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Multiple Maternal Lineages of Vietnamese Local Chickens Inferred by Mitochondrial DNA D-loop Sequences

  • Cuc, Ngo Thi Kim;Simianer, Henner;Groeneveld, Linn Fenna;Weigend, Steffen
    • Asian-Australasian Journal of Animal Sciences
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    • v.24 no.2
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    • pp.155-161
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    • 2011
  • In this study, mitochondrial DNA (mtDNA) sequence polymorphism was used to assess genetic diversity of nine Vietnamese local chicken breeds. In addition, two Chinese breeds kept in Vietnam were included in the analysis for comparison. A 455-bp fragment of the mtDNA D-loop region was sequenced in 222 chickens of these 11 breeds. As reference, a skeleton was constructed based on chicken mtDNA sequences taken from the Genbank. Haplotypes of the nine Vietnamese local and two Chinese breeds were aligned together with these sequences. The Vietnamese and Chinese breeds showed a high degree of variability. In total, 37 haplotypes were identified in the chicken breeds studied forming eight clades. Thereby, the majority of individuals of the two Chinese breeds grouped together in one clade which is assumed to have its roots in the Indian subcontinent. Although the Vietnamese chicken breeds were distributed across all eight clades, most of them clustered in three main clades. These results suggest that the Vietnamese domestic chickens have originated from multiple maternal lineages, presumably from Yunnan and adjacent areas in China, South and Southwest China and/or surrounding regions (i.e. Vietnam, Burma, Thailand, and India).

Evaluation of Single Nucleotide Polymorphisms (SNPs) Genotyped by the Illumina Bovine SNP50K in Cattle Focusing on Hanwoo Breed

  • Dadi, Hailu;Kim, Jong-Joo;Yoon, Du-Hak;Kim, Kwan-Suk
    • Asian-Australasian Journal of Animal Sciences
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    • v.25 no.1
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    • pp.28-32
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    • 2012
  • In the present study, we evaluated the informativeness of SNPs genotyped by the Illumina Bovine SNP50K assay in different cattle breeds. To investigate these on a genome-wide scale, we considered 52,678 SNPs spanning the whole autosomal and X chromosomes in cattle. Our study samples consists of six different cattle breeds. Across the breeds approximately 72 and 6% SNPs were found polymorphic and fixed or close to fix in all the breeds, respectively. The variations in the average minor allele frequency (MAF) were significantly different between the breeds studied. The level of average MAF observed in Hanwoo was significantly lower than the other breeds. Hanwoo breed also displayed the lowest number of polymorphic SNPs across all the chromosomes. More importantly, this study indicated that the Bovine SNP50K assay will have reduced power for genome-wide association studies in Hanwoo as compared to other cattle breeds. Overall, the Bovine SNP50K assay described in this study offer a useful genotyping platform for mapping quantitative trait loci (QTLs) in the cattle breeds. The assay data represent a vast and generally untapped resource to assist the investigation of the complex production traits and the development of marker-assisted selection programs.

Comparison of Carcass Characteristics and Meat Quality between Duroc and Crossbred Pigs

  • Choi, Jung-Seok;Lee, Hyun-Jin;Jin, Sang-Keun;Choi, Yang-Il;Lee, Jae-Joon
    • Food Science of Animal Resources
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    • v.34 no.2
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    • pp.238-244
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    • 2014
  • This study was conducted to compare the carcass characteristics and meat quality characteristics of Duroc breed and crossbred pigs (Landrace ${\times}$ Yorkshire ${\times}$ Duroc, LYD). Duroc and crossbred pigs did not show differences in carcass characteristics. Crossbred pigs had higher moisture and protein content than Duroc breeds. However, Duroc breeds had a higher fat content than the crossbred pigs. In meat quality characteristics, crossbred pigs showed higher values of drip loss and cooking loss over Duroc breeds, while Duroc breeds showed higher ultimate pH value compared to that of crossbred pigs. However, there were no differences in water holding capacity and shear force value. In myoglobin content, crossbred pigs had higher content compared to that in the Duroc population. In subjective evaluation and sensory characteristics, Duroc breeds showed significantly higher scores in all categories except for tenderness over the crossbred pigs. However, in storage characteristics, Duroc breeds showed reduced tendency relative to crossbred pigs. Crossbred pigs had higher unsaturated fatty acid content than Duroc breeds did. In these results, Duroc breeds showed excellent meat quality characteristics with its higher intramuscular fat content and pH value, lower drip loss and cooking loss and higher juiciness and flavor, compared to the crossbred pigs.

