开发，养鱼业似乎不可避免地将在很大程度上取代渔业，就像家畜饲养已经取代狩猎成为陆地动物的主要食物来源一样。不幸的是，许多养殖的鱼，如鲑鱼，本身就是捕食者，需要用鱼粉喂养。罗非鱼是一种热带淡水鱼，主要以蔬菜和农业废弃物为原料种植，因此为未来的可持续生产提供了很大希望。在截至2012年的10年里，全球罗非鱼产量增长了280%，产量约为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以少数几个品种为基础的，但整个非洲有50多个野生物种，它们可能含有生长、抗病、耐温和耐盐等方面的宝贵基因。许多罗非鱼会很容易杂交，因此可以很容易地将自然遗传特征培育成养殖品种，而不需要转基因技术。然而，这一特征也使它们容易受到基因淹没的影响，因为它们将外来养殖的菌株放养到自然水体中，这一做法目前在非洲很普遍。目前，人们对野生罗非鱼品系的状况知之甚少，国际机构似乎在很大程度上没有意识到正在进行广泛的放养，对其可能产生的后果也几乎没有认识到。我们建议调查坦桑尼亚的天然罗非鱼多样性，坦桑尼亚是野生罗非鱼品系的特别热点。我们将通过对原生和放养形式的基因组进行测序，在分子遗传水平上评估放牧的效果。我们将确定纯种原生物种的位置，并为原地和异地(例如池塘养殖或精子库)保护它们提出建议。我们将使用鳞片年轮估计纯种和杂交种在其自然栖息地的增长率，并将这些与特定的遗传特征联系起来，预测放牧可能产生的遗传后果。我们还将从稳定的同位素比率调查纯菌株和杂交菌株的生态位。有可能来自本土菌株的遗传物质实际上正在帮助杂交形式确立自己的地位，或者实际上，如果没有定期的放牧计划的补充，可能在一些栖息地，放养的形式可能无法建立。我们将为其他地方的渔业管理人员开发快速的杂交分子诊断测试，并使用这些测试来校准简单的视觉方法，以便在野外识别杂交物种。所有这些罗非鱼品系的基因组序列信息都将存储在在线公共数据库中，在那里它将为未来罗非鱼品系开发和保护的研究提供主要资源。我们还将建议坦桑尼亚政府和WorldFish等国际机构关于剩余的本地菌株的纯种群优先保护它们。这可以通过保存组织/精子样本进行长期冷冻储存来支持，这样这些独特的、濒危的遗传资源可能会被未来寻求改良罗非鱼品系的育种者获得。

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.