14TSB_ATC_IR Genome biobanking for the optimisation of valuable broiler genetic stocks

该项目将开发新的技术来保护和利用现有的家禽遗传资源，方法是：i)使用PGCs(哺乳动物干细胞的鸡肉功能等价物)为肉鸡品系建立遗传资源生物库，以保存基因类型，因此有可能根据需要将基因类型重新引入家禽生产系统。使用PGCS的最新发展为开发一种新技术来保护和管理独特的遗传谱系繁育群提供了一个商业机会。目前，如果因疾病或自然灾害而失去血统，就无法重建谱系种群。可能包含对发展中市场有用的等位基因的有价值的品系要么作为活的羊群保留，要么从生产过程中被淘汰。经过验证的生物库程序，再加上生物库材料的完整基因分型，将允许储存可根据需要恢复生产的PGC。与哺乳动物农业物种不同，肉鸡行业受到有限的精液冷冻计划和精液存储技术的阻碍，这些技术只能可靠地保存几个小时，而不是几天、几个月或几年。使用鸡PGCs(干细胞)作为冷冻保存系统是最近开发的(van de Lvoir，2006)，尚未由任何大型商业家禽饲养者开发。我们打算保留Vantress鸡的传统品系，这是我们在过去50年中一直存在的当前Cobb纯种肉鸡品系的创始品系。因此，它代表了一个祖先基因库，现代品系的基因组就是从这个基因库中挑选出来的。因此，它将包括可能有用的等位基因，这些等位基因已经从现代品系中丢失，或者在未来进一步选择时可能丢失。基因材料的冷冻保存只是获取和保存基因多样性的综合计划的一部分，该计划是为新兴市场和转型市场开发新产品所需的。仔细评估可用的遗传变异，以及了解哪些等位基因对驱动关键性能性状至关重要，对于开发商业和非商业遗传资源中现有的遗传多样性是必要的。测序技术和努力的最新进展提供了一个有价值的参考鸡基因组的组装。作为一个由公共和私人资助的财团的产品，这项努力的重点是现代鸡的祖先，红色丛林家禽。然而，为了在商业行业中有效地利用基因组选择策略，必须全面了解商业纯种的等位基因和相关的表型性状。为此，该项目将对肉鸡品系的基因组序列进行进一步的DNA测序和注释，以产生GeneAtlas；模型，以更好地了解现代肉鸡品系的遗传变异。目前，我们理解鸡品系内和品系之间的变异性的能力受到当前鸡基因组构建的不完整状态以及现代肉鸡品系与红色丛林家禽之间遥远关系的阻碍。肉鸡基因图谱将允许利用肉鸡的遗传变异性，将生物库遗传物质导入新的纯系种群。这款肉鸡图集将专门用于Cobb商业纯种肉鸡和祖先Cobb肉鸡系列。这将是一种独特的资源，将使Cobb能够从他们针对特定市场的各种生产群中选择性状。

This project will develop novel technology to safeguard and harness existing poultry genetic resources by i) biobanking genetic resources for broiler lines using PGCs (the chicken functional equivalent of the mammalian stem cell) to preserve genotypes and therefore have the potential to re-introduce genotypes as needed into poultry production systems. Recent developments using PGCs provide a business opportunity to exploit a novel technology to safeguard and manage unique genetic pedigree breeding flocks. Currently there is no way to reconstitute pedigree stocks if lost to disease or natural disaster. Valuable lines that could contain useful alleles for developing markets are either maintained as living flocks or are culled from the production process. A proven biobanking procedure, coupled with complete genotyping of the biobanked material, will permit the storage of PGCs which can be returned to production as needed. Unlike mammalian agricultural species, the broiler industry is hindered by the limited semen cryopreservation program and semen storage technologies that are only reliable for hours, not days, months, or years. The use of chicken PGCs (stem cells) as a cryopreservation system has recently developed (van de Lavoir, 2006) and has not yet been developed by any of the large commercial poultry breeders. We intend to preserve the Vantress heritage line of chickens, a/the founder line for the current Cobb pedigree broiler lines that we have kept extant for the last fifty years. It thus represents an ancestral pool of genes from which the genomes of the modern lines have been selected. It will therefore include potentially useful alleles that have already been lost from the modern lines, or may be lost in the future with further selection. Cryopreserving genetic material is only one part of an integrated program to access and preserve genetic diversity required for the development of new products for emerging and transforming market segments. A careful assessment of the available genetic variation, along with an understanding of which alleles are critical for driving key performance traits is necessary to exploit the existing genetic diversity in commercial and non-commercial genetic stocks. Recent advances in sequencing technologies and efforts have provided a valuable assembly of a reference chicken genome. As the product of a publically and privately funded consortium, the effort focused on the ancestor of the modern chicken, the red jungle fowl. However, to effectively utilize genomic selection strategies in the commercial industry, a comprehensive understanding of the alleles and associated phenotypic traits of commercial purelines must be completed. To this end, this project will undertake ii) further DNA sequencing and annotation of the genomic sequence of a broiler line to produce a GeneAtlas; model for better understanding genetic variation in modern broiler lines. Currently, our ability to understand variability within and between lines of chickens is hampered by the incomplete state of the current chicken genome build and the distant relationship between modern broiler lines and the red jungle fowl. A broiler GeneAtlas will allow the exploitation of broiler genetic variability for the introgression of biobanked genetic material into new pureline populations. This broiler Atlas will be specific for Cobb commercial purelines and ancestral Cobb broiler lines. This will be a unique resource that will enable Cobb to select traits from within their various production flocks for specific markets.