Assessment of Genetic Diversity, Relationships and Structure among Korean Native Cattle Breeds Using Microsatellite Markers

  • Suh, Sangwon;Kim, Young-Sin;Cho, Chang-Yeon;Byun, Mi-Jeong;Choi, Seong-Bok;Ko, Yeoung-Gyu;Lee, Chang Woo;Jung, Kyoung-Sub;Bae, Kyoung Hun;Kim, Jae-Hwan
    • Asian-Australasian Journal of Animal Sciences
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    • v.27 no.11
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    • pp.1548-1553
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    • 2014
  • Four Korean native cattle (KNC) breeds-Hanwoo, Chikso, Heugu, and Jeju black-are entered in the Domestic Animal Diversity Information System of the United Nations Food and Agriculture Organization (FAO). The objective of this study was to assess the genetic diversity, phylogenetic relationships and population structure of these KNC breeds (n = 120) and exotic breeds (Holstein and Charolais, n = 56). Thirty microsatellite loci recommended by the International Society for Animal Genetics/FAO were genotyped. These genotypes were used to determine the allele frequencies, allelic richness, heterozygosity and polymorphism information content per locus and breed. Genetic diversity was lower in Heugu and Jeju black breeds. Phylogenetic analysis, Factorial Correspondence Analysis and genetic clustering grouped each breed in its own cluster, which supported the genetic uniqueness of the KNC breeds. These results will be useful for conservation and management of KNC breeds as animal genetic resources.

Genetic diversity of Saudi native chicken breeds segregating for naked neck and frizzle genes using microsatellite markers

  • Fathi, Moataz;El-Zarei, Mohamed;Al-Homidan, Ibrahim;Abou-Emera, Osama
    • Asian-Australasian Journal of Animal Sciences
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    • v.31 no.12
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    • pp.1871-1880
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    • 2018
  • Objective: Recently, there has been an increasing interest in conservation of native genetic resources of chicken on a worldwide basis. Most of the native chicken breeds are threatened by extinction or crossing with ecotypes. Methods: Six Saudi native chicken breeds including black naked neck, brown frizzled, black, black barred, brown and gray were used in the current study. The aim of the current study was to evaluate genetic diversity, relationship and population structure of Saudi native chicken breeds based on 20 microsatellite markers. Results: A total of 172 alleles were detected in Saudi native chicken breeds across all 20 microsatellite loci. The mean number of alleles per breed ranged from 4.35 in gray breed to 5.45 in normally feathered black with an average of 8.6 alleles. All breeds were characterized by a high degree of genetic diversity, with the lowest heterozygosity found in the brown breed (72%) and the greatest in the frizzled and black barred populations (78%). Higher estimate of expected heterozygosity (0.68) was found in both black breeds (normal and naked neck) compared to the other chicken populations. All studied breeds showed no inbreeding within breed (negative inbreeding coefficient [$F_{IS}$]). The phylogenetic relationships of chickens were examined using neighbor-joining trees constructed at the level of breeds and individual samples. The neighbor-joining tree constructed at breed level revealed three main clusters, with naked neck and gray breeds in one cluster, and brown and frizzled in the second cluster leaving black barred in a separate one. Conclusion: It could be concluded that the genetic information derived from the current study can be used as a guide for genetic improvement and conservation in further breeding programs. Our findings indicate that the Saudi native chicken populations have a rich genetic diversity and show a high polymorphism.

Population Structure and Biodiversity of Chinese Indigenous Duck Breeds Revealed by 15 Microsatellite Markers

  • Liu, W.;Hou, Z.C.;Qu, L.J.;Huang, Y.H.;Yao, J.F.;Li, N.;Yang, N.
    • Asian-Australasian Journal of Animal Sciences
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    • v.21 no.3
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    • pp.314-319
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    • 2008
  • Duck (Anas platyrhynchos) is one of the most important domestic avian species in the world. In the present research, fifteen polymorphic microsatellite markers were used to evaluate the diversity and population structure of 26 Chinese indigenous duck breeds across the country. The Chinese breeds showed high variation with the observed heterozygosity (Ho) ranging from 0.401 (Jinding) to 0.615 (Enshi), and the expected heterozygosity (He) ranging from 0.498 (Jinding) to 0.707 (Jingjiang). In all of the breeds, the values of Ho were significantly lower than those of He, suggesting high selection pressure on these local breeds. AMOVA and Bayesian clustering analysis showed that some breeds had mixed together. The FST value for all breeds was 0.155, indicating medium differentiation of the Chinese indigenous breeds. The FST value also indicated the short domestication history of most of Chinese indigenous ducks and the admixture of these breeds after domestication. Understanding the genetic relationship and structure of these breeds will provide valuable information for further conservation and utilization of the genetic resources in ducks.

