• Asian-Australasian Journal of Animal Sciences
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• 제24권8호
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• pp.1048-1052
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• 2011

The Chinese Holstein cattle breed, an introduced breed in China, has been crossbred with native cattle breeds. We hypothesised that the Chinese Holstein local population in Beijing share haplotypes with native Asian cattle breeds, the result of a sudden population expansion in the recent past. We also hypothesised that crossbreeding and population expansion left traces that shaped the genetic makeup of the breed. Evaluation of this was performed by mitochondrial DNA (mtDNA) sequence analysis of Chinese Holstein cattle from Beijing (n = 41) and a comparison of them with the published mtDNA sequences (n = 293) of 14 Asian breeds with an emphasis on Chinese native cattle breeds. Three shared common haplotypes between Chinese Holstein cattle and native Asian cattle were found. Moreover, a high level of haplotype diversity in Chinese Holstein cattle (h = 0.9557) and low nucleotide diversity (${\pi}$ = 0.0052) was found, indicating a past population bottleneck followed by rapid population growth. These findings are supported by the significantly negative deviation of Tajima's D (-1.82085), the star-like pattern of dominant haplotypes and the pairwise mismatch distribution analysis, which showed a unimodal pattern.

• Asian-Australasian Journal of Animal Sciences
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• 제21권11호
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• pp.1535-1543
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• 2008

Microsatellites (MS) are useful for quantifying genetic variation within and between populations and for describing the evolutionary relationships of closely related populations. The main objectives of this work were to estimate genetic parameters, measure genetic distances and reconstruct phylogenetic relationships between Australian Angora/Angora_Aus/ and Cashmere/Cashmere_Aus/ populations and three Mongolian Cashmere goat (Bayandelger/BD/, Zavkhan Buural/ZB/, and Gobi Gurvan Saikhan/GGS/) populations based on variation at fourteen MS loci. The level and pattern of observed and expected heterozygosity and polymorphic information content of the fourteen loci studied across the populations were quite similar and high. Except for SRCRSP07, all studied microsatellites were in Hardy-Weinberg Equilibrium (p<0.001). Moderate genetic variation (7.5%) was found between the five goat populations with 92.5% of total genetic variation attributable to diversity existing between the individuals within each population. The greatest Nei's genetic distances were found between the Angora and four Cashmere populations (0.201-0.276) and the lowest distances were between the Mongolian Cashmere goat populations (0.026-0.031). Compared with other Cashmere goat populations, the GGS (crossbred with Russian Don Goats) population had the smallest pairwise genetic distance from the Australian Angora population (0.192). According to a three-factorial correspondence analysis (CA), the three different Mongolian Cashmere populations could hardly be distinguished from each other.

• Journal of Animal Science and Technology
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• 제65권1호
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• pp.57-68
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• 2023

Flavor is an important sensory trait of chicken meat. The free amino acid (FAA) and nucleotide (NT) components of meat are major factors affecting meat flavor during the cooking process. As a genetic approach to improve meat flavor, we performed a genome-wide association study (GWAS) to identify the potential candidate genes related to the FAA and NT components of chicken breast meat. Measurements of FAA and NT components were recorded at the age of 10 weeks from 764 and 767 birds, respectively, using a White leghorn and Yeonsan ogye crossbred F2 chicken population. For genotyping, we used 60K Illumina single-nucleotide polymorphism (SNP) chips. We found a total of nine significant SNPs for five FAA traits (arginine, glycine, lysine, threonine content, and the essential FAAs and one NT trait (inosine content), and six significant genomic regions were identified, including three regions shared among the essential FAAs, arginine, and inosine content traits. A list of potential candidate genes in significant genomic regions was detected, including the KCNRG, KCNIP4, HOXA3, THSD7B, and MMUT genes. The essential FAAs had significant gene regions the same as arginine. The genes related to arginine content were involved in nitric oxide metabolism, while the inosine content was possibly affected by insulin activity. Moreover, the threonine content could be related to methylmalonyl-CoA mutase. The genes and SNPs identified in this study might be useful markers in chicken selection and breeding for chicken meat flavor.

