Dataset Information

A Genetic Investigation of Island Jersey Cattle, the Foundation of the Jersey Breed: Comparing Population Structure and Selection to Guernsey, Holstein, and United States Jersey Cattle.

ABSTRACT: For two centuries, Jersey cattle were exported globally, adapting to varying climates and production systems, yet the founding population remained genetically isolated on the Island of Jersey. The Island of Jersey formally allowed the importation of pure Jersey cattle in 2008. This study characterized the genetic variation of 49 popular bulls from the Island of Jersey born from 1964 to 2004 and compared them to 47 non-Island Jersey bulls and cows, primarily from the United States In addition, 21 Guernsey cattle derived from the Island of Guernsey and 71 Holstein cattle served as reference populations for genetic comparison. Cattle were genotyped on the Illumina BovineHD Beadchip producing 777,962 SNPs spanning the genome. Principal component analysis revealed population stratification within breed reflective of individual animal's continental origin. When compared to Holstein and Guernsey, all Jersey clustered together by breed. The Jersey breed demonstrated increased inbreeding in comparison to Holstein or Guernsey with slightly higher estimates of inbreeding coefficients and identity-by-descent. The Island and United States Jersey have relatively similar, yet statistically different inbreeding estimates despite vastly different population sizes and gene flow. Signatures of selection within Island Jersey were identified using genome-wide homozygosity association and marker-based FST that provided population informative single-nucleotide polymorphism (SNPs). Biological significance of the homozygosity association results identified multiple genes on chromosomes 5, 24, and 27, involved in immune function and cellular processes. Overall, genomic variation was identified between the Island and non-Island Jersey cattle producing population informative SNPs and differing runs of homozygosity (ROH) over immune regulation and metabolic genes. Results on inbreeding measures and ROH may reflect varying effective population size or differential selection with grazing systems promoting natural selection for traits such as parasite resistance, whereas confinement systems demonstrate a more intensive artificial selection. More broadly, differences in breed formation, particularly between the two Channel Island breeds, likely contributed to the variation in ROH and inbreeding. This research provides a reference for the Jersey breed based on the genetic foundation of the Island cattle as compared to the intensively selected United States cattle, and identifies regions of the genome for future investigation of immune regulation and metabolic processes.

SUBMITTER: Huson HJ

PROVIDER: S-EPMC7181675 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Publications

A Genetic Investigation of Island Jersey Cattle, the Foundation of the Jersey Breed: Comparing Population Structure and Selection to Guernsey, Holstein, and United States Jersey Cattle.

Huson Heather J HJ Sonstegard Tad S TS Godfrey James J Hambrook David D Wolfe Cari C Wiggans George G Blackburn Harvey H VanTassell Curtis P CP

Frontiers in genetics 20200417

For two centuries, Jersey cattle were exported globally, adapting to varying climates and production systems, yet the founding population remained genetically isolated on the Island of Jersey. The Island of Jersey formally allowed the importation of pure Jersey cattle in 2008. This study characterized the genetic variation of 49 popular bulls from the Island of Jersey born from 1964 to 2004 and compared them to 47 non-Island Jersey bulls and cows, primarily from the United States In addition, 21 ...[more]

PMID: 32362912

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Project description:BACKGROUND:Calving difficulty or dystocia has a great economic impact in the US dairy industry. Reported risk factors associated with calving difficulty are feto-pelvic disproportion, gestation length and conformation. Different dairy cattle breeds have different incidence of calving difficulty, with Holstein having the highest dystocia rates and Jersey the lowest. Genomic selection becomes important especially for complex traits with low heritability, where the accuracy of conventional selection is lower. However, for complex traits where a large number of genes influence the phenotype, genome-wide association studies showed limitations. Biological networks could overcome some of these limitations and better capture the genetic architecture of complex traits. In this paper, we characterize Holstein, Brown Swiss and Jersey breed-specific dystocia networks and employ them in genomic predictions. RESULTS:Marker association analysis identified single nucleotide polymorphisms explaining the largest average proportion of genetic variance on BTA18 in Holstein, BTA25 in Brown Swiss, and BTA15 in Jersey. Gene networks derived from the genome-wide association included 1272 genes in Holstein, 1454 genes in Brown Swiss, and 1455 genes in Jersey. Furthermore, 256 genes in Holstein network, 275 genes in the Brown Swiss network, and 253 genes in the Jersey network were within previously reported dystocia quantitative trait loci. The across-breed network included 80 genes, with 9 genes being within previously reported dystocia quantitative trait loci. The gene-gene interactions in this network differed in the different breeds. Gene ontology enrichment analysis of genes in the networks showed Regulation of ARF GTPase was very significant (FDR ≤ 0.0098) on Holstein. Neuron morphogenesis and differentiation was the term most enriched (FDR ≤ 0.0539) on the across-breed network. Genomic prediction models enriched with network-derived relationship matrices did not outperform regular GBLUP models. CONCLUSIONS:Regions identified in the genome were in the proximity of previously described quantitative trait loci that would most likely affect calving difficulty by altering the feto-pelvic proportion. Inclusion of identified networks did not increase prediction accuracy. The approach used in this paper could be extended to any instance with asymmetric distribution of phenotypes, for example, resistance to disease data.

Project description:BACKGROUND:The main cattle breed in Korea is the brown Hanwoo, which has been under artificial selection within a national breeding program for several decades. Varieties of the Hanwoo known as Jeju Black and Chikso were not included in the breeding program and remained isolated from the effects of recent artificial selection advancements. We analysed the Jeju Black and Chikso populations in regards to their genetic variability, state of inbreeding, as well as level of differentiation from the mainland Hanwoo population. RESULTS:Jeju Black and Chikso were found to have small estimated effective population sizes (N e ) of only 11 and 7, respectively. Despite a small N e , higher than expected heterozygosity levels were observed (0.303 and 0.306), however, lower allelic richness was found for the two island populations (1.76 and 1.77) compared to the mainland population (1.81). The increase in heterozygosity could be due to environmental disease challenges that promoted maintenance of higher genetic variability; however, no direct proof exists. Increased heterozygosity due to a first generation crossing of genetically different populations is not recorded. The differentiation between the Korean populations had F ST values between 0.014 and 0.036 which is not as high as the differentiation within European beef or dairy cattle breeds (0.047-0.111). This suggests that the three populations have not separated into independent breeds. CONCLUSION:Results agree with an island model of speciation where the brown Hanwoo represents the ancestral breed, whilst the Jeju Black and Chikso diverge from this common ancestor, following different evolutionary trajectories. Nevertheless, differences are minor and whether Jeju Black and Chikso cattle will develop into discrete breeds or reintegrate with the main population has to be seen in the future and will largely depend on human management decisions. This offers a rare opportunity to accompany the development of new breeds but also poses challenges on how to preserve these incipient breeds and ensure their long term viability.

Dataset Information

A Genetic Investigation of Island Jersey Cattle, the Foundation of the Jersey Breed: Comparing Population Structure and Selection to Guernsey, Holstein, and United States Jersey Cattle.

Publications

A Genetic Investigation of Island Jersey Cattle, the Foundation of the Jersey Breed: Comparing Population Structure and Selection to Guernsey, Holstein, and United States Jersey Cattle.

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