WHOLE GENOME SEQUENCING OF CHANGTHANGI GOAT FOR IDENTIFICATION OF SELECTION FOOTPRINTS

S.T VANZAMPUII

WHOLE GENOME SEQUENCING OF CHANGTHANGI GOAT FOR IDENTIFICATION OF SELECTION FOOTPRINTS

Date

2022

Authors

S.T VANZAMPUII

Publisher

ICAR-NDRI, KARNAL

Abstract

The goat (Capra hircus) is one of the earliest domesticated livestock species, primarily raised for milk, meat, hair, cashmere, and skin to suit basic human requirements. Comprehensive study about genomic variants and selection signals, which would provide valuable genomic insights linked to key Changthangi goat traits, has not yet been investigated. The study included 10 random samples of Changthangi goat breed, domesticated by nomadic pastoralists in the Ladakh area of Jammu and Kashmir, which is one of the most valuable livestock breeds because it produces the finest and most costly animal fiber in the world, with an average fineness of 11-12 microns. The current research aimed to detect genetic variations of Changthangi goat and to examine selection footprints related to hair/fibre quality. To explore genetic composition, whole genome resequencing (~10X) of 10 Changthangi goat samples were performed on the Illumina NOVASEQ 6000 platform using 150bp paired-end chemistry. Additionally, we downloaded ten Angora goat whole genome resequencing data to compare the genomic variants with Changthangi goat. We identified 22.5 million single nucleotide polymorphisms (SNP) and 3.5 million insertions and deletions (INDEL) in Changthangi goat. We examined the selection footprints that selection had left behind using the composite likelihood ratio (CLR), nucleotide diversity (θπ), and fixation index (FST) approaches, and by using the top 1% of selection signatures, we obtained 1276, 206, and 700 genes, respectively. Candidate genes that are under selection pressure include genes like FGF5, FGF9, KRT17, KRT71, STK3, TCF7L1, FGF20, SOX10, CUX1 and IGFBP7 that may have a role in qualities associated to hair or fibre, as well as adaptive traits (NOS2, PRKCB). Significant enrichment of KEGG pathways like Ras signaling pathway, MAPK signaling pathway and Focal adhesion, which are associated with skin hair follicle developments and hair follicle morphogenesis, were identified. The enrichment of the HSF-1 signalling pathway in the top selection signatures also draws attention to Changthangi goat adaptation to the hypoxic environment at high altitudes. Our findings offer a comprehensive overview of the genomic variants in the Changthangi goat genome, and analysis of selection footprints revealed positive sites that may be connected to important traits. The improvement of this breed may be anticipated in the future through targeted screening of verified selection signatures in larger populations.