Comparison of linkage disequilibrium levels in Iranian indigenous cattle using whole genome SNPs data

  • Karimi, Karim;Koshkoiyeh, Ali Esmailizadeh;Gondro, Cedric
    • Journal of Animal Science and Technology
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    • v.57 no.12
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    • pp.47.1-47.10
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    • 2015
  • Background: Knowledge of linkage disequilibrium (LD) levels among different populations can be used to detect genetic diversity and to investigate the historical changes in population sizes. Availability of large numbers of SNP through new sequencing technologies has provided opportunities for extensive researches in quantifying LD patterns in cattle breeds. The aim of this study was to compare the extent of linkage disequilibrium among Iranian cattle breeds using high density SNP genotyping data. Results: A total of 70 samples, representing seven Iranian indigenous cattle breeds, were genotyped for 777962 SNPs. The average values of LD based on the $r^2$ criterion were computed by grouping all syntenic SNP pairwises for intermarker distances from 0 Kb up to 1 Mb using three distance sets. Average $r^2$ above 0.3 was observed at distances less than 30 Kb for Sistani and Kermani, 20 Kb for Najdi, Taleshi, Kurdi and Sarabi, and 10 Kb for Mazandarani. The LD levels were considerably different among the Iranian cattle breeds and the difference in LD extent was more detectable between the studied breeds at longer distances. Lower level of LD was observed for Mazandarani breed as compared to other breeds indicating larger ancestral population size in this breed. Kermani breed continued to have more slowly LD decay than all of the other breeds after 3 Kb distances. More slowly LD decay was observed in Kurdi and Sarabi breeds at larger distances (>100 Kb) showing that population decline has been more intense in more recent generations for these populations. Conclusions: A wide genetic diversity and different historical background were well reflected in the LD levels among Iranian cattle breeds. More LD fluctuation was observed in the shorter distances (less than 10 Kb) in different cattle populations. Despite of the sample size effects, High LD levels found in this study were in accordance with the presence of inbreeding and population decline in Iranian cattle breeds.

Genetic Distance among South Indian Breeds of Zebu Cattle Using Random Amplified DNA Markers

  • Ramesha, K.P.;Saravanan, T.;Rao, M.K.;Appannavar, M.M.;Obi Reddy, A.
    • Asian-Australasian Journal of Animal Sciences
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    • v.15 no.3
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    • pp.309-314
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    • 2002
  • Random Amplified Polymorphic DNA (RAPD) assay was conducted to identify polymorphic markers in Amrithmahal, Krishna Valley, Hallikar, Deoni, Khillari, Ongole and Malnad Gidda breeds of South Indian cattle using twenty six primers. Of the 93 RAPD markers obtained, 53 were present in all breeds, 22 were individual specific and 18 were polymorphic for different breeds. Dual purpose breeds viz., Krishna Valley and Ongole showed less genetic divergence between them as compared to their genetic divergence from draft breeds viz., Amrithmahal, Hallikar and Khillari. Malnad Gidda was found to be a distinctly different from others studied.

Identification of Promising Bivoltine Breeds based on Multiple Trait Analysis for Future Breeding Program in West Bengal, India

  • Chanda, Subhra;Saha, Lal Mohan;Das, Nirvan Kumar;Kar, Niharendu Bikash;Bindroo, Bharat Bhusan
    • International Journal of Industrial Entomology
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    • v.23 no.2
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    • pp.239-243
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    • 2011
  • Thirty five bivoltine breeds were acclimatized under controlled condition for three years during two seasons to evaluate their efficiency in Seri industry of tropical region. Out of thirty five ten breeds had been short listed based on ranking for individual trait. Three breeds out of those ten selected breeds viz. SK6, NB18 and B.Con.4 ranked top in respect of overall performance. The ten breeds based on average Evaluation Index value > 50 considering twelve economically important traits are the resource material for future course of breeding program in West Bengal.

Analysis of genetic diversity and distances in Asian cattle breeds using microsatellite markers

  • Shi, Zheng;Lee, Ji-Hong;Lee, Yoon-Seok;Oh, Dong-Yeub;Yeo, Jung-Sou
    • Journal of the Korean Data and Information Science Society
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    • v.21 no.4
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    • pp.795-802
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    • 2010
  • This study defined the genetic diversity of five breeds of cattle in Asia by analyzing 6 microsatellite markers in 270 animals. Based on expected mean heterozygosity, the lowest genetic diversity was exhibited in Japanese black cattle (HE=0.5849), and the highest in Chinese yellow cattle (HE=0.8073). Average proportion of genetic variation due to interpopulation subdivision among these five cattle breeds varied between 11.7 and 12.5%. The genetic distances were roughly divided into three groups: Japanese black cattle, Holstein, and the three remaining breeds. This clustering agrees with the origin and geographical distributions of these five cattle breeds.