Characterization of Genetic Diversity Conserved in the Gene Bank for Dutch Cattle Breeds

In this study, we characterized genetic diversity in the gene bank for Dutch native cattle breeds. A total of 715 bulls from seven native breeds and a sample of 165 Holstein Friesian bulls were included. Genotype data were used to calculate genetic similarities. Based on these similarities, most breeds were clearly differentiated, except for two breeds (Deep Red and Improved Red and White) that have recently been derived from the MRY breed, and for the Dutch Friesian and Dutch Friesian Red, which have frequently exchanged bulls. Optimal contribution selection (OCS) was used to construct core sets of bulls with a minimized similarity. The composition of the gene bank appeared to be partly optimized in the semen collection process, i.e., the mean similarity within breeds based on the current number of straws per bull was 0.32% to 1.49% lower than when each bull would have contributed equally. Mean similarity could be further reduced within core sets by 0.34% to 2.79% using OCS. Material not needed for the core sets can be made available for supporting in situ populations and for research. Our findings provide insight in genetic diversity in Dutch cattle breeds and help to prioritize material in gene banking.

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Genetic diversity and population structure of four cattle breeds raised in Turkey using microsatellite markers

Czech Journal of Animal Science ◽

10.17221/62/2019-cjas ◽

2019 ◽

Vol 64 (No. 10) ◽

pp. 411-419 ◽

Cited By ~ 2

Author(s):

Eymen Demir ◽

Murat Soner Balcioğlu

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Microsatellite Markers ◽

Factorial Correspondence Analysis ◽

Cattle Breeds ◽

Expected Heterozygosity ◽

Bottleneck Analysis ◽

Holstein Friesian ◽

Native Cattle ◽

Marker Level

In the present study, genetic diversity and population structure of Holstein Friesian and three native cattle breeds of Turkey including Turkish Grey Steppe, Eastern Anatolian Red and Anatolian Black were assessed. Totally 120 individuals of 4 breeds were genotyped using 20 microsatellite markers and 204 different alleles, of which 31 were private alleles, were detected. The average observed and expected heterozygosity values were 0.63 and 0.74, respectively. Observed heterozygosity at the marker level ranged from 0.30 (DRBP1) to 0.88 (ILSTS011), while expected heterozygosity ranged from 0.51 (INRABERN172) to 0.88 (SPS113). Inbreeding coefficient values for Turkish Grey Steppe, Eastern Anatolian Red, Anatolian Black and Holstein Friesian were 0.216, 0.202, 0.128 and 0.069, respectively. The lowest pairwise F<sub>ST</sub> value (0.030) was detected between Turkish Grey Steppe and Anatolian Black breeds, while the highest value (0.070) was detected between Turkish Grey Steppe and Holstein Friesian. Results of structure and factorial correspondence analysis revealed that Turkish native cattle breeds and Holstein Friesian were genetically different enough to separate the two breeds. Results of bottleneck analysis indicated heterozygosity deficiency in Turkish Grey Steppe (P < 0.05).

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163 Population structure and genetic diversity of Russian native cattle breeds

Journal of Animal Science ◽

10.2527/asasann.2017.163 ◽

2017 ◽

Vol 95 (suppl_4) ◽

pp. 80-80 ◽

Cited By ~ 1

Author(s):

A. V. Dotsev ◽

A. A. Sermyagin ◽

E. A. Gladyr' ◽

T. Deniskova ◽

K. Wimmers ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Cattle Breeds ◽

Native Cattle

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Genetic diversity and population structure of Turkish native cattle breeds

South African Journal of Animal Science ◽

10.4314/sajas.v49i4.4 ◽

2019 ◽

Vol 49 (4) ◽

pp. 628

Author(s):

Y Öner ◽

O Yılmaz ◽

C Eriş ◽

N Ata ◽

C Ünal ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Cattle Breeds ◽

Native Cattle

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Characterization of the long-term radiosonde temperature biases in the upper troposphere and lower stratosphere using COSMIC and Metop-A/GRAS data from 2006 to 2014

Atmospheric Chemistry and Physics ◽

10.5194/acp-17-4493-2017 ◽

2017 ◽

Vol 17 (7) ◽

pp. 4493-4511 ◽

Cited By ~ 21

Author(s):

Shu-peng Ho ◽

Liang Peng ◽

Holger Vömel

Keyword(s):

