• Asian-Australasian Journal of Animal Sciences
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• v.19 no.10
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• pp.1369-1378
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• 2006

This is the first study in which genetic variability and relationships of a large number of Japanese chicken breeds were revealed along with those of several foreign breeds by using microsatellite DNA polymorphisms. Twenty-eight breeds (34 populations) of native Japanese chickens and seven foreign breeds or varieties were analyzed. The mean number of alleles per locus, the proportion of the polymorphic loci, and the expected average heterozygosity ranged from 1.75 to 4.70, from 0.55 to 1.00, and from 0.21 to 0.67, respectively. Microsatellite alleles being unique to a particular population were detected in some populations. The $D_A$ genetic distance between populations was obtained from allele frequency for every pair of the populations to construct a neighbor-joining tree. According to the phylogenetic tree, excluding a few exceptions, native Japanese chicken breeds and foreign breeds were clearly separated from each other. Furthermore, the tree topology divided native Japanese chickens into four main classes, which was almost in accordance with the classification based on body morphology; that is, (1) Cochin type, (2) Malay type, (3) layer type, and (4) intermediate type between Malay and layer types. This is the first finding for native Japanese chickens.

• Asian-Australasian Journal of Animal Sciences
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• v.28 no.1
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• pp.25-36
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• 2015

The complex analysis of the pedigree records of Czech Landrace (CLA), Czech Large White-dam line (CLWd), Czech Large White-sire line (CLWs), Duroc (DC), and Pietrain (PN) was performed to determine trends of genetic diversity (GD), and to find the main sources of the GD loss. The total size of the pedigree was 132,365, 391,151, 32,913, 13,299, and 7,160 animals in CLA, CLWd, CLWs, DC, and PN, respectively. Animals born in the years 2011 through 2013 were assumed as the reference population. The average pedigree completeness index for one generation back was 95.9%, 97.4%, 91.2%, 89.8%, and 94.2% for appropriate breeds. Number of ancestors explaining 100% of gene pool was 186, 373, 125, 157, and 37 in CLA, CLWd, CLWs, DC, and PN, respectively. The relative proportion of inbred animals (58%, 58%, 54%, 47%, and 25%), the average inbreeding (2.7%, 1.4%, 2.5%, 3.6%, and 1.3%) and the average co-ancestry (3.1%, 1.6%, 3.3%, 4.2%, and 3.3%) were found over the past decade in analysed breeds. The expected inbreeding under random mating increased during the last 10 years in CLWs and PN and varied from 1.27% to 3.2%. The effective population size computed on the basis of inbreeding was 76, 74, 50, 35, and 83 in 2012 in CLA, CLWd, CLWs, DC, and PN, respectively. The shortest generation interval (1.45) was observed for CLWd in sire to son selection pathway. The longest generation interval obtained PN (1.95) in sire to daughter pathway. The average relative GD loss within last generation interval was 7.05%, 4.70%, 9.81%, 7.47%, and 10.46%, respectively. The relative proportion of GD loss due to genetic drift on total GD loss was 85.04%, 84.51%, 89.46%, 86.19%, and 83.68% in CLA, CLWd, CLWs, DC, and PN, respectively. All breeds were characterized by a high proportion of inbred animals, but the average inbreeding was low. The most vulnerable breeds to loss of GD are DC and PN. Therefore, a breeding program should be more oriented to prevent the increase of GD loss in these breeds.

• Asian-Australasian Journal of Animal Sciences
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• v.22 no.4
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• pp.598-604
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• 2009

This work was carried out to study the carcass characteristics, the chemical composition and the fatty acid profile in Longissimus muscle (LM) of bull breeds Nellore, NEL (11), Caracu, CAR (12) and Holstein-Friesian, HFR (12) finished in a feedlot. The bulls were fed twice a day with corn silage, cotton meal, cracked corn, urea, limestone and mineral salt. NEL and CAR bulls had similar (p>0.05) final weight and hot carcass weight. However, NEL and CAR bulls had higher (p<0.05) final weight and hot carcass weight than HFR bulls. Carcass hot dressing, carcass conformation, cushion thickness, Longissimus muscle area and texture were similar (p>0.05) among NEL, CAR and HFR bulls. NEL and HFR bulls had higher (p<0.05) carcass length in comparison to the CAR breed. Nellore breed had higher (p<0.05) leg length in comparison to CAR and HFR breeds. Leg length was similar (p>0.05) between CAR and HFR breeds. Thickness fat, color and marbling score were lower (p<0.05) in NEL breed in comparison to CAR and HFR breeds. LM of NEL bulls had higher (p<0.05) meat moisture content in comparison to CAR and HFR bulls. In contrast, lipid content was lower (p<0.10) in HFR bulls. LM ash and crude protein contents were similar (p>0.05) among breeds. Saturated fatty acids (SFA) were higher (p<0.10) in HFR animals. Monounsaturated fatty acids (MUFA), polyunsaturated fatty acids (PUFA), n-6, n-3 and PUFA/SFA ratio were similar (p>0.05) among the different breeds. N-6/n-3 ratio was higher (p<0.05) in CAR animals.

