Genome-wide runs of homozygosity signatures in diverse Indian goat breeds

Dibyasha Kar; Indrajit Ganguly; Sanjeev Singh; Avnish Kumar Bhatia; S P Dixit

doi:10.1007/s13205-024-03921-y

Genome-wide runs of homozygosity signatures in diverse Indian goat breeds

3 Biotech. 2024 Mar;14(3):81. doi: 10.1007/s13205-024-03921-y. Epub 2024 Feb 17.

Authors

Dibyasha Kar^{1

2}, Indrajit Ganguly¹, Sanjeev Singh¹, Avnish Kumar Bhatia¹, S P Dixit¹

Affiliations

¹ Division of Animal Genetics, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana 132001 India.
² Division of Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal, Haryana 132001 India.

PMID: 38375512
PMCID: PMC10874352 (available on 2025-03-01)
DOI: 10.1007/s13205-024-03921-y

Abstract

The present study analyzed ROH and consensus ROH regions in 102 animals of eleven diverse Indian goat (Capra hircus) breeds using whole genome sequencing. A total of 51,705 ROH and 21,271 consensus regions were identified. The mean number of ROH per animal was highest in the meat breed, Jharkhand Black (2693) and lowest in the pashmina breed, Changthangi (60). The average length of ROH (AL_ROH) was maximum in Kanniadu (974.11 Kb) and minimum in Tellicherry (146.98 Kb). Long ROH is typically associated with more recent inbreeding, whereas short ROH is connected to more ancient inbreeding. The overall ROH-based genomic inbreeding (F_ROH) was highest for Jharkhand Black (0.602) followed by Kanniadu (0.120) and Sangamneri (0.108) among all breeds. F_ROH of Jharkhand Black was higher than Kanniadu up to 5 Mb ROH length category. However, in > 20 Mb ROH length category, Kanniadu (0.98) exhibited significantly higher F_ROH than Jharkhand Black (0.46). This implies that Kanniadu had higher levels of recent inbreeding than Jharkhand Black. Despite this, due to the presence of both recent and ancient inbreeding, Jharkhand Black demonstrated higher overall F_ROH compared to Kanniadu. ROH patterns revealed dual purpose (meat and dairy) and pashmina breeds as less consanguineous while recent inbreeding was apparent in meat breeds. Analysis of ROH consensus regions identified selection sweeps in key genes governing intramuscular fat deposition, meat tenderisation, lean meat production and carcass weight (CDK4, ALOX15, CASP9, PRDM16, DVL1) in meat breeds; milk fat percentage and mammary gland development (POLD1, NOTCH2, ARHGAP35) in dual purpose (meat and dairy) breeds; while cold adaptation and hair follicle development (APOBEC1, DNAJC3, F2RL1, FGF9) in pashmina breed. MAPK, RAS, BMP and Wnt signaling pathways associated with hair follicle morphogenesis in Changthangi were also identified. PCA analysis based on ROH consensus regions revealed that meat breeds are more diverse than other goat breeds/populations.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-024-03921-y.

Keywords: FROH; PCA; ROH consensus regions; Runs of homozygosity; Selection sweeps.

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