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.

Possible relationship between IGF-1/SnaBI genotypes and milk yield of Holstein-Friesian cows

2019 ◽  
Vol 15 (4) ◽  
pp. 35-41
Author(s):  
Małgorzata WASIELEWSKA ◽  
Iwona SZATKOWSKA
Keyword(s):  
Milk Yield ◽  
Quality Characteristics ◽  
Production Traits ◽  
Performance Parameters ◽  
Milk Traits ◽  
White Variety ◽  
Black And White ◽  
Holstein Friesian ◽  
Milk Performance ◽  
Friesian Cows

The correlation between polymorphisms in the IGF-1 gene and production traits in beef cattle is well known. The effect of insulin-like growth factor on the value of milk traits is not yet adequately understood. The aim of the study was to attempt to describe the effect of IGF-1/SnaBI substitution on selected milk performance parameters of the Black-and-White variety of Holstein-Friesian cows. Three genotypes were identified: CC, CT and TT. The results showed a correlation between IGF-1/SnaBI genotypes and milk yield (highest for CC homozygotes and lowest for CT heterozygotes). No relationship could be established between the genotype and the quality characteristics of milk.

scholarly journals Holstein Friesian dairy cattle edited for diluted coat color as adaptation to climate change

2020 ◽  
Author(s):  
G. Laible ◽  
S-A. Cole ◽  
B. Brophy ◽  
J. Wei ◽  
S. Leath ◽  
...  
Keyword(s):  
Dairy Cattle ◽  
Coat Color ◽  
Dilution Effect ◽  
Climatic Conditions ◽  
White Coat ◽  
Production Traits ◽  
Adaptation To Climate Change ◽  
Black And White ◽  
Holstein Friesian ◽  
The Impact

AbstractHigh-producing Holstein Friesian dairy cattle have a characteristic black and white coat pattern where black frequently comprises a large proportion of the coat. Compared to a light coat color, black absorbs more solar radiation translating into radiative heat gain which is a contributing factor to heat stress in cattle, negatively impacting on their production levels, fertility and welfare. To better adapt dairy cattle to the rapidly changing climatic conditions with predictions for more frequent and prolonged hot temperature patterns, we aimed to lighten their coat color by genome editing. Using gRNA/Cas9-mediated editing, we introduced a three base pair (bp) deletion in the pre-melanosomal protein 17 gene (PMEL) proposed as the causative variant responsible for the semi-dominant color dilution phenotype seen in Galloway and Highland cattle. Calves generated from cells homozygous for the edited mutation revealed a strong color dilution effect. Instead of the characteristic black and white coat color patterning of control calves generated from unedited parental cells, the edited calves displayed a novel pattern of grey and white markings and absence of any black areas. This, for the first time, verified the causative nature of the PMEL mutation for diluting the black coat color in cattle. With these edited animals, it is now possible to dissect the effects of the introgressed edit and other interfering allelic variants that might exist in individual cattle and accurately determine the impact of only the three bp change on important health, welfare and production traits. In addition, our study proved targeted editing as a promising approach for the rapid adaptation of livestock to changing climatic conditions.

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 Holstein Friesian dairy cattle edited for diluted coat color as a potential adaptation to climate change

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
G. Laible ◽  
S.-A. Cole ◽  
B. Brophy ◽  
J. Wei ◽  
S. Leath ◽  
...  
Keyword(s):  
Dairy Cattle ◽  
Coat Color ◽  
Dilution Effect ◽  
White Coat ◽  
Adaptation To Climate Change ◽  
Black And White ◽  
Holstein Friesian ◽  
Coat Pattern ◽  
The Impact ◽  
First Time

Abstract Background High-producing Holstein Friesian dairy cattle have a characteristic black and white coat, often with large proportions of black. Compared to a light coat color, black absorbs more solar radiation which is a contributing factor to heat stress in cattle. To better adapt dairy cattle to rapidly warming climates, we aimed to lighten their coat color by genome editing. Results Using gRNA/Cas9-mediated editing, we introduced a three bp deletion in the pre-melanosomal protein 17 gene (PMEL) proposed as causative variant for the semi-dominant color dilution phenotype observed in Galloway and Highland cattle. Calves generated from cells with homozygous edits revealed a strong color dilution effect. Instead of the characteristic black and white markings of control calves generated from unedited cells, the edited calves displayed a novel grey and white coat pattern. Conclusion This, for the first time, verified the causative nature of the PMEL mutation for diluting the black coat color in cattle. Although only one of the calves was healthy at birth and later succumbed to a naval infection, the study showed the feasibility of generating such edited animals with the possibility to dissect the effects of the introgressed edit and other interfering allelic variants that might exist in individual cattle and accurately determine the impact of only the three bp change.

scholarly journals Semi-Intensive Fattening Suitability and Slaughter Value of Young Bulls of Three Polish Native Breeds in Comparison With Polish Holstein-Friesian and Simmental

2014 ◽  
Vol 14 (2) ◽  
pp. 453-460 ◽  
Author(s):  
Zygmunt Litwińczuk ◽  
Paweł Żółkiewski ◽  
Mariusz Florek ◽  
Witold Chabuz ◽  
Piotr Domaradzki
Keyword(s):  
Weight Gain ◽  
Reference Group ◽  
Daily Weight Gain ◽  
White Variety ◽  
Black And White ◽  
Holstein Friesian ◽  
Good Material ◽  
Fattening Period ◽  
The Difference ◽  
Intensive System

