Assessment of runs of homozygosity islands and estimates of genomic inbreeding in Gyr (Bos indicus) dairy cattle

The objective of this study was to investigate the genetic diversity of the Garfagnina (GRF) goat, a breed that currently risks extinction. For this purpose, 48 goats were genotyped with the Illumina CaprineSNP50 BeadChip and analyzed together with 214 goats belonging to 9 other Italian breeds (~25 goats/breed), whose genotypes were available from the AdaptMap project [Argentata (ARG), Bionda dell’Adamello (BIO), Ciociara Grigia (CCG), Di Teramo (DIT), Garganica (GAR), Girgentana (GGT), Orobica (ORO), Valdostana (VAL) and Valpassiria (VSS)]. Comparative analyses were conducted on i) runs of homozygosity (ROH), ii) admixture ancestries and iii) the accuracy of breed traceability via discriminant analysis on principal components (DAPC) based on cross-validation. ROH analyses was used to assess the genetic diversity of GRF, while admixture and DAPC to evaluate its relationship to the other breeds. For GRF, common ROH (more than 45% in GRF samples) was detected on CHR 12 at, roughly 50.25–50.94Mbp (ARS1 assembly), which spans the CENPJ (centromere protein) and IL17D (interleukin 17D) genes. The same area of common ROH was also present in DIT, while a broader region (~49.25–51.94Mbp) was shared among the ARG, CCG, and GGT. Admixture analysis revealed a small region of common ancestry from GRF shared by BIO, VSS, ARG and CCG breeds. The DAPC model yielded 100% assignment success for GRF. Overall, our results support the identification of GRF as a distinct native Italian goat breed. This work can contribute to planning conservation programmes to save GRF from extinction and will improve the understanding of the socio-agro-economic factors related with the farming of GRF.

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Level of Inbreeding in Norik of Muran Horse: Pedigree vs. Genomic Data

Acta Universitatis Agriculturae et Silviculturae Mendelianae Brunensis ◽

10.11118/actaun201967061457 ◽

2019 ◽

Vol 67 (6) ◽

pp. 1457-1463 ◽

Cited By ~ 2

Author(s):

Radovan Kasarda ◽

Nina Moravčíková ◽

Ondrej Kadlečík ◽

Anna Trakovická ◽

Marko Halo ◽

...

Keyword(s):

Genetic Diversity ◽

Quality Control ◽

Genomic Analysis ◽

Genomic Data ◽

Reference Population ◽

Pedigree Analysis ◽

Snp Markers ◽

Runs Of Homozygosity ◽

Current Generation ◽

Genomic Inbreeding

The objective of this study was to analyse the level of pedigree and genomic inbreeding in a herd of the Norik of Muran horses. The pedigree file included 1374 animals (603 stallions and 771 mares), while the reference population consisted of animals that were genotyped by using 70k SNP platform (n = 25). The trend of pedigree inbreeding was expressed as the probability that an animal has two identical alleles by descent according to classical formulas. The trend of genomic inbreeding was derived from the distribution of runs of homozygosity (ROHs) with various length in the genome based on the assumption that these regions reflect the autozygosity originated from past generations of ancestors. A maximum of 19 generations was found in pedigree file. As expected, the highest level of pedigree completeness was found in first five generations. Subsequent quality control of genomic data resulted in totally 54432 SNP markers covering 2.242 Mb of the autosomal genome. The pedigree analysis showed that in current generation can be expected the pedigree inbreeding at level 0.23% (ΔFPEDi = 0.19 ± 1.17%). Comparable results was obtained also by the genomic analysis, when the inbreeding in current generation reached level 0.11%. Thus, in term of genetic diversity both analyses reflected sufficient level of variability across analysed population of Norik of Muran horses.

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The German Shorthair Pointer Dog Breed (Canis lupus familiaris): Genomic Inbreeding and Variability

Animals ◽

10.3390/ani10030498 ◽

2020 ◽

Vol 10 (3) ◽

pp. 498 ◽

Cited By ~ 1

Author(s):

Antonio Boccardo ◽

Stefano Paolo Marelli ◽

Davide Pravettoni ◽

Alessandro Bagnato ◽

Giuseppe Achille Busca ◽

...

Keyword(s):

Canis Lupus ◽

Inbreeding Coefficient ◽

Nucleotide Polymorphisms ◽

Canis Lupus Familiaris ◽

Runs Of Homozygosity ◽

Single Nucleotide ◽

The Mean ◽

Dog Breed ◽

Genomic Inbreeding ◽

Genealogical Information

The German Shorthaired Pointer (GSHP) is a breed worldwide known for its hunting versatility. Dogs of this breed are appreciated as valuable companions, effective trackers, field trailers and obedience athletes. The aim of the present work is to describe the genomic architecture of the GSHP breed and to analyze inbreeding levels under a genomic and a genealogic perspective. A total of 34 samples were collected (24 Italian, 10 USA), and the genomic and pedigree coefficients of inbreeding have been calculated. A total of 3183 runs of homozygosity (ROH) across all 34 dogs have been identified. The minimum and maximum number of Single Nucleotide Polymorphisms (SNPs) defining all ROH are 40 and 3060. The mean number of ROH for the sample was 93.6. ROH were found on all chromosomes. A total of 854 SNPs (TOP_SNPs) defined 11 ROH island regions (TOP_ROH), in which some gene already associated with behavioral and morphological canine traits was annotated. The proportion of averaged observed homozygotes estimated on total number of SNPs was 0.70. The genomic inbreeding coefficient based on ROH was 0.17. The mean inbreeding based on genealogical information resulted 0.023. The results describe a low inbred population with quite a good level of genetic variability.

