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Related Concept Videos

Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

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,...
Incomplete Dominance01:43

Incomplete Dominance

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.
Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

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...
Principles of Pharmacogenetics: Types of Genetic Variants01:27

Principles of Pharmacogenetics: Types of Genetic Variants

The human genome is over 99.9% identical between individuals, yet genetic differences exist at millions of bases. The human genome contains approximately 3 million variant positions per individual, many of which are heterozygous, contributing to genetic diversity and individual traits. Genetic variations include single-nucleotide polymorphisms (SNPs), insertions, deletions, and copy number variations (CNVs).SNPs, the most common variation, involve single-base changes in DNA. These can be...
Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

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%...
Pharmacogenomics: Identification of New Drug Targets01:29

Pharmacogenomics: Identification of New Drug Targets

Advances in genomics have profoundly influenced drug discovery by increasing both the speed and accuracy of pharmaceutical development. Pharmacogenomics, which examines how genetic variation influences drug response, facilitates the identification of novel therapeutic targets and enables patient stratification for personalized treatment. These strategies contribute to improved drug efficacy, minimized adverse effects, and more efficient clinical trial design.Mapping genetic differences...

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Single nucleotide polymorphisms and haplotypes associated with feed efficiency in beef cattle.

Nick Vl Serão1, Dianelys González-Peña, Jonathan E Beever

  • 1Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA. rodrgzzs@illinois.edu.

BMC Genetics
|September 27, 2013
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Summary

Genomic variants associated with feed efficiency in beef cattle were identified using SNP panels. Both general and specific associations were found, aiding in genome-enabled selection for improved feed efficiency.

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Area of Science:

  • Animal Genetics
  • Quantitative Genetics
  • Livestock Production

Background:

  • Identified general, breed-dependent, and diet-dependent associations between feed efficiency indicators and SNPs/haplotypes in 1321 beef steers.
  • Compared traditional two-step indicators (RFI, RADG, RIG) with one-step indicators (EI, EG) for feed efficiency.
  • Utilized a 50K SNP panel for genomic analysis.

Purpose of the Study:

  • To identify genomic variants associated with feed efficiency in beef cattle.
  • To compare different indicators of feed efficiency and their genomic underpinnings.
  • To develop a multi-SNP model for predicting feed efficiency.

Main Methods:

  • Genomic association analysis using a 50K SNP panel on 1321 steers.
  • Evaluation of associations on an independent validation dataset.
  • Development of a multi-SNP model for feed efficiency prediction.
  • Functional analysis of associated genes and network visualization.

Main Results:

  • Discovered numerous SNP and haplotype associations with five feed efficiency indicators, including general, breed-dependent, and diet-dependent effects.
  • Confirmed complementary value of one-step and two-step feed efficiency indicators through overlapping associations.
  • Developed a multi-SNP model with 89 SNPs for precise prediction of feed efficiency.
  • Identified overrepresented Gene Ontology and KEGG pathway categories related to nucleotide binding, ion transport, and signaling pathways.

Conclusions:

  • General SNP associations suggest a universal genomic panel for feed efficiency, irrespective of breed and diet.
  • Breed- and diet-dependent associations highlight the need for tailored variant panels considering management practices.
  • Unique genomic variants for different indicator types confirm their complementary nature, valuable for genome-enabled selection.