COMPARATIVE GENOME ANALYSIS OF INTERNATIONAL TRANSBOUNDARY CATTLE BREEDS
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Date
2022
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Publisher
ICAR-NDRI, KARNAL
Abstract
Selection of the animals has resulted in differentiation of breeds exhibiting a wide range of
phenotypic variation in a short amount of time. Gir and Ongole are International
transboundary breeds of cattle of Indian origin, bred for dairy and meat production across
different countries viz Brazil, USA, Mexico, Malaysia, Panama etc. These breeds are well
adapted to Brazilian ecological niche and have undergone significant genetic differentiation
in recent years. 90 cattle samples belonging to Indian Gir (n=15), Ongole (n=17), Brazilian
Gyr (n=27) and Nellore (n=31) genotyped using Illumina BovineHD BeadChip were
included in the current investigation. All the samples were quality checked using Plink
software and after quality filtration 5.5 lakhs SNPs were retained for downstream analysis.
Three complementary approaches viz., Runs of homozygosity (ROH), Integrated haplotype
score (iHS) and Fixation index (FST) were implemented and these samples were analysis
further, for the identification of the selection signatures. The present investigation revealed
that the Pairwise FST differences between Gir versus Gyr and Ongole versus Nellore were
2.856 % and 2.354 %, respectively. Genomic regions under selection within (iHS and ROH)
and among breeds (FST) were identified. A total of 4004, 3322, 3437 and 3485 genes were
identified in Gir, Gyr, Ongole and Nellore, respectively under top 1% of the selected regions
using the integrated haplotype score (iHS) approach. ROH method based selected regions
(ROH consensus ≥20%) revealed 4285, 1768, 1663 and 1466 genes in Gir, Gyr, Ongole and
Nellore cattle, respectively. FST based approach identified 1966 genes for Gir-Gyr pair and
1897 genes for Ongole-Nellore pair under top 1% selected regions. Several candidate genes
were identified under top selected regions viz. IER5, MILR1, ARAP3 in Gir and PCDH9 in
Ongole. These genes are responsible for immunity and body shape traits in Indian breeds of
cattle. Gene related to mammary gland development, udder size and carcass (MYO16,
AGAP2, MYO1B, ABCA7) in Gyr and carcass traits (PARP2, ATP10D and KCNJ11) were
identified in Nellore breed of cattle. These findings suggests that selection in Indian
population (Gir and Ongole) is more towards immunity and adaptation traits while Brazilian
population is more selected towards carcass and milk production traits. Further studies on
larger sample size using GWAS will be helpful in the validation of the present results.