• Journal of Animal Science and Technology
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• 제56권7호
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• pp.25.1-25.6
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• 2014

This study was carried out to investigate the association of POU1F1 (POU domain, class 1, transcription factor 1, Pit1, renamed as POU1F1) gene with backfat thickness (mm), carcass weight (kg), pH, and color values ($L^*$, $a^*$, $b^*$) in crossbred pigs (Landrace ${\times}$ Yorkshire ${\times}$ Duroc). Frequency of the AA genotype indel was at the highest level (66.67%). Frequency of A allele (0.81) was higher than that of b allele (0.19). This population followed Hardy-Weinberg equilibrium. Carcass weights and $a^*$ values of the three genotypes were all significantly different (p < 0.05), respectively. However, backfat thickness, $L^*$, $b^*$, visual color, and pH of the three genotypes were not significantly different (p > 0.05). Visual color was negatively correlated with $L^*$ (r = -0.521) and $b^*$ (r = -0.390) values, $L^*$ value was correlated with $b^*$ (r = 0.419) value, and $a^*$ value was positively correlated with $b^*$ (r = 0.612) value. These results indicate that the POU1F1 gene affected carcass weight and meat redness.

• Asian-Australasian Journal of Animal Sciences
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• 제32권12호
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• pp.1907-1913
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• 2019

Objective: Homoacetogens play important roles in the production of acetate in the large intestine of monogastric mammals. However, their diversity in the porcine large intestine is still unknown. Marker gene analysis was performed to assess the effects of energy level on the diversity and population densities of homoacetogens in porcine feces. Methods: Crossbred pigs were fed high or low energy-level diets. The high-intake (HI) diet was sufficient to allow a daily gain of 1.2 kg. The low-intake (LI) diet provided 0.6 times the amount of energy as the HI diet. Genetic diversity was analyzed using formyltetrahydrofolate synthetase gene (FHS) clone libraries derived from fecal DNA samples. FHS DNA copy numbers were quantified using real-time polymerase chain reaction. Results: A wide variety of FHS sequences was recovered from animals in both treatments. No differences in FHS clone libraries between the HI and LI groups were found. During the experimental period, no significant differences in the proportion of FHS copy numbers were observed between the two treatment groups. Conclusion: This is the first reported molecular diversity analysis using specific homoacetogen marker genes from the large intestines of pigs. There was no observable effect of feed intake on acetogen diversity.

• Asian-Australasian Journal of Animal Sciences
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• 제27권3호
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• pp.316-323
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• 2014

We previously identified quantitative trait loci (QTL) for body weight and average daily gain in a common region between ADL0198 (chr 1: 171.7 Mb) and ABR0287 (chr 1: 173.4 Mb) on chicken chromosome 1 in an $F_2$ resource population produced by crossing low- and high-growth lines of the Hinai-dori breed. Motilin receptor (MLNR) is a candidate gene affecting growth traits in the region. In this study, we genotyped polymorphisms of the MLNR gene and investigated its association with growth traits in a Hinai-dori $F_2$ intercross population. All the exons of the MLNR gene in the parental population were subjected to PCR amplification, nucleotide sequenced and haplotypes identified. To distinguish resultant diplotype individuals in the $F_2$ population, a mismatch amplification mutation assay was performed. Three haplotypes (Haplotypes 1-3) were accordingly identified. Six genotypes produced by the combination of three haplotypes (Haplotype 1, 2, and 3) were examined in order to identify associations between MLNR haplotypes and growth traits. The data showed that Haplotype 1 was superior to Haplotype 2 and 3 in body weight at 10 and 14 weeks of age, average daily gain between 4 and 10 weeks, 10 and 14 weeks, and 0 and 14 weeks of age in female in $F_2$ females. It was concluded that MLNR is a useful marker of growth traits and could be used to develop strategies for improving growth traits in the Hinai-dori breed.

