GCRF-BBR: A compendium of structural variation across African cattle breeds

GCRF-BBR：非洲牛品种结构变异概要

• 批准号: BB/R015155/1
• 负责人: James Prendergast
• 金额: $ 15.41万
• 依托单位: University of Edinburgh
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2018
• 资助国家: 英国
• 起止时间: 2018 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FR015155%2F1
• 关键词: GCRF; BBR; compendium; structural; variation

Cattle are a vital component of the economies of low and middle income countries across the globe. They are a source of meat and dairy products, provide leather and other by-products and are often used as working animals. Cattle can be grazed where crops are not easily grown, provide manure as effective fertiliser and can convert forage into high-protein food. Often cattle are the most valuable possession individuals in low and middle income countries own, but are susceptible to a range of infectious diseases, which not only inflict a heavy economic burden on these countries but can also often be transmissible to humans.Over two-thirds of the global cattle population are in low and middle income countries. Reducing the burden of cattle infectious diseases would consequently have major benefits to these areas. However for many diseases no vaccine or treatment is available. Where they are available, poor veterinary services generally mean the livestock keepers must pay for vaccines and treatments themselves. Consequently these diseases are major barriers to escaping poverty. Due to the co-evolution of pathogens and cattle there are various examples of cattle breeds that show natural tolerance or resistance to important infectious diseases. Although these breeds are often less productive, making them less attractive to LMIC farmers, if the mechanisms underlying their resistance could be identified and harnessed, then breeds of both higher productivity and tolerance could be developed. Likewise certain breeds have been shown to be better adapted to particular environmental conditions. With certain breeds better able to tolerate extreme temperatures and limited access to feed and water for example.Structural variants (SVs), large alterations in an animal's genome sequence, have been linked in livestock to adaptation to environments and natural tolerance to important diseases. Despite their potential value, little is currently known about the genome-wide location of SVs in cattle and almost nothing in African cattle breeds. Native African cattle are particularly well adapted to African environments and pathogens, with structural variants expected to underlie many such important traits. Knowledge of the location of structural variants in African cattle breeds will enable researchers to determine their functional consequences and develop better breeding programs. In this project we will develop a database of structural variants focused on African cattle breeds to enable studies of their role in shaping important phenotypes.

牛是地球仪中低收入国家经济的重要组成部分。它们是肉类和奶制品的来源，提供皮革和其他副产品，并经常被用作工作动物。牛可以在作物不易生长的地方放牧，提供粪便作为有效的肥料，并可以将饲料转化为高蛋白质食物。牛通常是低收入和中等收入国家个人拥有的最有价值的财产，但容易感染一系列传染病，这不仅给这些国家造成沉重的经济负担，而且往往还可以传染给人类。全球三分之二以上的牛种群在低收入和中等收入国家。因此，减少牛传染病的负担将对这些地区产生重大利益。然而，对于许多疾病，没有疫苗或治疗方法。在有兽医服务的地方，糟糕的兽医服务通常意味着牲畜饲养者必须自己支付疫苗和治疗费用。因此，这些疾病是摆脱贫困的主要障碍。由于病原体和牛的共同进化，有各种各样的牛品种表现出对重要传染病的天然耐受性或抗性。虽然这些品种的生产力往往较低，使它们对LMIC农民的吸引力较低，但如果能够确定和利用它们的抗性机制，那么就可以开发出生产力和耐受性都较高的品种。同样，某些品种已被证明更好地适应特定的环境条件。例如，某些品种能够更好地耐受极端温度和有限的饲料和水。结构变异（SV），动物基因组序列的大幅度改变，已在牲畜中与适应环境和对重要疾病的天然耐受性联系起来。尽管它们具有潜在的价值，但目前对SV在牛中的全基因组位置知之甚少，在非洲牛品种中几乎一无所知。非洲本土牛特别适应非洲的环境和病原体，预计结构变异是许多重要特征的基础。了解非洲牛品种结构变异的位置将使研究人员能够确定其功能后果，并制定更好的育种计划。在这个项目中，我们将开发一个专注于非洲牛品种的结构变异数据库，以研究它们在形成重要表型中的作用。

项目成果

A cattle graph genome incorporating global breed diversity

纳入全球品种多样性的牛图基因组

• DOI: 10.1101/2021.06.23.449389
• 发表时间: 2021
• 作者: Talenti A

Bionano Solve outputs (PT2) for: Optical mapping compendium of structural variants across global cattle breeds

Bionano Solve 输出 (PT2)： 全球牛品种结构变异的光学测绘概要

• DOI: 10.5281/zenodo.6517171
• 发表时间: 2022
• 作者: Talenti A

VCF files from: Optical mapping compendium of structural variants across global cattle breeds

VCF 文件来自：全球牛品种结构变异的光学映射概要

• DOI: 10.5281/zenodo.6516932
• 发表时间: 2022
• 作者: Talenti A

Optical mapping compendium of structural variants across global cattle breeds

全球牛品种结构变异的光学测绘概要

• DOI: 10.1101/2022.05.05.490773
• 发表时间: 2022
• 作者: Talenti A

Bionano Solve outputs (PT1) for: Optical mapping compendium of structural variants across global cattle breeds

Bionano Solve 输出 (PT1)： 全球牛品种结构变异的光学测绘概要

• DOI: 10.5281/zenodo.6516992
• 发表时间: 2022
• 作者: Talenti A