• Asian-Australasian Journal of Animal Sciences
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• v.29 no.3
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• pp.321-326
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• 2016

The porcine major histocompatibility complex (MHC) is called swine leukocyte antigen (SLA), which controls immune responses and transplantation reactions. The SLA is mapped on pig chromosome 7 (SSC7) near the centromere. In this study, 3 class I (SLA-1, SLA-3, and SLA-2) and 3 class II (DRB1, DQB1, and DQA) genes were used for investigation of SLA haplotypes in Yucatan miniature pigs in Korea. This pig breed is a well-known model organism for biomedical research worldwide. The current study indicated that Korean Yucatan pig population had 3 Class I haplotypes (Lr-4.0, Lr-6.0, and Lr-25.0) and 3 class II haplotypes (Lr-0.5, Lr-0.7, and Lr-0.25). The combinations of SLA class I and II haplotype together, 2 homozygous (Lr-4.5/4.5 and Lr-6.7/6.7) and 3 heterozygous (Lr-4.5/6.7, Lr-4.5/25.25, and Lr-6.7/25.25) haplotypes were identified, including previously unidentified new heterozygous haplotypes (Lr-4.5/4.7). In addition, a new SLA allele typing method using Agilent 2100 bioanalyzer was developed that permitted more rapid identification of SLA haplotypes. These results will facilitate the breeding of SLA homozygous Yucatan pigs and will expedite the possible use of these pigs for the biomedical research, especially xenotransplantation research.

• Asian-Australasian Journal of Animal Sciences
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• v.25 no.2
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• pp.278-285
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• 2012

Poultry products are an important source of Salmonella enterica. An effective way to reduce food poisoning due to Salmonella would be to breed chickens more resistant to infection. Unfortunately host responses to Salmonella are complex with many factors involved. To learn more about responses to Salmonella in young chickens of 2 wk old, a cDNA Microarray containing 13,319 probes was performed to compare gene expression profiles between two chicken groups under control and Salmonella infected conditions. Newly hatched chickens were orally infected with S. enterica serovar Enteritidis. Since the intestine is one of the important barriers the bacteria encounter after oral inoculation, intestine gene expression was investigated at 2 wk old. There were 588 differentially expressed genes detected, of which 276 were known genes, and of the total number 266 were up-regulated and 322 were down-regulated. Differences in gene expression between the two chicken groups were found in control as well as Salmonella infected conditions indicating a difference in the intestine development between the two chicken groups which might be linked to the difference in Salmonella susceptibility. The differential expressions of 4 genes were confirmed by quantitative real-time PCR and the results indicated that the expression changes of these genes were generally consistent with the results of GeneChips. The findings in this study have lead to the identification of novel genes and possible cellular pathways, which are host dependent.

• Parasites, Hosts and Diseases
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• v.43 no.3 s.135
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• pp.75-92
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• 2005

Extensive previous studies on taxonomy, behavior/bionomics and control of Anopheles sinensis are reviewed and summarized. Recent molecular identification revealed that the population of An. sinensis complex includes An. sinensis, An. pullus, An. lesteri and at least two new species, and An. yatsushiroensis is synonmy of An. pullus. An. sinensis is the main vector specie of vivax malaria in Korea. Larvae of An. sinensis breed in wide range of habitats which are naturally-made clean water, stagnant or flowing; main habitats include rice fields, ditches, streams, irrigation cannals, marshes, ponds, ground pools, etc. Their host preferences are highly zoophilic. Human blood rate is very low ($0.7-1.7\%$); nevertheless An. sinensis readily feeds on man when domestic animals are not found near by. They feed on hosts throughout the night from dusk to dawn with a peak period of 02:00-04:00 hours; they are slightly more exophagic (biting outdoors); much larger numbers come into the room when light is on. Main resting places are outdoors such as grasses, vegetable fields and rice fields. A mark-release-recapture study resulted that $37.1\%$ was recaptured within 1 km, $29.4\%$ at 1-3 km, $21.1\%$ at 3-6 km, $10.3\%$ at 6-9 km and $2.1\%$ at 9-12 km distance. An. sinensis hibernate outdoors (mostly under part of dense grasses) during October-March. At the end of the hibernation period (March-April) they feed on cows at daytime. Until today any single measure to effectively control An. sinensis population has not been found. Indoor residual spray with a long-lasting insecticide can not reduce vector population densities, but shorten their life spans in some degree, so contributes to malaria control.