Lower Stratosphere ◽

Temperature Measurements ◽

Climate Data ◽

Upper Troposphere ◽

Global Trend ◽

The Mean ◽

Temperature Climate

Abstract. Radiosonde observations (RAOBs) have provided the only long-term global in situ temperature measurements in the troposphere and lower stratosphere since 1958. In this study, we use consistently reprocessed Global Positioning System (GPS) radio occultation (RO) temperature data derived from the COSMIC and Metop-A/GRAS missions from 2006 to 2014 to characterize the inter-seasonal and interannual variability of temperature biases in the upper troposphere and lower stratosphere for different radiosonde sensor types. The results show that the temperature biases for different sensor types are mainly due to (i) uncorrected solar-zenith-angle-dependent errors and (ii) change of radiation correction. The mean radiosonde–RO global daytime temperature difference in the layer from 200 to 20 hPa for Vaisala RS92 is equal to 0.20 K. The corresponding difference is equal to −0.06 K for Sippican, 0.71 K for VIZ-B2, 0.66 K for Russian AVK-MRZ, and 0.18 K for Shanghai. The global daytime trend of differences for Vaisala RS92 and RO temperature at 50 hPa is equal to 0.07 K/5 yr. Although there still exist uncertainties for Vaisala RS92 temperature measurement over different geographical locations, the global trend of temperature differences between Vaisala RS92 and RO from June 2006 to April 2014 is within ±0.09 K/5 yr. Compared with Vaisala RS80, Vaisala RS90, and sondes from other manufacturers, the Vaisala RS92 seems to provide the most accurate RAOB temperature measurements, and these can potentially be used to construct long-term temperature climate data records (CDRs). Results from this study also demonstrate the feasibility of using RO data to correct RAOB temperature biases for different sensor types.

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Genetic Characterization of the Bovine Y-chromosomal Microsatellite Markers in the Korean Native Cattle Breeds

Annals of Animal Resource Sciences ◽

10.12718/aars.2013.24.2.89 ◽

2013 ◽

Vol 24 (2) ◽

pp. 89-96 ◽

Cited By ~ 2

Author(s):

Sawgwon Suh ◽

◽

Young-Sin Kim ◽

Chang-Yeon Cho ◽

Mi-Jeong Byun ◽

...

Keyword(s):

Microsatellite Markers ◽

Genetic Characterization ◽

Cattle Breeds ◽

Native Cattle

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Characterization of the Long-term Radiosonde Temperature Biases in the Lower Stratosphere using COSMIC and Metop-A/GRAS Data from 2006 to 2014

10.5194/acp-2016-801 ◽

2016 ◽

Author(s):

Shu-Peng Ho ◽

Liang Peng ◽

Holger Vömel

Keyword(s):

Global Positioning System ◽

Lower Stratosphere ◽

Temperature Measurements ◽

Global Trend ◽

Global Positioning ◽

The Mean ◽

Geographical Locations

Abstract. Radiosonde observations (RAOBs) have provided the only long-term global in situ temperature measurements in the troposphere and lower stratosphere since 1958. In this study, we use consistently reprocessed Global Positioning System (GPS) radio occultation (RO) temperature data derived from COSMIC and Metop-A/GRAS missions from 2006 to 2014 to characterize the inter-seasonal and inter-annual variability of temperature biases in the lower stratosphere for different sensor types. The results show that the RAOB temperature biases for different RAOB sensor types are mainly owing to i) uncorrected solar zenith angle dependent errors, and ii) change of radiation correction. The mean daytime temperature difference (ΔT) for Vaisala RS92 is equal to 0.18 K in Australia, 0.20 K in Germany, 0.10 K in Canada, 0.13 K in England, and 0.33 K in Brazil. The mean daytime ΔT is equal to −0.06 K for Sippican, 0.71 K for VIZ-B2, 0.66 K for AVK-MRZ, and 0.18 K for Shanghai. The daytime trend of anomalies for Vaisala RS92 and RO temperature at 50 hPa is equal to 0.00 K/5 yrs over United States, −0.02 K/5 yrs over Germany, 0.17 K/5 yrs over Australia, 0.23 K/5 yrs over Canada, 0.26 K/5 yrs over England, and 0.12 K/5 yrs over Brazil, respectively. Although there still exist uncertainties for Vaisala RS92 temperature measurements over different geographical locations, the global trend of temperature anomaly between Vaisala RS92 and RO from June 2006 to April 2014 is within +/−0.09 K/5 yrs globally. Comparing with Vaisala RS80, Vaisala RS90 and sondes from other manufacturers, the Vaisala RS92 seems to provide the best RAOB temperature measurements, which can potentially be used to construct long term temperature CDRs. Results from this study also demonstrate the feasibility to use RO data to correct RAOB temperature biases for different sensor types.

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Genomic relatedness and diversity of Swedish native cattle breeds

Genetics Selection Evolution ◽

10.1186/s12711-019-0496-0 ◽

2019 ◽

Vol 51 (1) ◽

Cited By ~ 7

Author(s):

Maulik Upadhyay ◽

Susanne Eriksson ◽

Sofia Mikko ◽

Erling Strandberg ◽

Hans Stålhammar ◽

...