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Differential expression of microRNAs associated with thermal stress in Frieswal (Bos taurus x Bos indicus) crossbred dairy cattle

Cell Stress and Chaperones ◽

10.1007/s12192-017-0833-6 ◽

2017 ◽

Vol 23 (1) ◽

pp. 155-170 ◽

Cited By ~ 15

Author(s):

Gyanendra Singh Sengar ◽

Rajib Deb ◽

Umesh Singh ◽

T. V. Raja ◽

Rajiv Kant ◽

...

Keyword(s):

Thermal Stress ◽

Dairy Cattle ◽

Differential Expression ◽

Bos Taurus ◽

Bos Indicus ◽

Crossbred Dairy Cattle

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Genome‐wide identification of runs of homozygosity islands in the Gyr breed ( Bos indicus )

Reproduction in Domestic Animals ◽

10.1111/rda.13639 ◽

2020 ◽

Vol 55 (3) ◽

pp. 333-342 ◽

Cited By ~ 1

Author(s):

Alejandra Maria Toro Ospina ◽

Ricardo António Silva Faria ◽

Anibal Eugenio Vercesi Filho ◽

Joslaine Noely dos Santos Goncalves Cyrillo ◽

Maria Eugenia Zerlotti Mercadante ◽

...

Keyword(s):

Bos Indicus ◽

Runs Of Homozygosity ◽

Genome Wide

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A Comprehensive Analysis of Runs of Homozygosity of Eleven Cattle Breeds Representing Different Production Types

Animals ◽

10.3390/ani9121024 ◽

2019 ◽

Vol 9 (12) ◽

pp. 1024 ◽

Cited By ~ 11

Author(s):

Tomasz Szmatoła ◽

Artur Gurgul ◽

Igor Jasielczuk ◽

Tomasz Ząbek ◽

Katarzyna Ropka-Molik ◽

...

Keyword(s):

High Frequency ◽

Production Traits ◽

Runs Of Homozygosity ◽

White Variety ◽

Black And White ◽

Cattle Breeds ◽

Hereford Cattle ◽

Holstein Friesian ◽

Genomic Inbreeding ◽

The Impact

In the presented research, BovineSNP50 microarrays (Illumina) were applied to determine runs of homozygosity in the genomes of 11 cattle breeds maintained in Poland. These cattle breeds represent three basic utility types: milk, meat and dual purpose. Analysis of runs of homozygosity allowed the evaluation of the level of autozygosity within each breed in order to calculate the genomic inbreeding coefficient (FROH), as well as to identify regions of the genome with a high frequency of ROH occurrence, which may reflect traces of directional selectin left in their genomes. Visible differences in the length and distribution of runs of homozygosity in the genomes of the analyzed cattle breeds have been observed. The highest mean number and mean sums of lengths of runs of homozygosity were characteristic for Hereford cattle and intermediate for the Holstein-Friesian Black-and-White variety, Holstein-Friesian Red-and-White variety, Simmental, Limousin, Montbeliarde and Charolais breeds. However, lower values were observed for cattle of conserved breeds. Moreover, the selected livestock differed in the level of inbreeding estimated using the FROH coefficient. In regions of the genome with a high frequency of ROH occurrence, which may reflect the impact of directional selection, a number of genes were observed that can be potentially related to the production traits which are under selection pressure for specific production types. The most important detected genes were GHR, MSTN, DGAT1, FABP4, and TRH, with a known influence on the milk and meat traits of the studied cattle breeds.

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Bos indicus and Bos taurus crossbred dairy cattle in Australia. IV.* Progeny testing and expected rate of genetic improvement

Australian Journal of Agricultural Research ◽

10.1071/ar9760309 ◽

1976 ◽

Vol 27 (2) ◽

pp. 309 ◽

Cited By ~ 4

Author(s):

IR Franklin ◽

RH Hayman ◽

RO Hewetson

Keyword(s):

Dairy Cattle ◽

Heat Tolerance ◽

Genetic Improvement ◽

Bos Taurus ◽

Bos Indicus ◽

Progeny Testing ◽

Dairy Farmers ◽

Improvement Program ◽

Tropical Environments ◽

Tick Resistance

A dairy improvement program designed to develop a breed of cattle adapted to tropical environments is described. Each year young crossbred (Bos indicus x Bos taurus) bulls are screened for heat tolerance and tick resistance, and then progeny-tested in the herds of cooperating dairy farmers. Estimates of phenotypic and genetic means, variances and correlations are presented for production of milk and milk components, and the rate of genetic improvement is discussed. In particular the heritability of milk yield in the crossbred progeny is 0.27, and the theoretical rate of improvement is 2.6% per year. ____________________ *Part III, Aust. J. Agric. Res., 25: 1023 (1974).

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