• Animal Bioscience
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• v.37 no.4
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• pp.622-630
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• 2024

Objective: Pig breeders cannot obtain phenotypic information at the time of selection for sow lifetime productivity (SLP). They would benefit from obtaining genetic information of candidate sows. Genomic data interpreted using deep learning (DL) techniques could contribute to the genetic improvement of SLP to maximize farm profitability because DL models capture nonlinear genetic effects such as dominance and epistasis more efficiently than conventional genomic prediction methods based on linear models. This study aimed to investigate the usefulness of DL for the genomic prediction of two SLP-related traits; lifetime number of litters (LNL) and lifetime pig production (LPP). Methods: Two bivariate DL models, convolutional neural network (CNN) and local convolutional neural network (LCNN), were compared with conventional bivariate linear models (i.e., genomic best linear unbiased prediction, Bayesian ridge regression, Bayes A, and Bayes B). Phenotype and pedigree data were collected from 40,011 sows that had husbandry records. Among these, 3,652 pigs were genotyped using the PorcineSNP60K BeadChip. Results: The best predictive correlation for LNL was obtained with CNN (0.28), followed by LCNN (0.26) and conventional linear models (approximately 0.21). For LPP, the best predictive correlation was also obtained with CNN (0.29), followed by LCNN (0.27) and conventional linear models (approximately 0.25). A similar trend was observed with the mean squared error of prediction for the SLP traits. Conclusion: This study provides an example of a CNN that can outperform against the linear model-based genomic prediction approaches when the nonlinear interaction components are important because LNL and LPP exhibited strong epistatic interaction components. Additionally, our results suggest that applying bivariate DL models could also contribute to the prediction accuracy by utilizing the genetic correlation between LNL and LPP.

• Korean Journal of Poultry Science
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• v.38 no.2
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• pp.81-87
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• 2011

The study was conducted to select and optimize microsatellite (MS) markers for evaluate Korean Native Chicken (KNC) breeds in order to provide standard for the classification and breed definition of the indigenous breeds. The study also aimed to characterize and classify each KNC populations for inventory and management of avian genetic resources. A total of 462 chickens from 11 populations of chicken breeds including eight KNC breeds and three commercial chicken breeds were analyzed with 19 MS markers. KNC breeds, especially Long-Tail Chicken breeds, formed separate cluster from those commercial chicken breeds. Genetic distances between KNC populations (0.11~0.18) were relatively shorter. Genetic uniformity of KNC (except KNCR breed) (0.86~0.88) were higher than that of commercial breeds (except Cornish) (0.95~0.97). On the other hand, genetic uniformity of KNC Long Tail (KNCLT) were relatively higher (0.91~0.97). The result can be used to evaluate and manage animal genetic resources at national scale.

• Food Science of Animal Resources
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• v.38 no.4
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• pp.653-663
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• 2018

Lamb has long been considered a traditional meal within Australia; however as consumer preferences have changed since the 1950's, consumption of lamb has decreased from the 1980's. This is the result of changing societal roles, particularly for females, decreasing household sizes and increasing awareness of the impact of food choices on human health. Since the 1980's improvement of farm practices and increases in genetic gains has addressed part of this decline by increasing the amount of lean meat and decreasing fat in lamb retail cuts. Yet, this has created a challenge for the industry to utilise the larger carcases now being produced. Thus, a whole value chain approach to increasing consumption has been undertaken through several research programs to create cuts which suit the modern consumer, examine nutritional and eating quality and increase adoption of value added cuts. Therefore, this paper outlines this history of changing consumer patterns and the consequent research to address these changes.

• Asian-Australasian Journal of Animal Sciences
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• v.28 no.9
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• pp.1244-1251
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• 2015

A herd of Berkshire pigs was established in 2003 and subjected to selection without introduction of any genetic resources until 2007. The complete pedigree, including 410 boars and 916 sows, as well as the records from 5,845 pigs and 822 litters were used to investigate the results obtained from the selections. The index of selection for breeding values included days to 90 kg (D90kg), backfat thickness (BF) and number of piglets born alive (NBA). The average inbreeding coefficients of pigs were found to be 0.023, 0.008, 0.013, 0.025, 0.026, and 0.005 from 2003 to 2007, respectively. The genetic gains per year were 12.1 g, -0.04 mm, -3.13 days, and 0.181 head for average daily gain (ADG), BF, D90kg, and NBA, respectively. Breeding values of ADG, BF and D90kg were not significantly correlated with inbreeding coefficients of individuals, except for NBA (-0.21). The response per additional 1% of inbreeding was 0.0278 head reduction in NBA. The annual increase of inbreeding was 0.23% and the annual decrease in NBA due to inbreeding was 0.0064 head. This magnitude could be disregarded when compared with the annual gain in NBA (0.181 head). These results suggest that inbreeding and inbreeding depression on ordinary farms can be controlled with a proper breeding scheme and that breeding programs are economical and safe relative to the risks associated with importation of pigs.

