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Genome-wide association study and functional annotation analyses for nitrogen efficiency index and its composition
1TERRA Teaching and Research Center, University of Liège, Gembloux Agro-Bio Tech (ULiège-GxABT), 5030 Gembloux, Belgium.
Journal of Dairy Science
|March 9, 2023
Summary
This study identified key genomic regions and candidate genes linked to nitrogen efficiency in cattle, improving understanding of genetic mechanisms for nitrogen use. The findings provide insights into milk production and animal health traits.
Area of Science:
- Animal Genetics and Genomics
- Nutritional Biochemistry
- Quantitative Genetics
Background:
- Nitrogen (N) efficiency is crucial for sustainable cattle production and environmental impact.
- Identifying genetic factors influencing N efficiency can aid breeding programs.
- Previous studies have explored genetic components of N utilization, but comprehensive analysis of N efficiency index (NEI) and its traits is needed.
Purpose of the Study:
- To identify genomic regions associated with a comprehensive Nitrogen Efficiency Index (NEI) and its constituent traits in cattle.
- To perform functional annotation of these identified genomic regions.
- To uncover candidate genes and Quantitative Trait Loci (QTL) related to nitrogen utilization in dairy cattle.
Main Methods:
- Utilized a large dataset of over 1 million records from 342,847 cows across 1,931 herds.
- Employed a single-step genomic Best Linear Unbiased Prediction (BLUP) approach to estimate SNP effects.
- Analyzed additive genetic variance explained by SNP windows and identified top genomic regions for candidate gene and QTL annotation.
Main Results:
- Identified specific genomic regions on Bos taurus autosomes 14, 26, 16, 6, and 11 associated with NEI and its composition traits (N intake, milk true protein N, milk urea N yield).
- These top regions explained up to 0.58% of the total additive genetic variance for NEI.
- Identified 16 key candidate genes, primarily expressed in milk, mammary, and liver tissues, and found numerous enriched QTL related to milk production, health, and overall performance.
Conclusions:
- This study successfully pinpointed significant genomic regions and candidate genes underlying nitrogen efficiency in cattle.
- The identified genes provide insights into the genetic mechanisms governing nitrogen use efficiency and its related traits.
- The NEI effectively captures not only its component traits but also their complex interactions, offering a valuable tool for genetic selection.
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