• Korean Journal of Agricultural Science
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• v.38 no.3
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• pp.465-471
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• 2011

The commercial Korean native chickens (WR_CC) was developed by crossing a few native chicken breeds in Korea. In order to investigate the breed identification markers, SNPs from TYR gene and MC1R gene, which are associated with skin and feather colors respectively, were initially identified. In case of 3 identified SNPs in the TYR gene, yellow shank color was identified in Loss, Harvard, AA, RIR and CC, which have the fixed SNPs in most of the animals. On the other hand, SNP variations were observed in KNC_RB, C_B, WR_CC and HH_CC, which have the black, yellow and mixed color with black and yellow shank colors. Also, the investigation of 3 SNPs in the MC1R gene indicated that there were associations between shank and feather colors in RIR, SF, KNC_B, C_B and RIR. However, these results are not consistent among breeds. These SNP type inconsistencies within breeds suggested that the selection was performed based on the phenotypes, which is not include the genotype information. Thus, selection based on genetic information is required in the future.

• Asian-Australasian Journal of Animal Sciences
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• v.26 no.5
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• pp.625-629
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• 2013

The melanocortin 1 receptor (MC1R) gene is related to the plumage color variations in chicken. Initially, the MC1R gene from 30 individuals was sequenced and nine polymorphisms were obtained. Of these, three and six single nucleotide polymorphisms (SNPs) were confirmed as synonymous and nonsynonymous mutations, respectively. Among these, three selected SNPs were genotyped using the restriction fragment length polymorphism (RFLP) method in 150 individuals from five chicken breeds, which identified the plumage color responding alleles. The neighbor-joining phylogenetic tree using MC1R gene sequences indicated three well-differentiated different plumage pigmentations (eumelanin, pheomelanin and albino). Also, the genotype analyses indicated that the TT, AA and GG genotypes corresponded to the eumelanin, pheomelanin and albino plumage pigmentations at nucleotide positions 69, 376 and 427, respectively. In contrast, high allele frequencies with T, A and G alleles corresponded to black, red/yellow and white plumage color in 69, 376 and 427 nucleotide positions, respectively. Also, amino acids changes at position Asn23Asn, Val126Ile and Thr143Ala were observed in melanin synthesis with identified possible alleles, respectively. In addition, high haplotype frequencies in TGA, CGG and CAA haplotypes were well discriminated based on the plumage pigmentation in chicken breeds. The results obtained in this study can be used for designing proper breeding and conservation strategies for the Korean native chicken breeds, as well as for the developing breed identification markers in chicken.

• Asian-Australasian Journal of Animal Sciences
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• v.10 no.1
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• pp.141-146
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• 1997

Postmortem examination was conducted on 350 (three hundred and fifty) chickens. Related samples (Liver, heart, ovary, spleen, bone-marrow, and caecal junction) were collected. The appropriate materials from the samples were cultured into different media. A total 40(forty) isolates of salmonella pullorum and S. gallinarum were identified and preserved. Characterization of the isolates were done by cultural, morphological, biochemical, and serological tests. Salmonella pullorum antigen was prepared from the local isolate, standardized and tested. This antigen was used in the field for the detection of pullorum or fowl typhoid infection or carrier birds. The antigen consisted of suspension of Salmonella pullorum in 0.50 percent sodium chloride plus 1.5 percent sodium sulfate and inactivated with 1% formalin U.S.P. and standardized with McFarland scale iv or by pour plate method containing 800 million organisms per milliliter and stained by the addition of alcoholic crystal violet. Sterility, safety and potency were tested and found as good as other international antigens. The antigen was found to retain its quality for six months when preserved at room temperatures. The test was made by mixing one drop of the antigen with a drop of blood or a drop of serum, on a glass plate or white tile. The locally produced antigen was as good as antigens from Japan, Hungary, Holland and India. A serological study was conducted with the locally prepared antigen in different farms, and the incidence was 0-4% in government farms, 5-10% in commercial imported breeds and 0-3% in cross breed local farms respectively.

• Journal of Crop Science and Biotechnology
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• v.10 no.3
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• pp.175-184
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• 2007

Two subspecies, japonica and indica, have been reported in rice, which differ in several ecotypic traits. However, reproductive barriers in hybrid progenies between subspecies have been major obstacles in breeding programs using inter-subspecific hybridization. As the first step to elucidate the reproductive barriers, we developed subspecies-specific(SS) STS markers in this study. A total of 765 STS primers were designed through comparing DNA sequences at every $2{\sim}3$cM interval between japonica and indica rices, which are available at Web DBs such as IRGSP, NCBI, TIGR, and GRAMENE, and tested for subspecies-specificity using 15 indica and 15 japonica varieties of diverse origin. Of them, 67 STS markers were identified as SS STS markers and their subspecies-specificity scores were estimated. The SS markers were dispersed throughout the genome along chromosomes. Of them, 64 SS markers were mapped on an RIL population derived from a Dasanbyeo(indica)/TR22183(japonica) cross. Genomic inclination of RILs was evaluated based on the genotyping with different types of markers. Association test between markers and segregation distortion revealed that segregation distortion might not be the cause of generating SS markers. The SS markers will be applicable to estimate the genomic inclination of varieties or lines and to study the differentiation of indica and japonica, and ultimately to breed true hybrid rice varieties in which desirable characters from both subspecies are recombined.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.12
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• pp.1816-1825
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• 2019

