Dataset Information

Assessing genomic diversity and signatures of selection in Original Braunvieh cattle using whole-genome sequencing data.

ABSTRACT: BACKGROUND:Autochthonous cattle breeds are an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and food conditions. Original Braunvieh (OB) is a local cattle breed of Switzerland used for beef and milk production in alpine areas. Using whole-genome sequencing (WGS) data of 49 key ancestors, we characterize genomic diversity, genomic inbreeding, and signatures of selection in Swiss OB cattle at nucleotide resolution. RESULTS:We annotated 15,722,811 SNPs and 1,580,878 Indels including 10,738 and 2763 missense deleterious and high impact variants, respectively, that were discovered in 49 OB key ancestors. Six Mendelian trait-associated variants that were previously detected in breeds other than OB, segregated in the sequenced key ancestors including variants causal for recessive xanthinuria and albinism. The average nucleotide diversity (1.6 ? ×?10-?3) was higher in OB than many mainstream European cattle breeds. Accordingly, the average genomic inbreeding derived from runs of homozygosity (ROH) was relatively low (FROH =?0.14) in the 49 OB key ancestor animals. However, genomic inbreeding was higher in OB cattle of more recent generations (FROH =?0.16) due to a higher number of long (>?1?Mb) runs of homozygosity. Using two complementary approaches, composite likelihood ratio test and integrated haplotype score, we identified 95 and 162 genomic regions encompassing 136 and 157 protein-coding genes, respectively, that showed evidence (P

SUBMITTER: Bhati M

PROVIDER: S-EPMC6950892 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature

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Assessing genomic diversity and signatures of selection in Original Braunvieh cattle using whole-genome sequencing data.

Bhati Meenu M Kadri Naveen Kumar NK Crysnanto Danang D Pausch Hubert H

BMC genomics 20200108 1

<h4>Background</h4>Autochthonous cattle breeds are an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and food conditions. Original Braunvieh (OB) is a local cattle breed of Switzerland used for beef and milk production in alpine areas. Using whole-genome sequencing (WGS) data of 49 key ancestors, we characterize genomic diversity, genomic inbreeding, and signatures of selection in Swiss OB cattle at nucleotide resolution.<h4> ...[more]

PMID: 31914939

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Project description:Yanbian cattle is inhabitant of North of China, exhibiting many phenotypic features, such as long, dense body hair, and abundant intramuscular fat, designed to combat the extreme cold climate adaption. In the current study, we studied the cold tolerance of nine Yanbian cattle by whole genome resequencing and compared with African tropical cattle, N'Dama, as a control group. Yanbian cattle was aligned to the Bos taurus reference genome (ARS-UCD1.2) yielding an average of 10.8 fold coverage. The positive selective sweep analysis for the cold adaption in Yanbian cattle were analyzed using composite likelihood ratio (CLR) and nucleotide diversity (??), resulting in 292 overlapped genes. The strongest selective signal was found on BTA16 with potential mutation in CORT gene, a regulatory gene of primary hormone in the hypothalamic-pituitary-adrenal (HPA) axis, is reported to be associated with the cold stress, representedfour missense mutations (c.269C > T, p.Lys90Ile; c.251A > G, p.Glu84Gly; c.112C > T, p.Pro38Ser; c.86G > A, p.Pro29His). Meanwhile another gene on BTA6, showed significantly higher selective sweep signals for a cold adapted trait for hair follicle and length development, FGF5 (fibroblast growth factor 5) with a missense mutation (c.191C > T, p.Ser64Phe). Moreover, cold adapted Yanbian cattle was statistically compared with the hot adapted N'Dama cattle, a taurine cattle reported to show superior heat tolerance than zebu cattle, making them better adapted to the hot regions of Africa. XP-CLR, Fst, and ?? ratio were used to compare both breeds, yielding 487, 924, and 346 genes respectively. Among the 12 overlapped genes, (CD36) (c.638A > G, p.Lys 213Arg) involved in fat digestion and absorption plays an important role in membrane transport of long-chain fatty acid and its expression could increase in cold exposure. Henceforth, our study provides a novel genetic insights into the cold climate adaptation of Yanbian cattle and identified three candidate genes (CORT, FGF5, and CD36), which can add to an understanding of the cold climate adaptation of Yanbian cattle.

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Dataset Information

Assessing genomic diversity and signatures of selection in Original Braunvieh cattle using whole-genome sequencing data.

Publications

Assessing genomic diversity and signatures of selection in Original Braunvieh cattle using whole-genome sequencing data.

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