scholarly journals Comparative analysis of inbreeding parameters and runs of homozygosity islands in 2 Italian autochthonous cattle breeds mainly raised in the Parmigiano-Reggiano cheese production region

2021 ◽  
Author(s):  
Giuseppina Schiavo ◽  
Samuele Bovo ◽  
Anisa Ribani ◽  
Giulia Moscatelli ◽  
Massimo Bonacini ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Runs Of Homozygosity ◽  
Production Region ◽  
Cattle Breeds ◽  
Parmigiano Reggiano ◽  
Cheese Production

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

Animals ◽  
2019 ◽  
Vol 9 (12) ◽  
pp. 1024 ◽  
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.

scholarly journals Analysis of runs of homozygosity and their relationship with inbreeding in five cattle breeds farmed in Italy

2014 ◽  
Vol 46 (2) ◽  
pp. 110-121 ◽  
Author(s):  
Gabriele Marras ◽  
Giustino Gaspa ◽  
Silvia Sorbolini ◽  
Corrado Dimauro ◽  
Paolo Ajmone-Marsan ◽  
...  
Keyword(s):  
Runs Of Homozygosity ◽  
Cattle Breeds

scholarly journals Whole-Genome comparative analysis reveals genetic mechanisms of disease resistance and heat tolerance of tropical Bos indicus cattle breeds

Genome ◽  
2021 ◽  
Author(s):  
Periyasamy Vijayakumar ◽  
Arunasalam Singaravadivelan ◽  
Anamika Mishra ◽  
Krishnan Jagadeesan ◽  
Sanniyasi Bakyaraj ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Comparative Analysis ◽  
Stress Response ◽  
Functional Annotation ◽  
Indian Subcontinent ◽  
Bos Indicus ◽  
Whole Genome ◽  
Immune Genes ◽  
Cattle Breeds ◽  
Genetic Mechanisms

The Bos indicus cattle breeds have been naturally selected over thousands of years for disease resistance and thermo-tolerance. However, a genetic mechanism of these specific inherited characteristics needs to be discovered. Hence, in this study, the whole-genome comparative analysis of Bos indicus cattle breeds of Kangayam, Tharparkar, Sahiwal, Red Sindhi, and Hariana of the Indian subcontinent was conducted. The genetic variants identification analysis revealed a total of 15,58,51,012 SNPs and 1,00,62,805 InDels in the mapped reads across all Bos indicus cattle breeds. The functional annotation of 17,252 genes that comprised both, SNPs and InDels, of high functional impact on proteins, has been carried out. The functional annotation results revealed the pathways that were involved in the innate immune response including toll-like receptors, a retinoic acid-inducible gene I like receptors, NOD-like receptors, Jak-STAT signaling pathways, and the non-synonymous variants in the candidate immune genes. Further, we also identified several pathways involved in heat shock response, hair and skin properties, oxidative stress response, osmotic stress response, thermal sweating, feed intake, metabolism, and the non-synonymous variants in the candidate thermo-tolerant genes. These pathways and genes were directly or indirectly contributing to the disease resistance and thermo-tolerance adaptations of Bos indicus cattle breeds.

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

2019 ◽  
Author(s):  
Meenu Bhati ◽  
Naveen Kumar Kadri ◽  
Danang Crysnanto ◽  
Hubert Pausch
Keyword(s):  
Whole Genome Sequencing ◽  
Meat Quality ◽  
Genome Sequencing ◽  
Genomic Diversity ◽  
Whole Genome ◽  
Runs Of Homozygosity ◽  
Cattle Breeds ◽  
Signatures Of Selection ◽  
Genomic Inbreeding ◽  
Genomic Regions

AbstractBackgroundAutochthonous cattle breeds represent an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and food conditions. Original Braunvieh (OB) is a local cattle breed of Switzerland used for beef and milk production in alpine areas. Using whole-genome sequencing (WGS) data of 49 key ancestors, we characterize genomic diversity, genomic inbreeding, and signatures of selection in Swiss OB cattle at nucleotide resolution.ResultsWe annotated 15,722,811 million SNPs and 1,580,878 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 quantified using runs of homozygosity (ROH) was relatively low (FROH=0.14) in the 49 OB key ancestor animals. However, genomic inbreeding was higher in more recent generations of OB cattle (FROH=0.16) due to a higher number of long (> 1 Mb) runs of homozygosity. Using two complementary approaches, 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.ConclusionsWe provide a comprehensive overview of sequence variation in Swiss OB cattle genomes. With WGS 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 local environmental conditions. Considering that the population size is low and genomic inbreeding increased in the past generations, the implementation and adoption of optimal mating strategies seems warranted to maintain genetic diversity in the Swiss OB cattle population.

