Related Experiment Video
Updated: Jun 11, 2025
09:34
Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
Published on: April 4, 2018
33.7K
A large structural variant collection in Holstein cattle and associated database for variant discovery,
Jason R Grant1, Emily K Herman1, Lael D Barlow1
1Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada.
BMC Genomics
|September 30, 2024
Summary
This study identified thousands of structural variants (SVs) in Holstein cattle, creating a valuable resource for understanding their role in traits. The findings highlight challenges in SV genotyping and emphasize the need for advanced methods to link these variants to cattle phenotypes.
Area of Science:
- Genomics
- Animal Genetics
- Bioinformatics
Background:
- Structural variants (SVs) like deletions and duplications contribute to phenotypic variation but are difficult to identify and genotype.
- A comprehensive collection of SVs is crucial for studying their function in cattle and for improving animal evaluation.
Purpose of the Study:
- To generate a large, well-characterized collection of structural variants (SVs) in Holstein cattle.
- To create an accessible database for SVs to facilitate research into their functional roles and phenotypic impacts.
Main Methods:
- Whole-genome sequencing (WGS) data from 310 Holstein cattle samples were analyzed using Manta and Smoove SV callers.
- Genotype data were used to assess SV accuracy and relationships with SNP genotypes.
- Overlapping and tag single nucleotide polymorphisms (SNPs) were identified for SVs using bovine SNP chip data.
Main Results:
- Thousands of SVs were identified, covering a significant portion of the cattle genome.
- Manta SV genotypes accurately recapitulated animal relationships, outperforming Smoove.
- A custom interactive database was developed, containing annotated SVs for prioritization and study.
Conclusions:
- The developed resources aid in exploring sequence variation and studying SVs in Holstein cattle.
- Most SVs lack overlapping or tag SNPs, necessitating alternative genotyping approaches for phenotype association.
- Challenges in SV characterization with short-read data highlight the need for long-read sequencing.
Related Concept Videos
02:26Comparing Copy Number Variations and SNPs
17.6K
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%...
17.6K
01:05Single Nucleotide Polymorphisms-SNPs
14.8K
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,...
14.8K
01:43Incomplete Dominance
22.0K
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.
22.0K
01:11Genome-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
02:54Evolutionary 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
02:51Multi-species Conserved Sequences
3.9K
Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
3.9K