Related Experiment Video
Updated: Jan 15, 2026

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
Published on: June 21, 2018
Utilitarian selection signatures co-localized with copy number variation regions in Indian goat breeds revealed
Nidhi Sukhija1,2, Indrajit Ganguly1, K K Kanaka1,2
1Division of Animal Genetics, ICAR-National Bureau of Animal Genetics Resources, Karnal, India.
Abstract:
This study investigates the selection signatures of 11 Indigenous goat breeds from diverse eco-topographies of India, using whole-genome re-sequencing data from 103 individuals. We identified population-wide copy number variation regions (as well as selection signatures through a variance-stabilizing transformation approach for utility traits. A total of 32 711 polymorphic sites were analyzed, revealing 327 significant and 32 highly significant signatures under selection. Key genes identified in selection signatures include GHR, PLAG1, and MTOR, which play crucial roles in growth, development, and reproductive traits across different utility groups. Notable reproduction-related genes such as ITPR3, ESRRG, and SOX6 were found to be associated with fertility, hormone regulation, and reproductive system. Network analysis revealed ESR1 as a central hub gene forming significant interactions with RUNX2, HDAC2, and BCL2, indicating its vital role in muscle development and metabolism. The MTOR signaling pathway emerged as another crucial hub, connecting with DEPDC5 and SESN1, suggesting its importance in nutrient sensing and metabolic regulation for production traits. Gene ontology analysis of the selection signatures revealed pathways for functional categories between meat, milk, and fiber-producing breeds, reflecting the genetic architecture underlying their specialized phenotypes. Identified selection signatures and hub genes can be used in marker-assisted and genomic selection to improve growth, reproduction, and adaptability in indigenous goats, aiding precision breeding and conservation programs.
Related Concept Videos
Comparing Copy Number Variations and SNPs
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%...
Single Nucleotide Polymorphisms-SNPs
Genetic Variation
Genes exist in different versions called alleles,...
Multi-species Conserved Sequences
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
Genome-wide Association Studies-GWAS
GWAS does not require the identification of the target gene involved in...
Incomplete Dominance