scholarly journals “In vivo” and “in vitro” degradability of diets for Parmigiano Reggiano cheese production

2009 ◽  
Vol 8 (sup2) ◽  
pp. 331-333 ◽  
Author(s):  
Federico Righi ◽  
Simone Romanelli ◽  
Marco Renzi ◽  
Afro Quarantelli
Keyword(s):  
Parmigiano Reggiano ◽  
Cheese Production

scholarly journals Genetic diversity and effective population sizes of thirteen Indian cattle breeds

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Eva M. Strucken ◽  
Netsanet Z. Gebrehiwot ◽  
Marimuthu Swaminathan ◽  
Sachin Joshi ◽  
Mohammad Al Kalaldeh ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Bos Taurus ◽  
Bos Indicus ◽  
Allele Frequencies ◽  
Runs Of Homozygosity ◽  
Effective Population ◽  
Indigenous Cattle ◽  
Cattle Breeds ◽  
Population Sizes ◽  
Indian Cattle

Abstract Background The genetic structure of a diverse set of 15 Indian indigenous breeds and non-descript indigenous cattle sampled from eight states was examined, based on 777 k single nucleotide polymorphism (SNP) genotypes obtained on 699 animals, with sample sizes ranging from 17 to 140 animals per breed. To date, this is the largest and most detailed assessment of the genetic diversity of Indian cattle breeds. Results Admixture analyses revealed that 109 of the indigenous animals analyzed had more than 1% Bos taurus admixture of relatively recent origin. Pure indigenous animals were defined as having more than 99% Bos indicus ancestry. Assessment of the genetic diversity within and between breeds using principal component analyses, F statistics, runs of homozygosity, the genomic relationship matrix, and maximum likelihood clustering based on allele frequencies revealed a low level of genetic diversity among the indigenous breeds compared to that of Bos taurus breeds. Correlations of SNP allele frequencies between breeds indicated that the genetic variation among the Bos indicus breeds was remarkably low. In addition, the variance in allele frequencies represented less than 1.5% between the Indian indigenous breeds compared to about 40% between Bos taurus dairy breeds. Effective population sizes (Ne) increased during a period post-domestication, notably for Ongole cattle, and then declined during the last 100 generations. Although we found that most of the identified runs of homozygosity are short in the Indian indigenous breeds, indicating no recent inbreeding, the high FROH coefficients and low FIS values point towards small population sizes. Nonetheless, the Ne of the Indian indigenous breeds is currently still larger than that of Bos taurus dairy breeds. Conclusions The changes in the estimates of effective population size are consistent with domestication from a large native population followed by consolidation into breeds with a more limited population size. The surprisingly low genetic diversity among Indian indigenous cattle breeds might be due to their large Ne since their domestication, which started to decline only 100 generations ago, compared to approximately 250 to 500 generations for Bos taurus dairy cattle.

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

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Meenu Bhati ◽  
Naveen Kumar Kadri ◽  
Danang Crysnanto ◽  
Hubert Pausch
Keyword(s):  
Whole Genome Sequencing ◽  
Meat Quality ◽  
Genome Sequencing ◽  
Genomic Diversity ◽  
Whole Genome ◽  
Runs Of Homozygosity ◽  
Cattle Breeds ◽  
Signatures Of Selection ◽  
Genomic Inbreeding ◽  
Genomic Regions

Abstract Background Autochthonous cattle breeds are an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and food conditions. Original Braunvieh (OB) is a local cattle breed of Switzerland used for beef and milk production in alpine areas. Using whole-genome sequencing (WGS) 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 15,722,811 SNPs and 1,580,878 Indels including 10,738 and 2763 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 derived from runs of homozygosity (ROH) was relatively low (FROH = 0.14) in the 49 OB key ancestor animals. However, genomic inbreeding was higher in OB cattle of more recent generations (FROH = 0.16) due to a higher number of long (> 1 Mb) runs of homozygosity. Using two complementary approaches, 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 sequence variation in Swiss OB cattle genomes. With WGS 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 local environmental conditions. Considering that the population size is low and genomic inbreeding increased in the past generations, the implementation of optimal mating strategies seems warranted to maintain genetic diversity in the Swiss OB cattle population.

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