Cattle genome-wide analysis reveals genetic signatures in trypanotolerant N'Dama

BMC Genomics
Soo-Jin KimHeebal Kim

Abstract

Indigenous cattle in Africa have adapted to various local environments to acquire superior phenotypes that enhance their survival under harsh conditions. While many studies investigated the adaptation of overall African cattle, genetic characteristics of each breed have been poorly studied. We performed the comparative genome-wide analysis to assess evidence for subspeciation within species at the genetic level in trypanotolerant N'Dama cattle. We analysed genetic variation patterns in N'Dama from the genomes of 101 cattle breeds including 48 samples of five indigenous African cattle breeds and 53 samples of various commercial breeds. Analysis of SNP variances between cattle breeds using wMI, XP-CLR, and XP-EHH detected genes containing N'Dama-specific genetic variants and their potential associations. Functional annotation analysis revealed that these genes are associated with ossification, neurological and immune system. Particularly, the genes involved in bone formation indicate that local adaptation of N'Dama may engage in skeletal growth as well as immune systems. Our results imply that N'Dama might have acquired distinct genotypes associated with growth and regulation of regional diseases including trypanosomiasis. Moreov...Continue Reading

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Citations

Sep 3, 2019·Animal Genetics·Y T UtsunomiyaP Ajmone-Marsan
Aug 10, 2020·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·Qiuming ChenChuzhao Lei
Jan 9, 2019·Frontiers in Genetics·Evans Kiptoo CheruiyotFidalis D N Mujibi
Jan 13, 2021·International Journal of Molecular Sciences·Abirami RajavelMehmet Gültas

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Methods Mentioned

BETA
PCR
Genotyping
chip

Software Mentioned

UnifiedGenotyper
XP
Python
DAVID
snpEff
SNPSift
Picard
IndelRealigner
BEAGLE
GATK

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