Keyword(s):

Genetic Diversity ◽

Phylogenetic Trees ◽

Genetic Relatedness ◽

Demographic History ◽

Genomic Diversity ◽

Founder Population ◽

Southern Sweden ◽

Cattle Breeds ◽

Genome Wide ◽

Native Cattle

Abstract Background Native cattle breeds are important genetic resources given their adaptation to the local environment in which they are bred. However, the widespread use of commercial cattle breeds has resulted in a marked reduction in population size of several native cattle breeds worldwide. Therefore, conservation management of native cattle breeds requires urgent attention to avoid their extinction. To this end, we genotyped nine Swedish native cattle breeds with genome-wide 150 K single nucleotide polymorphisms (SNPs) to investigate the level of genetic diversity and relatedness between these breeds. Results We used various SNP-based approaches on this dataset to connect the demographic history with the genetic diversity and population structure of these Swedish cattle breeds. Our results suggest that the Väne and Ringamåla breeds originating from southern Sweden have experienced population isolation and have a low genetic diversity, whereas the Fjäll breed has a large founder population and a relatively high genetic diversity. Based on the shared ancestry and the constructed phylogenetic trees, we identified two major clusters in Swedish native cattle. In the first cluster, which includes Swedish mountain cattle breeds, there was little differentiation among the Fjäll, Fjällnära, Swedish Polled, and Bohus Polled breeds. The second cluster consists of breeds from southern Sweden: Väne, Ringamåla and Swedish Red. Interestingly, we also identified sub-structuring in the Fjällnära breed, which indicates different breeding practices on the farms that maintain this breed. Conclusions This study represents the first comprehensive genome-wide analysis of the genetic relatedness and diversity in Swedish native cattle breeds. Our results show that different demographic patterns such as genetic isolation and cross-breeding have shaped the genomic diversity of Swedish native cattle breeds and that the Swedish mountain breeds have retained their authentic distinct gene pool without significant contribution from any of the other European cattle breeds that were included in this study.

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Characterization of bovine MHC DRB3 diversity in global cattle breeds, with a focus on cattle in Myanmar

10.21203/rs.3.rs-20143/v3 ◽

2020 ◽

Author(s):

Guillermo Giovambattista ◽

Kyaw Kyaw Moe ◽

Meripet Polat ◽

Liushiqi Borjigin ◽

Si Thu Hein ◽

...

Keyword(s):

Genetic Diversity ◽

Immune Response ◽

Latin American ◽

Coat Color ◽

Genetic Locus ◽

The Philippines ◽

Typing Method ◽

Cattle Breeds ◽

Holstein Friesian ◽

Native Populations

Abstract Background: Myanmar cattle populations predominantly consist of native cattle breeds (Pyer Sein and Shwe), characterized by their geographical location and coat color, and the Holstein-Friesian crossbreed, which is highly adapted to the harsh tropical climates of this region. Here, we analyzed the diversity and genetic structure of the BoLA-DRB3 gene, a genetic locus that has been linked to the immune response, in Myanmar cattle populations.Methods: Blood samples (n=294) were taken from two native breeds (Pyer Sein, n=163 and Shwe Ni, n=69) and a cattle crossbreed (Holstein-Friesian, n=62) distributed across six regions of Myanmar (Bago, n=38; Sagaing, n=77; Mandalay, n=46; Magway, n=46; Kayin, n=43; Yangon, n=44). In addition, a database that included 2,428 BoLA-DRB3 genotypes from European (Angus, Hereford, Holstein, Shorthorn, Overo Negro, Overo Colorado, and Jersey), Zebuine (Nellore, Brahman and Gir), Asian Native from Japan and Philippine and Latin-American Creole breeds was also included. Furthermore, the information from the IPD–MHC database was also used in the present analysis. DNA was genotyped using the sequence-based typing method. DNA electropherograms were analyzed using the Assign 400ATF software.Results: We detected 71 distinct alleles, including three new variants for the BoLA-DRB3 gene. Venn analysis showed that 11 of these alleles were only detected in Myanmar native breeds and 26 were only shared with Asian native and/or Zebu groups. The number of alleles ranged from 33 in Holstein-Friesians to 58 in Pyer Seins, and the observed versus unbiased expected heterozygosity were higher than 0.84 in all the three the populations analyzed. The FST analysis showed a low level of genetic differentiation between the two Myanmar native breeds (FST=0.003), and between these native breeds and the Holstein-Friesians (FST < 0.021). The average FST value for all the Myanmar Holstein-Friesian crossbred and Myanmar native populations was 0.0136 and 0.0121, respectively. Principal component analysis (PCA) and tree analysis showed that Myanmar native populations grouped in a narrow cluster that diverged clearly from the Holstein-Friesian populations. Furthermore, the BoLA-DRB3 allele frequencies suggested that while some Myanmar native populations from Bago, Mandalay and Yangon regions were more closely related to Zebu breeds (Gir and Brahman), populations from Kayin, Magway and Sagaing regions were more related to the Philippines native breeds. On the contrary, PCA showed that the Holstein-Friesian populations demonstrated a high degree of dispersion, which is likely the result of the different degrees of native admixture in these populations.Conclusion: This study is the first to report the genetic diversity of the BoLA-DRB3 gene in two native breeds and one exotic cattle crossbreed from Myanmar. The results obtained contribute to our understanding of the genetic diversity and distribution of BoLA-DRB3 gene alleles in Myanmar, and increases our knowledge of the worldwide variability of cattle BoLA-DRB3 genes, an important locus for immune response and protection against pathogens.

