What question did this study set out to answer?

To identify immune-related structural and sequence variations, runs of homozygosity, and selective sweeps across the genomes of Indicine cattle breeds to understand the genetic basis of their disease resilience.

December 10, 2024Open Access

Genetic basis of immunity in Indian cattle as revealed by comparative analysis of Bos genome

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Authors

MTMenaka Thambiraja SIShukkruthi K. Iyengar BSBrintha Satishkumar

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Overview

Comparative genomic analysis reveals distinct immune variations and selection sweeps in Indicine cattle, indicating candidate targets for breeding disease-resistant livestock.

Key Points

To identify immune-related structural and sequence variations, runs of homozygosity, and selective sweeps across the genomes of Indicine cattle breeds to understand the genetic basis of their disease resilience.
Analyzed whole-genome sequencing data from Nelore (n=14) and Gir (n=20) breeds aligned to the Bos taurus ARS-UCD2.0 reference genome.
Identified and annotated single nucleotide variants and indels using GATK HaplotypeCaller, SnpEff, InnateDB, and Animal QTLdb.
Mapped runs of homozygosity islands using PLINK, detected selective-sweep signatures using RAiSD, and performed pathway enrichment via DAVID.
Identified 1,884,058 indels and 13,997,533 SNVs in Nelore cattle and 1,457,337 indels and 11,627,881 SNVs in Gir cattle, with transition-to-transversion ratios of ~2.26 and ~2.25.
Detected shared frameshift insertions in TLR3 and LOC508441 (CD33) along with selective sweeps in 707 candidate genes in Nelore and 165 in Gir, prioritizing loci such as ANKRD11, FOXP2, and MEFV.
Found significant enrichment (P < 0.05) among variant-bearing genes in key immune pathways, including NF-kappaB, T-cell receptor, and MAPK signaling.

Cite This Study

Thambiraja et al. (2024) studied this question.

synapsesocial.com/papers/6a7592ea72c9f0ed5b5fffe3 https://doi.org/10.1101/2024.12.09.627532

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December 10, 2024Open Access

Genetic basis of immunity in Indian cattle as revealed by comparative analysis of Bos genome

View Full Paper

Ask AI

Bookmark

Authors

MTMenaka Thambiraja SIShukkruthi K. Iyengar BSBrintha Satishkumar

Discussion

Member takes

Overview

Comparative genomic analysis reveals distinct immune variations and selection sweeps in Indicine cattle, indicating candidate targets for breeding disease-resistant livestock.

Key Points

To identify immune-related structural and sequence variations, runs of homozygosity, and selective sweeps across the genomes of Indicine cattle breeds to understand the genetic basis of their disease resilience.
Analyzed whole-genome sequencing data from Nelore (n=14) and Gir (n=20) breeds aligned to the Bos taurus ARS-UCD2.0 reference genome.
Identified and annotated single nucleotide variants and indels using GATK HaplotypeCaller, SnpEff, InnateDB, and Animal QTLdb.
Mapped runs of homozygosity islands using PLINK, detected selective-sweep signatures using RAiSD, and performed pathway enrichment via DAVID.
Identified 1,884,058 indels and 13,997,533 SNVs in Nelore cattle and 1,457,337 indels and 11,627,881 SNVs in Gir cattle, with transition-to-transversion ratios of ~2.26 and ~2.25.
Detected shared frameshift insertions in TLR3 and LOC508441 (CD33) along with selective sweeps in 707 candidate genes in Nelore and 165 in Gir, prioritizing loci such as ANKRD11, FOXP2, and MEFV.
Found significant enrichment (P < 0.05) among variant-bearing genes in key immune pathways, including NF-kappaB, T-cell receptor, and MAPK signaling.

Cite This Study

Thambiraja et al. (2024) studied this question.

synapsesocial.com/papers/6a7592ea72c9f0ed5b5fffe3 https://doi.org/10.1101/2024.12.09.627532

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