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

Authors: HUSON, HEATHER - Cornell University; SONSTEGARD, TAD - Recombinetics, Inc; GODFREY, JAMES - Royal Jersey Agricultural & Horticultural Society; HAMBROOK, DAVID - Royal Jersey Agricultural & Horticultural Society; WOLFE, CARI - American Jersey Cattle Association; WIGGANS, GEORGE - Council On Dairy Cattle Breeding; Blackburn, Harvey; Van Tassell, Curtis - Curt

Submitted to: Frontiers in Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/25/2020
Publication Date: N/A
Citation: N/A
DOI: https://doi.org/10.3389/fgene.2020.00366

Interpretive Summary: For 2 centuries, Jersey cattle were exported globally from the Island of Jersey in the English Channel. They adapted to varying climates and production systems, but the founding population remained genetically isolated. Recognizing the performance gap (depressed productivity and economic viability) between the populations of Jerseys on the Island and internationally traded Jersey genetics, the Island of Jersey formally allowed importation of pure Jersey cattle from other countries 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 with 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. Stratification of cattle populations within breed were found to reflect continental origin. Inbreeding was slightly higher for Jerseys than for Holsteins or Guernseys. Although Island and U.S. Jerseys have vastly different population sizes and gene flow, their inbreeding estimates were similar. Overall, genomic variation was identified between Island and non-Island Jersey cattle; population informative genetic markers were identified as well as differing conserved genomic regions for immune regulation and metabolic genes. These results may reflect varying effective population size or differential selection with grazing systems promoting natural selection for traits such as parasite resistance and confinement systems demonstrating a more intensive artificial selection. More broadly, differences in breed formation, particularly between the 2 Channel Island breeds, likely contributed to the variation in conserved genomic regions and inbreeding. This research provides a reference for the Jersey breed based on the genetic foundation of the Island cattle as compared with intensively selected U.S. cattle and identifies regions of the genome for future investigation of immune regulation and metabolic processes.

Technical Abstract: For 2 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 with 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 with 777,962 single-nucleotide polymorphisms (SNPs) spanning the genome. Principal component analysis revealed population stratification within breed reflective of individual animal’s continental origin. When compared with Holsteins and Guernseys, all Jerseys 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 U.S. Jerseys have relatively similar, yet statistically different, inbreeding estimates despite vastly different population sizes and gene flow. Signatures of selection within Island Jerseys were identified using genomewide homozygosity association and a marker-based fixation index that provided population informative 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; population informative SNPs were identified as well as 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 and confinement systems demonstrating a more intensive artificial selection. More broadly, differences in breed formation, particularly between the 2 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 with intensively selected U.S. cattle and identifies regions of the genome for future investigation of immune regulation and metabolic processes.