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.; Sonstegard, Tad S.; Godfrey, James; Hambrook, David; Wolfe, C. W.; Wiggans, G.R.; Blackburn, Harvey D.; Vantassell, Curtis P.

doi:10.3389/fgene.2020.00366

Cited by 24 publications

(18 citation statements)

References 23 publications

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“…We observed slight excess of heterozygotes in both the Russian breeds ( U F IS = -0.022 and -0.013 for Kholmogor and Yaroslavl breeds, respectively), which agrees with the findings obtained using DNA chips of lower density [9,10]. The detected inbreeding coefficient in Holsteins ( U F IS = -0.010) was similar or lower than one which was discovered in recent reports (F IS = −0.004 [60], F IS = 0.0526 [15]), which might reflect the differences in sample origins and population sizes.…”

Section: Plos Onesupporting

confidence: 90%

Selection signatures in two oldest Russian native cattle breeds revealed using high-density single nucleotide polymorphism analysis

et al. 2020

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Native cattle breeds can carry specific signatures of selection reflecting their adaptation to the local environmental conditions and response to the breeding strategy used. In this study, we comprehensively analysed high-density single nucleotide polymorphism (SNP) genotypes to characterise the population structure and detect the selection signatures in Russian native Yaroslavl and Kholmogor dairy cattle breeds, which have been little influenced by introgression with transboundary breeds. Fifty-six samples of pedigree-recorded purebred animals, originating from different breeding farms and representing different sire lines, of the two studied breeds were genotyped using a genome-wide bovine genotyping array (Bovine HD BeadChip). Three statistical analyses—calculation of fixation index (FST) for each SNP for the comparison of the pairs of breeds, hapFLK analysis, and estimation of the runs of homozygosity (ROH) islands shared in more than 50% of animals—were combined for detecting the selection signatures in the genome of the studied cattle breeds. We confirmed nine and six known regions under putative selection in the genomes of Yaroslavl and Kholmogor cattle, respectively; the flanking positions of most of these regions were elucidated. Only two of the selected regions (localised on BTA 14 at 24.4–25.1 Mbp and on BTA 16 at 42.5–43.5 Mb) overlapped in Yaroslavl, Kholmogor and Holstein breeds. In addition, we detected three novel selection sweeps in the genome of Yaroslavl (BTA 4 at 4.74–5.36 Mbp, BTA 15 at 17.80–18.77 Mbp, and BTA 17 at 45.59–45.61 Mbp) and Kholmogor breeds (BTA 12 at 82.40–81.69 Mbp, BTA 15 at 16.04–16.62 Mbp, and BTA 18 at 0.19–1.46 Mbp) by using at least two of the above-mentioned methods. We expanded the list of candidate genes associated with the selected genomic regions and performed their functional annotation. We discussed the possible involvement of the identified candidate genes in artificial selection in connection with the origin and development of the breeds. Our findings on the Yaroslavl and Kholmogor breeds obtained using high-density SNP genotyping and three different statistical methods allowed the detection of novel putative genomic regions and candidate genes that might be under selection. These results might be useful for the sustainable development and conservation of these two oldest Russian native cattle breeds.

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Section: Plos Onesupporting

confidence: 90%

Selection signatures in two oldest Russian native cattle breeds revealed using high-density single nucleotide polymorphism analysis

et al. 2020

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“…Figure 1 indicated that Slovak Spotted and Ayrshire populations were partially linked together probably due to use of Ayrshire in the grading-up of Slovak Spotted. Huson et al (2020) reported for Jersey cattle bred in different areas homogeneity despite a various geographic origin, compared with Holstein and Guernsey. In contrary, Ahmad et al (2020) found among breeds Holstein, Jersey and Brown Swiss high degree of differentiation depending on the geographical origin.…”