• Asian-Australasian Journal of Animal Sciences
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• v.22 no.4
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• pp.459-464
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• 2009

Data and pedigree information for Lori-Bakhtiari sheep used in this study were 6,239 records of lamb mortality from 246 sires and 1,721 dams, collected from 1989 through 2007 from a Lori-Bakhtiari flock at Shooli station in Shahrekord. The traits investigated were cumulative lamb mortality from birth up to 7 days, up to 14 days, up to 21 days, and up to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 and 12 months of age. The models included fixed factors that had significant effects and random direct genetic, maternal genetic and maternal permanent environmental effects. Variance components were estimated using the restricted maximum likelihood procedure applying three animal models with and without maternal and common environmental effects. The overall mean of cumulative lamb mortality rate was 22.95% from birth to 1 year of age, while the overall mortality rate up to 3 and from 3 to 6 months of age was 6.14% and 12.76%, respectively. The mortality rate after 6 months of age declined as the lambs grew older. The age of dam had no important effect on lamb mortality. The type of birth was more important during the preweaning period than at later ages, and lamb mortality rate was higher in twins. The year of birth, month of birth and sex of lamb significantly (p${\leq}$0.01) affected the cumulative lamb mortality rate at all ages. The least square mean of mortality during the final one-third of the lambing period was higher than the first and middle onethird of the lambing period. Male lambs were found to be at a higher risk of mortality than females. Birth weight of the lamb had a highly significant (p${\leq}$0.01) effect on lamb mortality at all ages as a quadratic regression. Direct and maternal heritability estimates of lamb mortality ranged from 0.01 to 0.13 and 0.01 to 0.05, respectively. Direct heritability increased with age of lamb, while maternal effects (genetic and common environmental) were important in the preweaning period. These results indicate that lamb mortality can be reduced first through farm management practices and secondly by genetic selection. Both animal and maternal effects should be considered in breeding programmes for reducing lamb mortality at preweaning.

• Asian-Australasian Journal of Animal Sciences
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• v.19 no.1
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• pp.7-12
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• 2006

The objective of this study was to estimate genetic parameters between first and later parities as different traits in reproductive traits of pigs using multiple trait animal model procedures. Data related to reproductive traits from a total of 2,371 individuals maintained at a farm were taken from the pedigree file. Sires and dams were consisted of Duroc, Landrace, and Yorkshire breeds, respectively. The first and later parity records were considered as different traits. Traits included in analyses were total pigs born (TB1), number of pigs born alive (NBA1), number of pigs weaned (NW1), and litter weaning weight (LWT1) in the first parity, and total pigs born (TB2), number of pigs born alive (NBA2), number of pigs weaned (NW2), litter weaning weight (LWT2) and interval between farrowing events (FTF) in later parities. Heritability estimates of TB1, NBA1, NW1 and LWT1 in the first parity were 0.27, 0.25, 0.16 and 0.20, respectively. For TB2, NBA2, NW2, LWT2 and FTF in later parities, heritabilities were estimated as 0.15, 0.15, 0.08, 0.11 and 0.07, respectively. Genetic correlations between sow reproductive traits in the first parity and in the second and later parity were estimated to be 0.89, 0.77, 0.58 and 0.66, respectively, between TB1 and TB2, NBA1 and NBA2, NW1 and NW2, and LWT1 and LWT2. While phenotypic correlations between TB1 and TB2, NBA1 and NBA2, NW1 and NW2, and LWT1 and LWT2 were estimated as 0.18, 0.15, 0.06 and 0.10, respectively. Genetic correlations between reproductive traits of first and later parities were not high indicating that reproductive traits for sows should be analyzed while considering the parities as different traits.

• Journal of Embryo Transfer
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• v.21 no.2
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• pp.147-156
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• 2006

The objective of this study was to supply excellent genetic resources to livestock farms by transferring embryos produced by genetically superior Korean cows (Hanwoo). Eighty Hanwoo donors were superovulated with gonadotropin ($Folltrpin^(R)\;or\;Antorin^(R)$) for 4 days combined with or without progesterone releasing intravaginal device (CIDR) insertion. The collected fresh or frozen-thawed embryos were transferred to 226 farm recipients. In this study, the effect of CIDR insertion in combination with gonadotropin ($Folltrpin^(R)$) treatments initiated at the random stage of estrous cycle on embryo production was evaluated and compared to conventional superovulation protocol. Moreover, the effect of gonadotropin ($Antorin^(R)$) dose in CIDR-treated Hanwoo donors on the embryo yield was determined. In addition, the effects of embryos (fresh vs. frozen-thawed), embryo transfer person, seasons and farms on the pregnancy rate were evaluated. In Hanwoo donors, CIDR insertion in combination with $Folltrpin^(R)$ treatments regardless of estrous detection resulted in increased numbers of total ova (6.5 vs. 5.8) and transferable embryos (3.9 vs. 3.2) compared to the conventional superovulation protocol (p<0.01). In CIDR-treated Hanwoo donors, the higher dose of $Antorin^(R)$ (36 vs. 28 mg) resulted in the increased number of transferable embryos (8.3 vs. 5.4, p<0.05). The embryos (fresh 43.9% vs. frozen-thawed 23.1%) and embryo transfer person (53.9 vs. $0{\sim}16.7%$) significantly affected the pregnancy rate after embryo transfer (p<0.01). These results suggest that CIDR-based superovulation protocol may be effectively used for production of superior Hanwoo embryos and, multiple ovulation and embryo transfer in Hanwoo might be effectively applied for livestock improvement if pregmancy rate with frozen-thawed embryos and embryo transfer skill would be improved.