Objective: We tried to analyze allele-specific expression in the pig neocortex using bioinformatic analysis of high-throughput sequencing results from the parental genomes and offspring transcriptomes from reciprocal crosses between Korean Native and Landrace pigs. Methods: We carried out sequencing of parental genomes and offspring transcriptomes using next generation sequencing. We subsequently carried out genome scale identification of single nucleotide polymorphisms (SNPs) in two different ways using either individual genome mapping or joint genome mapping of the same breed parents that were used for the reciprocal crosses. Using parent-specific SNPs, allele-specifically expressed genes were analyzed. Results: Because of the low genome coverage (${\sim}4{\times}$) of the sequencing results, most SNPs were non-informative for parental lineage determination of the expressed alleles in the offspring and were thus excluded from our analysis. Consequently, 436 SNPs covering 336 genes were applicable to measure the imbalanced expression of paternal alleles in the offspring. By calculating the read ratios of parental alleles in the offspring, we identified seven genes showing allele-biased expression (p<0.05) including three previously reported and four newly identified genes in this study. Conclusion: The newly identified allele-specifically expressing genes in the neocortex of pigs should contribute to improving our knowledge on genomic imprinting in pigs. To our knowledge, this is the first study of allelic imbalance using high throughput analysis of both parental genomes and offspring transcriptomes of the reciprocal cross in outbred animals. Our study also showed the effect of the number of informative animals on the genome level investigation of allele-specific expression using RNA-seq analysis in livestock species.

• Journal of Animal Reproduction and Biotechnology
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• v.36 no.1
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• pp.35-44
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• 2021

A pregnancy diagnosis is an important standard for control of livestock's reproduction in paricular dairy cattle. High reproductive performance in dairy animals is a essential condition to realize of high life-time production. Pregnancy diagnosis is crucial to shortening the calving interval by enabling the farmer to identify open animals so as to treat or re-breed them at the earliest opportunity. MicroRNAs are short RNA molecules which are critically involved in regulating gene expression during both health and disease. This study is sought to establish the feasible of circulating miRNAs as biomarkers of early pregnancy in cattle. We applied Illumina small-RNA sequencing to profile miRNAs in plasma samples collected from 12 non-pregnant cows ("open" cows: samples were collected before insemination (non-pregnant state) and after pregnancy check at the indicated time points) on weeks 0, 4, 8, 12 and 16. Using small RNA sequencing we identified a total of 115 miRNAs that were differentially expressed weeks 16 relative to non-pregnancy ("open" cows). Weeks 8, 12 and 16 of pregnancy commonly showed a distinct increase in circulating levels of miR-221 and miR-320a. Through genome-wide analyses we have successfully profiled plasma miRNA populations associated with pregnancy in cattle. Their application in the field of reproductive biology has opened up opportunities for research communities to look for pregnancy biomarker molecules in dairy cattle.

• International Journal of Industrial Entomology and Biomaterials
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• v.47 no.1
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• pp.34-43
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• 2023

The eighteen (18) F₁ hybrid combinations were tested to identify potential combinations adaptable to type 1 climatic conditions in the Philippines. The six (6) bivoltine purelines (DMMMSU 108, DMMMSU 109, DMMMSU 110, DMMMSU 111, DMMMSU 113, and DMMMSU 119); and three (3) multivoltine purelines (DMMMSU 1000, DMMMSU 1007, and DMMMSU 1014), were crossed (multivoltine x bivoltine) in a mating plan. These were arranged in a Completely Randomized Design (CRD), replicated three times, and analyzed using Analysis of Variance (ANOVA). A test of significance was done using ANOVA across years and Tukey's Honest Significant Difference Test (HSD). The multiple trait evaluation index (EI) method was also used in the identification of potential F₁ hybrids. Three major phases were done: (1) parental rearing of multivoltine and bivoltine pure lines for breed multiplication; (2) hybridization process; and (3) evaluation of F₁ hybrids. Rearing evaluations were conducted for three consecutive years. Based from the three evaluations, 10 potential crosses were identified: DMMMSU MV-12, DMMMSU MV-11, DMMMSU MV-13, DMMMSU MV-16, DMMMSU MV-07, DMMMSU MV-14, DMMMSU MV-05, DMMMSU MV-09, DMMMSU MV-03, and DMMSU MV-10. The topmost combinations with the best economic and commercial characters and are consistently adaptable during two (2) cropping seasons were DMMMSU MV-07, DMMMSU MV-12, DMMMSU MV-05, DMMMSU MV-09 and DMMMSU MV-11. These newly-identified F₁ hybrids are considered potential breeds that could improve cocoon production.