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Characterization of bovine MHC DRB3 diversity in global cattle breeds, with a focus on cattle in Myanmar

10.21203/rs.3.rs-20143/v2 ◽

2020 ◽

Cited By ~ 1

Author(s):

Guillermo Giovambattista ◽

Kyaw Kyaw Moe ◽

Meripet Polat ◽

Liushiqi Borjigin ◽

Si Thu Hein ◽

...

Keyword(s):

Genetic Diversity ◽

Immune Response ◽

Latin American ◽

Coat Color ◽

Genetic Locus ◽

The Philippines ◽

Typing Method ◽

Cattle Breeds ◽

Holstein Friesian ◽

Native Populations

Abstract Background: Myanmar cattle populations predominantly consist of native cattle breeds (Pyer Sein and Shwe), characterized by their geographical location and coat color, and the Holstein-Friesian crossbreed, which is highly adapted to the harsh tropical climates of this region. Here, we analyzed the diversity and genetic structure of the BoLA-DRB3 gene, a genetic locus that has been linked to the immune response, in Myanmar cattle populations.Methods: Blood samples (n=294) were taken from two native breeds (Pyer Sein, n=163 and Shwe Ni, n=69) and a cattle crossbreed (Holstein-Friesian, n=62) distributed across six regions of Myanmar (Bago, n=38; Sagaing, n=77; Mandalay, n=46; Magway, n=46; Kayin, n=43; Yangon, n=44). In addition, a database that included 2,428 BoLA-DRB3 genotypes from European (Angus, Hereford, Holstein, Shorthorn, Overo Negro, Overo Colorado, and Jersey), Zebuine (Nellore, Brahman and Gir), Asian Native form Japan and Philippine and Latin-American Creole breeds was also included. Furthermore, the information from the IPD–MHC database was also used in the present analysis. DNA was genotyped using the sequence-based typing method. DNA electropherograms were analyzed using the Assign 400ATF software. Results: We detected 71 distinct alleles, including three new variants for the BoLA-DRB3 gene. Venn analysis showed that 11 of these alleles were only detected in Myanmar native breeds and 26 were only shared with Asian native and/or Zebu groups. The number of alleles ranged from 33 in Holstein-Friesians to 58 in Pyer Seins, and the observed versus unbiased expected heterozygosity were higher than 0.84 in all the three the populations analyzed. The FST analysis showed a low level of genetic differentiation between the two Myanmar native breeds (FST=0.003), and between these native breeds and the Holstein-Friesians (FST < 0.021). The average FST value for all the Myanmar Holstein-Friesian crossbred and Myanmar native populations was 0.0136 and 0.0121, respectively. Principal component analysis and tree analysis showed that Myanmar native populations grouped in a narrow cluster that diverged clearly from the Holstein-Friesian populations. Furthermore, the BoLA-DRB3 allele frequencies suggested that while some Myanmar native populations form Bago, Mandalay and Yangon regions were more closely related to Zebu breeds (Gir and Brahman), while populations from Kayin, Magway and Sagaing regions were more related to the Philippines native breeds. On the contrary, PCA showed that the Holstein-Friesian populations demonstrated a high degree of dispersion, which is likely the result of the different degrees of native admixture in these populations. Conclusion: This study is the first to report the genetic diversity of the BoLA-DRB3 gene in two native breeds and one exotic cattle crossbreed from Myanmar. The results obtained contribute to our understanding of the genetic diversity and distribution of BoLA-DRB3 gene alleles in Myanmar, and increases our knowledge of the worldwide variability of cattle BoLA-DRB3 genes, an important locus for immune response and protection against pathogens.

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