Harnessing genomic information for livestock improvement

Georges, Michel; Charlier, Carole; Hayes, Ben J.

doi:10.1038/s41576-018-0082-2

Cited by 262 publications

(277 citation statements)

References 261 publications

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“…With the advancement of high-throughput genotyping technology, millions of cattle have been genotyped using low, medium or high-density SNP arrays [6,7]. The availability of dense genotype data is a prerequisite to characterize genomic diversity and detect signatures of selection within and between cattle breeds [8][9][10][11][12][13][14].…”

Section: Introductionmentioning

confidence: 99%

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

Bhati

Kadri

Crysnanto

et al. 2019

Preprint

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Background: Local cattle breeds represent an important source of genetic variation because they might carry alleles that enable them to adapt to harsh environments and scarce food conditions. One such local Swiss cattle breed is Original Braunvieh (OB) which is used for beef and milk production in alpine areas. Using whole-genome sequencing 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 15.7 million SNPs and 1.5 million Indels including 10,738 and 2,763 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 (F ROH =0.14) was relatively low in OB cattle. However, genomic inbreeding increased in recent years due to a higher number of long (> 1 Mb) runs of homozygosity in cattle born in more recent generations. Using two complementary approaches, i.e., 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 < 0.005) of past and ongoing selection. These selection signals were enriched for quantitative trait loci related to beef traits including meat quality, feed efficiency and body weight and pathways related to blood coagulation, nervous and sensory stimulus. Conclusions:We provide a comprehensive overview of genomic variation segregating in Swiss OB cattle. Using whole-genome sequencing data, we observe higher genomic diversity and less inbreeding in OB than many European mainstream cattle breeds.Footprints of selection were detected in genomic regions that are possibly relevant for meat quality and adaptation to harsh environments. Considering the low population size and increasing rates of genomic inbreeding in the past generations, the implementation and adoption of genomic mating programs seems warranted to maintain genetic diversity in the Swiss OB cattle population.

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Section: Introductionmentioning

confidence: 99%

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

Bhati

Kadri

Crysnanto

et al. 2019

Preprint

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“…This information may be very useful both from a farm health management point of view as well as from a downstream dairy processing point of view. Whole genome sequence data of bulk milk also informs about the herd frequency of functional variants such casein variants affecting consumer health or processing properties 10 , or variants causing inherited defects or embryonic lethality in cows 4 . In many countries, it is not allowed to add milk from cows being treated with antibiotics to the tank.…”

Section: Discussionmentioning

confidence: 99%

“…Prior to ~2010 estimation of breeding values to select the best dairy sires and dams used pedigree-based estimates of kinship. Since then, selection methods increasingly use genome-wide SNP information in a process referred to as “genomic selection” (GS) (Georges et al, 2019). As GS is becoming routine in dairy cattle (including for dams), herds that are fully genotyped with genome-wide SNP arrays are becoming standard, and the proposed method feasible.…”

Section: Introductionmentioning

confidence: 99%

SNP-based quantitative deconvolution of biological mixtures: application to the detection of cows with subclinical mastitis by whole genome sequencing of tank milk

Coppieters

Karim

Georges

2019

Preprint

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11Biological products of importance in food (f.i. milk) and medical (f.i. donor blood derived products) 12 sciences often correspond to mixtures of samples contributed by multiple individuals. Identifying 13 which individuals contributed to the mixture and in what proportions may be of interest in several 14 circumstances. We herein present a method that allows to do this by shallow whole genome 15 sequencing of the DNA in mixed samples from hundreds of donors. We demonstrate the efficacy of 16

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“…Single‐nucleotide polymorphism (SNP) arrays have the potential to identify thousands to hundreds of thousands of SNPs in the genome simultaneously (Matukumalli et al, ; Rincon, Weber, Eenennaam, Golden, & Medrano, ); therefore, they have been widely used for genetic and genomic analysis during cattle breeding, particularly in the genomic selection for economic traits (Garcia‐Ruiz et al, ; Georges, Charlier, & Hayes, ; Taylor et al, ). The data derived from these SNP arrays have accumulated on a large scale nationwide.…”

Section: Introductionmentioning

confidence: 99%

Genotypes and allele frequencies of buried SNPs in a bovine single‐nucleotide polymorphism array in Japanese Black cattle

Sasaki

Muraki

Inoue

et al. 2019

Animal Science Journal

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Single nucleotide polymorphism (SNP) arrays are widely used for genetic and genomic analyses in cattle breeding; thus, data derived from SNP arrays have accumulated on a large scale nationwide. Commercial SNP arrays contain a considerable number of unassigned SNPs on the chromosome/position on the genome; these SNPs are excluded in subsequent analyses. Notably, the position‐unassigned SNPs, or “buried SNPs” include some of the markers associated with genetic disease. In this study, we identified the position of buried SNPs using the Basic Local Alignment Search Tool against the surrounding sequences and characterized the relationship between SNPs and genetic diseases in Online Mendelian Inheritance in Animals based on the genomic position. We determined the position of 285 buried SNPs on the genome and surveyed the genotype and allele frequencies of these SNPs in 5,955 individual Japanese Black cattle. Eleven SNPs associated with genetic disease, which contained five buried SNPs, were found in the population with the risk allele frequency ranging from 0.00008396 to 0.46. These results indicate that buried SNPs in the bovine SNP array can be utilized to identify associations with genetic disorders from large scale accumulated SNP genotype data in Japanese Black cattle.

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Harnessing genomic information for livestock improvement

Cited by 262 publications

References 261 publications

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

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

SNP-based quantitative deconvolution of biological mixtures: application to the detection of cows with subclinical mastitis by whole genome sequencing of tank milk

Genotypes and allele frequencies of buried SNPs in a bovine single‐nucleotide polymorphism array in Japanese Black cattle

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