• Asian-Australasian Journal of Animal Sciences
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• 제15권3호
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• pp.326-329
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• 2002

A population of exotic Holstein Friesian, Jersey, their crossbreds and the indigenous Murrah breed of buffalo bulls (n=486), used in artificial insemination breeding program were screened for the allelic distribution of the ${\kappa}$-casein and ${\beta}$-lactoglobulin genotypes. The preferred "B" allele frequency was highest in Murrah buffalo bulls followed by Jersey and Holstein Friesian. The increase in this particular allele frequency in the Holstein Friesian crossbred bulls was more when compared to their Jersey counterparts. Hardy-Weinberg's equilibrium was maintained albeit with some deviations, which was higher in crossbreds than in purebreds. The feasibility of using such large-scale molecular diagnostic tools in the field and their significance with regards to the dairy economy is discussed.

• Communications for Statistical Applications and Methods
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• 제14권3호
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• pp.541-549
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• 2007

Testing the sibling relationship becomes more important issue in many cases such as the reunion of dispersed family members whose parents have already passed away and the discrimination between pure-bred and crossbred dogs. Analysis of the sibling case is different from that of the paternity case. In this paper, we describe how to evaluate and determine the sibling relationship by comparing sibling pairs with unrelated pairs. We use the Korean population with 17 independent STR loci system to propose a discrimination rule.

• 한국가금학회지
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• 제39권4호
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• pp.311-315
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• 2012

The increasing demand for Korean native chicken meat indicates that the discovery of haplotypes is very important from both economic and conservation points of view. In this study, mtDNA D-loop sequences from two crossbred Korean native chicken populations of 138 individuals were investigated. Twenty six nucleotide substitutions were identified from sequence analysis and were classified into 12 haplotypes. The haplotype H_8 represents 73.47% of Woorimatdag (chicken population) sequences, which were identified in all five Woorimatdag chicken populations investigated. The H_7 haplotype (Dhap1) for D population covers 45% sequences, which indicate maternal inheritance from black Korean native chicken. On the other hand, Chap3 and Chap4 for C population are specific haplotypes, as H_5 and H_2, respectively. Based on the network profiles, six SNPs (C199T, A239G, G242A, A291G, T330C and C391A) of the D-loop region are effective markers for discrimination between Woorimatdag and Hanhyup chicken populations. Also, the phylogenetic analyses of Woorimatdag and Hanhyup chicken populations were used to identify the genetic relationships among the haplotypes. The results presented here can be used for developing molecular markers to discriminate between two commercial Korean native chickens.

• Asian-Australasian Journal of Animal Sciences
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• 제32권10호
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• pp.1491-1500
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• 2019

Objective: European pigs have been imported to improve the economically important traits of Thai pigs by crossbreeding and was finally completely replaced. Currently Thai indigenous pigs are particularly kept in a small population. Therefore, indigenous pigs risk losing their genetic diversity and identity. Thus, this study was conducted to perform large-scale genetic diversity and phylogenetic analyses on the many pig breeds available in Thailand. Methods: Genetic diversity and phylogenetics analyses of 222 pigs belonging to Thai native pigs (TNP), Thai wild boars (TWB), European commercial pigs, commercial crossbred pigs, and Chinese indigenous pigs were investigated by genotyping using 26 microsatellite markers. Results: The results showed that Thai pig populations had a high genetic diversity with mean total and effective ($N_e$) number of alleles of 14.59 and 3.71, respectively, and expected heterozygosity ($H_e$) across loci (0.710). The polymorphic information content per locus ranged between 0.651 and 0.914 leading to an average value above all loci of 0.789, and private alleles were found in six populations. The higher $H_e$ compared to observed heterozygosity ($H_o$) in TNP, TWB, and the commercial pigs indicated some inbreeding within a population. The Nei's genetic distance, mean $F_{ST}$ estimates, neighbour-joining tree of populations and individual, as well as multidimensional analysis indicated close genetic relationship between Thai indigenous pigs and some Chinese pigs, and they are distinctly different from European pigs. Conclusion: Our study reveals a close genetic relationship between TNP and Chinese pigs. The genetic introgression from European breeds is found in some TNP populations, and signs of genetic erosion are shown. Private alleles found in this study should be taken into consideration for the breeding program. The genetic information from this study will be a benefit for both conservation and utilization of Thai pig genetic resources.