• Journal of Embryo Transfer
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• v.21 no.4
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• pp.331-338
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• 2006

This survey was carried out to investigate the occurrence of reproductive disorders in Korean native cattle (Hanwoo). The general management status such as barn type, feed intake, parity and type of reproductive disorders were examined in the Hanwoo farms. In this survey, the total incidence of reproductive disorders that was assessed from 54 Hanwoo farms was 11.6% (73/ 631). We first examined the incidence of reproductive disorders following herd size per farm. The rates of reproductive disorders in under 10 heads, 10 to 20 heads and over 20 heads were 25.2%, 9.4% and 8.3%, respectively (P<0.05). The rate of reproductive disorders in tie stall barn was significantly (P<0.05) higher than that in free stall barn (14.9% vs. 8.1%). The major types of reproductive disorders were follicular cysts (21.8%), fat necrosis (21.8%), and repeat breeding (17.8%). The rate of reproductive disorders assessed by the parity tended to decrease as the parity increased. The relationship between incidence of reproductive disorders and body condition score (BCS) was investigated in 203 Hanwoo. The incidence of reproductive disorder was 80.0%, 8.8%, 9.4%, 10.0%, 33.3% and 57.1% at 1.5, 2.0, 2.5, 3.0, 3.5 and 4.0 of BCS, respectively. These data show that the increase of herd size, barn type and BCS affect the incidence of reproductive disorders such as follicular cysts, fat necrosis and repeat breeding in Hanwoo.

• Clinical and Experimental Vaccine Research
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• v.12 no.3
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• pp.179-192
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• 2023

The world has watched the emergence of numerous animal viruses that may threaten animal health which were added to the perpetual growing list of animal pathogens. This emergence drew the attention of the experts and animal health groups to the fact that it has become necessary to work on vaccine development. The current review aims to explore the perspective vaccines for emerging viral diseases in farm animals. This aim was fulfilled by focusing on modern technologies as well as next generation vaccines that have been introduced in the field of vaccines, either in clinical developments pending approval, or have already come to light and have been applied to animals with acceptable results such as viral-vectored vaccines, virus-like particles, and messenger RNA-based platforms. Besides, it shed the light on the importance of differentiation of infected from vaccinated animals technology in eradication programs of emerging viral diseases. The new science of nanomaterials was explored to elucidate its role in vaccinology. Finally, the role of Bioinformatics or Vaccinomics and its assist in vaccine designing and developments were discussed. The reviewing of the published manuscripts concluded that the use of conventional vaccines is considered an out-of-date approach in eliminating emerging diseases. However, these types of vaccines are considered the suitable plan especially in countries with few resources and capabilities. Piloted vaccines that rely on genetic-based technologies with continuous analyses of current viruses should be the aim of future vaccinology. Smart genomics of emerging viruses will be the gateway to choosing appropriate vaccines, regardless of the evolutionary rates of viruses.

• Food Science of Animal Resources
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• v.28 no.1
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• pp.1-8
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• 2008

More safe and natural food was recently needed by consumers. Antimicrobials including sodium azide, penicillin, and vancomycin were used for therapeutic agents against pathogens such as Listeria monocytogenes, Staphylococcus aureus, Escherichia coli O157:H7 in dairy and meat industry. These antimicrobials and preservatives were prohibited in stock farm and food because they were caused resistant strain and side effects. Bacteriocins are proteinaceous compounds that may present antimicrobial activity towards important food-borne pathogens and spoilage-related microflora. Therefore, bacteriocins were reported as an alternative of antimicrobials. Due to these properties, bacteriocin-producing strains or purified bacteriocins have a great potential of use in biologically based food preservation systems. Despite the growing number of articles regarding on the isolation of bacteriocinogenic strains, genetic determinants for production, purification and biochemical characterization of these inhibitory substances, there are only limited reports of successful application of bacteriocins to dairy and meats. This review describes bacteriocins related to dairy and meat products for the further use.