• Asian-Australasian Journal of Animal Sciences
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• v.27 no.10
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• pp.1399-1405
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• 2014

The effective management of endangered animal genetic resources is one of the most important concerns of modern breeding. Evaluation of genetic diversity and relationship of local breeds is an important factor towards the identification of unique and valuable genetic resources. This study aimed to analyze the genetic diversity and population structure of six Korean native chicken breeds (n = 300), which were compared with three imported breeds in Korea (n = 150). For the analysis of genetic diversity, 30 microsatellite markers from FAO/ISAG recommended diversity panel or previously reported microsatellite markers were used. The number of alleles ranged from 2 to 15 per locus, with a mean of 8.13. The average observed heterozygosity within native breeds varied between 0.46 and 0.59. The overall heterozygote deficiency ($F_{IT}$) in native chicken was $0.234{\pm}0.025$. Over 30.7% of $F_{IT}$ was contributed by within-population deficiency ($F_{IS}$). Bayesian clustering analysis, using the STRUCTURE software suggested 9 clusters. This study may provide the background for future studies to identify the genetic uniqueness of the Korean native chicken breeds.

• Asian-Australasian Journal of Animal Sciences
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• v.30 no.5
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• pp.603-621
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• 2017

The current review focuses on characterization and conservation efforts vital for the development of breeding programmes for indigenous beef cattle genetic resources in Southern Africa. Indigenous African cattle breeds were identified and characterized using information from refereed journals, conference papers and research reports. Results of this current review reviewed that smallholder beef cattle production in Southern Africa is extensive and dominated by indigenous beef cattle strains adaptable to the local environment. The breeds include Nguni, Mashona, Tuli, Malawi Zebu, Bovino de Tete, Angoni, Landim, Barotse, Twsana and Ankole. These breeds have important functions ranging from provision of food and income to socio-economic, cultural and ecological roles. They also have adaptive traits ranging from drought tolerant, resistance to ticks and tick borne diseases, heat tolerance and resistance to trypanosomosis. Stakeholders in the conservation of beef cattle were also identified and they included farmers, national government, research institutes and universities as well as breeding companies and societies in Southern Africa. Research efforts made to evaluate threats and opportunities of indigenous beef cattle production systems, assess the contribution of indigenous cattle to household food security and income, genetically and phenotypically characterize and conserve indigenous breeds, and develop breeding programs for smallholder beef production are highlighted. Although smallholder beef cattle production in the smallholder farming systems contributes substantially to household food security and income, their productivity is hindered by several constraints that include high prevalence of diseases and parasites, limited feed availability and poor marketing. The majority of the African cattle populations remain largely uncharacterized although most of the indigenous cattle breeds have been identified.

• Asian-Australasian Journal of Animal Sciences
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• v.29 no.11
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• pp.1547-1554
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• 2016

To assess genetic diversity and maternal origin of Turkish and Iranian native chicken breeds, we analyzed the mtDNA D-loop sequences of 222 chickens from 2 Turkish (Denizli and Gerze) and 7 Iranian (White Marandi, Black Marandi, Naked Neck, Common Breed, Lari, West Azarbaijan, and New Hampshire) native chicken breeds, together with the available reference sequences of G. gallus gallus in GenBank. The haplotype diversity was estimated as $0.24{\pm}0.01$ and $0.36{\pm}0.02$ for Turkish and Iranian populations, respectively. In total, 19 haplotypes were observed from 24 polymorphic sites in Turkish and Iranian native chicken populations. Two different clades or haplogroups (A and E) were found in Turkish and Iranian chickens. Clade A haplotypes were found only in White Marandi, Common Breed and New Hampshire populations. Clade E haplotypes, which are quite common, were observed in Turkish and Iranian populations with 18 different haplotypes, of which Turkish and Iranian chickens, Clade E, haplotype 1 (TRIRE1) was a major haplotype with the frequency of 81.5% (181/222) across all breeds. Compared to red jungle fowl, Turkish and Iranian chicken breeds are closely related to each other. These results suggest that Turkish and Iranian chickens originated from the same region, the Indian subcontinent. Our results will provide reliable basic information for mtDNA haplotypes of Turkish and Iranian chickens and for studying the origin of domestic chickens.