Abstract An evaluation was conducted of the suitability for fattening in a semi-intensive system (mainly with fodders from permanent grassland) and the slaughter value of 15 young bulls of the Polish Red (PR) breed and 10 each of the White-Backed (WB) and Polish Black-and-White (BW) breeds. The reference group consisted of young bulls of the Black-and-White variety of the Polish Holstein- Friesian (HF) breed and the Simmental (SIM) breed, fattened on the same farms. Control fattening was carried out until the age of 18 months. Mean daily weight gain in the bulls of the native breeds during the control fattening period (which lasted 314-358 days) was 0.9 kg, similarly to HF, but significantly lower (P≤0.05) than in the Simmentals (986 g). During the entire fattening period, i.e. from birth to the age of 18 months, daily weight gain was 832 g in PR and 889-919 g in WB and BW. Dressing percentage was lowest in PR bulls (51.69%), and higher in WB (53.1%) and BW (53.49%), with values similar to the reference group, i.e. young bulls of the Simmental (52.97%) and HF (53.29%) breeds. The difference between PR and BW (1.8%) and HF (1.6%) was statistically significant (P≤0.05). In the EUROP classification system, the carcasses of the young bulls of the native breeds were most often placed in classes R- and O+ (conformation) and 2+ and 3- (fat cover), as in the case of young HF bulls. Carcasses of young Simmental bulls were assigned to much higher classes. The young bulls of the three Polish native breeds evaluated are good material for fattening in a semi-intensive system (mainly with fodder from permanent grasslands), while the young PR bulls were the least suitable

CATHL2 gene polymorphism in relation to production traits in Holstein-Friesian cows

2019 ◽  
Vol 15 (2) ◽  
pp. 23-30
Author(s):  
Sonia Hiller ◽  
Inga Kowalewska-Łuczak ◽  
Ewa Czerniawska-Piątkowska
Keyword(s):  
Statistical Analysis ◽  
Gene Polymorphism ◽  
Somatic Cell Count ◽  
The Other ◽  
Production Traits ◽  
Black And White ◽  
Potential Association ◽  
Holstein Friesian ◽  
Pcr Rflp ◽  
Friesian Cows

The aim of this study was to identify SNPs mutations in the CATHL2 gene and determine their potential association with dairy performance traits in Polish Black-and-White Holstein-Friesian (phf) cows. Genotypes of individuals were identified by PCR-RFLP. The frequencies of CATHL2/DdeI alleles were C ‒ 0.693 and T ‒ 0.307, and for CATHL2/HhaI polymorphisms, G ‒ 0.763 and C ‒ 0.237. The statistical analysis showed that cows with the CC (CATHL2/DdeI) and CG (CATHL2/HhaI) genotype produced higher milk yield than the other cattle genotypes. In the case of CATHL2/DdeI and CATHL2/HhaI polymorphisms, the highest somatic cell count was found in heterozygous CT and CG cows.

scholarly journals Food Resources Biodiversity: The Case of Local Cattle in Slovakia

2021 ◽  
Vol 13 (3) ◽  
pp. 1296
Author(s):  
Radovan Kasarda ◽  
Luboš Vostrý ◽  
Hana Vostrá-Vydrová ◽  
Kristína Candráková ◽  
Nina Moravčíková
Keyword(s):  
Food Resources ◽  
Significant Loss ◽  
Phenotypic Traits ◽  
Production Traits ◽  
Effective Population ◽  
Production Type ◽  
Genome Wide Data ◽  
Differentiation Degree ◽  
Genomic Inbreeding ◽  
The Impact

This study aimed to assess the level of biodiversity in selected local cattle populations as important food resources in Slovakia. The biodiversity level was derived from the genome-wide data collected for dairy (Jersey), dual-purpose (Slovak Pinzgau, Slovak Spotted), and beef breeds (Charolais, Limousine). The commonly used indices, genomic inbreeding (FROH, FGRM, FHOM, FUNI) and effective population size (NeLD), were used to quantify the impact of relatives mating on the genome of analysed populations. Even if the low NeLD estimates signalise significant loss of genetic variability within populations, the genomic inbreeding under 1% (except Jersey) showed that the intensity of diversity loss is not so rapid and can be managed by the re-arrangement of long-term breeding strategies. The analysis of genetic differentiation degree across populations assumed that the specialisation of breeds during their grading-up led to the specific nucleotide changes, especially in genes responsible for preferred phenotypic traits. The breed-specific differences observed mainly in the genome of Charolais (carcass traits) and Jersey (milk production traits) populations resulted from the polymorphisms in CAPN1 (μ-calpain) and CSN1S2 (casein alpha s2) genes, respectively. Obtained results confirmed that the specific haplotypes are strongly associated with the genetic nature of breed depending on production type.

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.

scholarly journals Associations between <i>Leu/Val</i> polymorphism of growth hormone gene and milk production traits in Black-and-White cattle

2002 ◽  
Vol 45 (5) ◽  
pp. 421-428 ◽  
Author(s):  
A. Dybus
Keyword(s):  
Growth Hormone ◽  
Milk Production ◽  
Milk Fat ◽  
Growth Hormone Gene ◽  
Production Traits ◽  
Milk Production Traits ◽  
Black And White ◽  
Holstein Friesian ◽  
Pcr Rflp ◽  
White Cattle

Abstract. Associations between polymorphism of the bovine growth hormone (GH) gene (Leu/Val) and milk production traits of Black-and-White cattle with different proportional share of Holstein Friesian genes were analysed. A total of 1086 cows were included in the study. PCR-RFLP method was used for genotyping. The frequencies of genotypes and alleles were as follows: 0.653 for LL genotype, 0.324 for LV and 0.023 for VV, and 0.815 for GHL and 0.185 for GHV. Associations between Leu/Val polymorphism and milk production traits of cows were found only in first lactation. Cows with LL genotype had higher milk, fat and protein yield compared to LV individuals (P ≤ 0.01).

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