中国本土绵羊品种的种群结构和品种鉴定使用全基因 SNPs 和 InDels
Chang-Heng Zhao1, Dan Wang1, Cheng Yang1
1Shandong Provincial Key Laboratory for Livestock Germplasm Innovation & Utilization, College of Animal Science, Shandong Agricultural University, Tai'an, 271018, China.
Genetics, selection, evolution : GSE
|September 3, 2024
概括
准确的羊品种识别对于保护至关重要. 将SNP和InDel标记物与先进方法相结合,在识别中国本土品种方面获得了超过97.5%的准确性.
科学领域:
- 基因组学就是基因组学.
- 动物科学动物科学
- 保护生物学 保护生物学
背景情况:
- 准确的品种鉴定对于保护本土农场动物遗传资源至关重要.
- 全基因组测序 (WGS) 为分析遗传多样性和品种组成提供了强大的工具.
- 了解家族遗传关系有助于制定有针对性的保护战略.
研究的目的:
- 评估13种绵羊品种的遗传学关系和基因组品种组成 (11种中国本土,2种外国).
- 用各种标记类型和分析方法比较不同的品种识别策略.
- 为了确定最优的方法,准确的品种分配和纯度估计.
主要方法:
- 全基因组测序 (WGS) 数据用于单核酸多态 (SNPs) 和插入/删除 (InDels) 的数据.
- 使用组合方法进行品种信息标记检测 (DFI_union: Delta,Pairwise Wright的FST,信息性分配).
- 使用集成机器学习策略进行品种分配 (KSR:K-最近邻居,支持矢量机器,随机森林).
主要成果:
- 结合SNP和InDel (SI) 标记器,比单个标记器类型提高了识别准确度.
- DFI_union和KSR策略产生了最佳的品种识别.
- 实现了高准确度:用1000个最具品种信息性的SI标记器达到97.5%,用5000个SI标记器达到100%.
结论:
- 这项研究为识别中国本土绵羊品种提供了强有力的框架.
- 开发的方法提供了适用于各种土著农场动物品种识别的一般方法.
- 这些发现支持当地绵羊品种的保护工作和遗传资源管理.
相关概念视频
Comparing Copy Number Variations and SNPs
17.7K
Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
17.7K
Single Nucleotide Polymorphisms-SNPs
14.9K
A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
14.9K
Cloning of Dolly the Sheep
3.4K
The first successfully cloned mammal was Dolly, a sheep, born on 5th July 1996 at Roslin Institute, Scotland. The cloned sheep was named after the American singer Dolly Parton. Dolly lived for seven years and died of respiratory complications, which is speculated to be due to the actual age of her DNA. Because the DNA in cloned cells belongs to an older individual, the cloned individual’s life expectancy may be affected. Indeed, analysis of Dolly’s DNA revealed shorter...
3.4K
Evolutionary Relationships through Genome Comparisons
5.7K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
5.7K
Genome-wide Association Studies-GWAS
13.2K
Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
GWAS does not require the identification of the target gene involved in...
13.2K
Incomplete Dominance
22.1K
Gregor Mendel's work (1822 - 1884) was primarily focused on pea plants. Through his initial experiments, he determined that every gene in a diploid cell has two variants called alleles inherited from each parent. He suggested that amongst these two alleles, one allele is dominant in character and the other recessive. The combination of alleles determines the phenotype of a gene in an organism.
22.1K