• Asian-Australasian Journal of Animal Sciences
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• v.17 no.7
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• pp.903-909
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• 2004

The variability of mtDNA hypervariable segment I (HVS I) sequences was investigated in a total of 48 birds belonging to 12 Chinese native chicken breeds. Sixteen haplotypes were identified from 35 polymorphic nucleotide sites which accounted for 6.4% of a sequenced 544 bp fragment. Diversity analysis of the haplotypes showed that Tibetan, Langshan and Henan cockfight chicken had only one haplotype, while ancient haplotypes existed in Taihe silky and Chahua chicken. Phylogenetic analysis of the haplotypes suggested that Chinese native chicken breeds shared 5 maternal lineages and some breeds would share the same maternal lineage, regardless of their external features and ecological types. Both divergent and phylogenetic analysis of the haplotypes indicated the close genetic relationships between the Chinese native chicken breeds and G. g. gallus and G. g. spadiceus from different areas, which implied that G. g. gallus and G. g. spadiceus were the original ancestors of the Chinese native chicken breeds.

• Asian-Australasian Journal of Animal Sciences
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• v.17 no.5
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• pp.603-607
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• 2004

Randomly Amplified Polymorphic DNA-Polymerase Chain Reaction (RAPD-PCR) analysis was carried out with a battery of 11 random decamer primers to study band frequency (BF), genetic identity index (I) and mean average percentage difference (MAPD) between Bhadawari and Murrah breeds of buffalo. The primers OPA04 and BG15 resolved a band of 460 bp, which was present only in animals of Bhadawari breed. Whereas, the primers OPA14, BG27 and BG28 produced Murrah specific fragments of sizes 730 bp and 1,230 bp, respectively. The estimate of genetic identity index was highest (0.845) with the primer OPA01 and the lowest (0.479) with the primer BG27. The genetic identity index pooled over the primers was 0.596${\pm}$0.037 between these two breeds. The highest MAPD estimate (53.9) between the two breeds was obtained with the primer BG27 and the lowest (14.3) with the primer OPA01. It might be concluded that the genetic identity index between these two breeds calculated on the basis of BF showed moderate level of genetic identity with the primers employed. MAPD calculated on the basis of uncommon bands also demonstrated lower to medium level of genetic difference between Bhadawari and Murrah breeds of buffalo.

• Asian-Australasian Journal of Animal Sciences
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• v.27 no.6
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• pp.898-906
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• 2014

The objective of this study was to investigate differences in the faecal microbial composition among Lantang, Bama, Erhualian, Meishan, Xiaomeishan, Duroc, Landrace, and Yorkshire sows and to explore the possible link of the pig breed with the gut microbial community. Among the sows, the Meishan, Landrace, Duroc, and Yorkshire sows were from the same breeding farm with the same feed. Fresh faeces were collected from three sows of each purebred breed for microbiota analysis and volatile fatty acid (VFA) determination. Denaturing gradient gel electrophoresis (DGGE) analysis revealed that samples from Bama, Erhualian, and Xiaomeishan sows, which from different farms, were generally grouped in one cluster, with similarity higher than 67.2%, and those from Duroc, Landrace, and Yorkshire sows were grouped in another cluster. Principal component analysis of the DGGE profile showed that samples from the foreign breeds and the samples from the Chinese indigenous breeds were scattered in two different groups, irrespective of the farm origin. Faecal VFA concentrations were significantly affected by the pig breed. The proportion of acetate was higher in the Bama sows than in the other breeds. The real-time PCR analysis showed that 16S rRNA gene copies of total bacteria, Firmicutes and Bacteroidetes were significantly higher in the Bama sows compared to Xiaomeishan and Duroc sows. Both Meishan and Erhualian sows had higher numbers of total bacteria, Firmicutes, Bacteroidetes and sulphate-reducing bacteria as compared to Duroc sows. The results suggest that the pig breed affects the composition of gut microbiota. The microbial composition is different with different breeds, especially between overseas breeds (lean type) and Chinese breeds (relatively obese type).

• Asian-Australasian Journal of Animal Sciences
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• v.17 no.3
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• pp.301-304
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• 2004

The polymorphism of insulin-like growth factor I (IGF I) in 6 chicken breeds (total n=515) was detected by PCR-Pst IRFLP, and allele A (621 bp) or allele B (364 and 257 bp) were observed. In these chicken breeds, it was found that exotic chicken carried high frequencies of allele B, while Chinese native chicken breeds carried high frequencies of allele A. Meanwhile the role of IGF I was investigated in 133 Ningdu Yellow chicken and 162 Wanzhai Yellow chicken. Five growth traits were recorded for analyzing the association between IGFI gene polymorphism and performance. In both the Ningdu and Wanzhai Yellow breeds, body weight at 4 months was significantly higher with BB genotype than with AA genotype (p<0.05). Furthermore, body weight at 2 months in the Wanzhai Yellow breeds was also higher with BB genotype than with AA genotype (p<0.05). There were no differences among the genotypes for the other traits studied. Based on these results, it is necessary to do more studies on IGFI before making the IGFI locus into the application of maker-assisted selection programms.