Genome-Wide Analysis Revealed Homozygosity and Demographic History of Five Chinese Sheep Breeds Adapted to Different Environments.
Adaptation, Physiological
/ genetics
Animals
Breeding
/ methods
China
Demography
Female
Genetic Variation
/ genetics
Genetics, Population
/ methods
Genome
/ genetics
Genome-Wide Association Study
/ methods
Genomics
/ methods
Genotype
Haplotypes
/ genetics
Homozygote
Male
Phenotype
Polymorphism, Genetic
/ genetics
Selection, Genetic
/ genetics
Sheep
/ classification
SNPs
high-density
inbreeding
minor allele frequency
sheep
Journal
Genes
ISSN: 2073-4425
Titre abrégé: Genes (Basel)
Pays: Switzerland
ID NLM: 101551097
Informations de publication
Date de publication:
09 12 2020
09 12 2020
Historique:
received:
30
08
2020
revised:
06
12
2020
accepted:
07
12
2020
entrez:
15
12
2020
pubmed:
16
12
2020
medline:
23
7
2021
Statut:
epublish
Résumé
Homozygosity of long sequence genotypes are a result of parents transmitting identical haplotypes, which can be used to estimate their auto-zygosity. Therefore, we used high-density SNP Chip data to characterize the auto-zygosity of each breed according to the occurrence and distribution of runs of homozygosity (ROH). Subsequently, we identified the genomic regions with high runs of homozygosity frequencies within individuals of each breed. We selected 96 sheep samples from five local Chinese sheep breeds belonging to different geographical locations. We identified 3046 ROHs within the study breed individuals, among which the longer segments (>1-5 Mb) were dominant. On average, ROH segments covered about 12% of the genomes; the coverage rate of OAR20 was the lowest and that of OAR2 was the highest. The distribution analysis of runs of homozygosity showed that the detected ROH mainly distributed between >26 and 28 Mb. The Hetian and Hu sheep showed the lowest ROH distribution. The estimation of homozygosity level reflects the history of modern and ancient inbreeding, which may affect the genomes of Chinese indigenous sheep breeds and indicate that some animals have experienced recent self-pollination events (Yabuyi, Karakul and Wadi). In these sheep breeds, the genomic regions were assumed to be under selection signatures frequently in line with long ROH. These regions included candidate genes associated with disease resistance traits (
Identifiants
pubmed: 33317115
pii: genes11121480
doi: 10.3390/genes11121480
pmc: PMC7764688
pii:
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
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