Section: Resultsmentioning

confidence: 93%

Detection of Selection Signals in Cattle Populations by Pca

Olšanská

Kasarda

Lehocká

et al. 2020

AGR

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The presented study provides a genome-wide scan of selection signals in cattle by principal component analysis (PCA). The aim was to identify SNP affected by intensive selection based on package PCAdapt implemented under software R. This analysis provided insight into the association between the SNP frequencies related to population differentiation. The four cattle populations were involved in the analysis (Slovak Spotted cattle, Ayrshire, Swiss Simmental and Holstein) with overall 272 of genotyped individuals. After applying quality control, the final dataset consisted of 35 675 SNPs, with an overall length of 2496.14 Mb and average space between adjacent SNP 70.03 ± 76.1 kb. After performing PCA analysis, the uniqueness of the breeds was revealed. On the other hand, a close genetic relationship and eleven SNPs affected by selection were found, with a position close to 162 genes involved in the various biological processes. The majority of genes were involved in the positive regulation of adenylate cyclase activity, embryo development and somatic diversification of immune receptors via somatic mutation. Several candidate genes for genetic control of the immune system (DNAJB9), muscle development (SEPT7, TRIM32, ROCK1, NRAP, PZDZ8, HSPA12A and FGFR2), milk production (SOCS5, CD46), reproduction (LHCGR, EEPD1, FSHR) and coat colour (KIT) were identified. Our results provide insights into the regions of the genome affected by the intensive selection of analysed cattle populations.

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“…At K = 4, a light green taurine ancestry was highlighted in the JER breed. This could be explained by the fact that this breed was only "discovered" around 200 years ago in the Jersey island, and this fact could have contributed to the maintenance of a conserved and distinct genetic composition of this breed, especially when compared with HOL, as also observed by Huson et al (2020).…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Analyses Reveal the Genetic Architecture and Candidate Genes of Indicine, Taurine, Synthetic Crossbreds, and Locally Adapted Cattle in Brazil

Verardo

Silva

Machado³

et al. 2021

Front. Genet.

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Cattle population history, breeding systems, and geographic subdivision may be reflected in runs of homozygosity (ROH), effective population size (Ne), and linkage disequilibrium (LD) patterns. Thus, the assessment of this information has become essential to the implementation of genomic selection on purebred and crossbred cattle breeding programs. In this way, we assessed the genotype of 19 cattle breeds raised in Brazil belonging to taurine, indicine, synthetic crossbreds, and Iberian-derived locally adapted ancestries to evaluate the overall LD decay patterns, Ne, ROH, and breed composition. We were able to obtain a general overview of the genomic architecture of cattle breeds currently raised in Brazil and other tropical countries. We found that, among the evaluated breeds, different marker densities should be used to improve the genomic prediction accuracy and power of genome-wide association studies. Breeds showing low Ne values indicate a recent inbreeding, also reflected by the occurrence of longer ROH, which demand special attention in the matting schemes to avoid extensive inbreeding. Candidate genes (e.g., ABCA7, PENK, SPP1, IFNAR1, IFNAR2, SPEF2, PRLR, LRRTM1, and LRRTM4) located in the identified ROH islands were evaluated, highlighting biological processes involved with milk production, behavior, rusticity, and fertility. Furthermore, we were successful in obtaining the breed composition regarding the taurine and indicine composition using single-nucleotide polymorphism (SNP) data. Our results were able to observe in detail the genomic backgrounds that are present in each breed and allowed to better understand the various contributions of ancestor breeds to the modern breed composition to the Brazilian cattle.

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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

Cited by 24 publications

References 23 publications

Selection signatures in two oldest Russian native cattle breeds revealed using high-density single nucleotide polymorphism analysis

Selection signatures in two oldest Russian native cattle breeds revealed using high-density single nucleotide polymorphism analysis

Detection of Selection Signals in Cattle Populations by Pca

Genome-Wide Analyses Reveal the Genetic Architecture and Candidate Genes of Indicine, Taurine, Synthetic Crossbreds, and Locally Adapted Cattle in Brazil

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