Sung-Soo Lee

Phylogenetic Relationships of Northeast Asian Cattle to Other Cattle Populations Determined Using Mitochondrial DNA D-Loop Sequence Polymorphism

Phylogenetic relationships of Northeast Asian cattle to various other cattle breeds including Bos taurus, Bos indicus, and Bison bison were assessed using mtDNA D-loop sequences. A neighbor-joining tree was constructed using sequences determined for 4 Cheju Black, 4 Cheju Yellow, 4 Korean Yellow cattle (Bos taurus), and 2 American Brahman cattle (Bos indicus), and also published sequences for 31 Japanese Black cattle, 45 European breed cattle, 6 African zebus, 2 African taurines, and 6 Indian zebus. Five American bisons (Bison bison) were used as an outgroup. The neighbor-joining tree showed that American bisons and Indian zebus are clearly separate from other cattle breeds, respectively, and African cattle clustered together, although with a low bootstrap probability (<50%). Results indicate that cattle in Northeast Asia, Europe, and Africa are closely related to each other–suggesting their recent divergence, but are separate from Indian zebus.

Length difference between equine ZFX and ZFY genes and its application for molecular sex determination

PurposeWe analyzed the sex chromosome-encoding ZFX-ZFY genes and tested molecular sexing using the amplification patterns of intron 9 of ZFX-ZFY in the horse.Methods and resultsThe amplification of the ZFX-ZFY produced two distinct patterns, reflecting sexual dimorphism based on a length difference between the X and Y chromosomes. The amplification products from foals showed two distinct bands: one was common to all foals and mares, indicating that this band was amplified from ZFX, while the other was specific to some foals, indicating that it was from ZFY. The result based on the PCR assay was identical to the results of amplification of the Y chromosome-specific SRY gene and those of investigations of the phenotypic gender in three different horse populations.ConclusionWe suggest that this PCR strategy for determining sexes by comparing the amplification patterns of ZFX-ZFY genes is a convenient and precise method for discriminating sexes in horses.

Discrimination of Korean Native Chicken Lines Using Fifteen Selected Microsatellite Markers

In order to evaluate the genetic diversity and discrimination among five Korean native chicken lines, a total of 86 individuals were genotyped using 150 microsatellite (MS) markers, and 15 highly polymorphic MS markers were selected. Based on the highest value of the number of alleles, the expected heterozygosity (He) and polymorphic information content (PIC) for the selected markers ranged from 6 to 12, 0.466 to 0.852, 0.709 to 0.882 and 0.648 to 0.865, respectively. Using these markers, the calculated genetic distance (Fst), the heterozygote deficit among chicken lines (Fit) and the heterozygote deficit within chicken line (Fis) values ranged from 0.0309 to 0.2473, 0.0013 to 0.4513 and −0.1002 to 0.271, respectively. The expected probability of identity values in random individuals (PI), random half-sib (PIhalf-sibs) and random sibs (PIsibs) were estimated at 7.98×10−29, 2.88×10−20 and 1.25×10−08, respectively, indicating that these markers can be used for traceability systems in Korean native chickens. The unrooted phylogenetic neighbor-joining (NJ) tree was constructed using 15 MS markers that clearly differentiated among the five native chicken lines. Also, the structure was estimated by the individual clustering with the K value of 5. The selected 15 MS markers were found to be useful for the conservation, breeding plan, and traceability system in Korean native chickens.

The robust phylogeny of Korean wild boar (Sus scrofa coreanus) using partial D-loop sequence of mtDNA.

In order to elucidate the precise phylogenetic relationships of Korean wild boar (Sus scrofa coreanus), a partial mtDNA D-loop region (1,274 bp, NC_000845 nucleotide positions 16576-1236) was sequenced among 56 Korean wild boars. In total, 25 haplotypes were identified and classified into four distinct subgroups (K1 to K4) based on Bayesian phylogenetic analysis using Markov chain Monte Carlo methods. An extended analysis, adding 139 wild boars sampled worldwide, confirmed that Korean wild boars clearly belong to the Asian wild boar cluster. Unexpectedly, the Myanmarese/Thai wild boar population was detected on the same branch as Korean wild boar subgroups K3 and K4. A parsimonious median-joining network analysis including all Asian wild boar haplotypes again revealed four maternal lineages of Korean wild boars, which corresponded to the four Korean wild boar subgroups identified previously. In an additional analysis, we supplemented the Asian wild boar network with 34 Korean and Chinese domestic pig haplotypes. We found only one haplotype, C31, that was shared by Chinese wild, Chinese domestic and Korean domestic pigs. In contrast to our expectation that Korean wild boars contributed to the gene pool of Korean native pigs, these data clearly suggest that Korean native pigs would be introduced from China after domestication from Chinese wild boars.

AGHR polymorphism and its associations with carcass traits in Harrwoo cattle

The growth hormone receptor (GHR) is a membrane transmitter for the growth hormone signal transduction pathway that regulates various metabolic activities, including cell growth and expressions of cytokine genes. The presence or absence of a genetic polymorphism for the LINE-1 retroposon in the PI promoter, which specifically regulates theGHR gene expression in the liver, was screened by a novel detection method and examined for its relationships with carcass traits in Hanwoo cattle. Han woo cattle had taurine type LINE-1 present (alleleI) as well as incidine type LINE-1 absent (alleleA) promoter sequences. Three genotypes,I/I, I/A andA/A, showed frequencies of 49.1, 36.7 and 14.2%, respectively. The effects of allele A were significant on mean differences for final weight, eye muscle area, marbling score and fat color (p<0.05), but not for carcass weight, backfat thickness, final meat quality grade or meat color (p>0.05). Most 30-month old Hanwoo steers bearing the LINE-1 absent promoter had whiter fat color, heavier live weight and higher marbling score, reflecting intramuscular fat deposition inM. longissimus dorsi, compared to animals bearing a LINE-1 present promoter. This suggests that aGHR polymorphism could be a potential genetic marker for improving beef production of Hanwoo cattle.

Establishment of a resource population of SLA haplotype-defined Korean native pigs.

The highly polymorphic porcine major histocompatibility complex (MHC), or the swine leukocyte antigens (SLA), has been repeatedly associated with variations in swine immune response to pathogens and vaccines as well as with production traits. The SLA antigens are also important targets for immunological recognition of foreign tissue grafts. We recently established a resource population of Korean native pigs as models for human transplantation and xenotransplantation research. In this study, 115 animals derived from three generations of the Korean native pigs were genotyped for three SLA class I (SLA-2, SLA-3 and SLA-1) and three SLA class II loci (DRB1, DQB1, DQA) using PCR with sequence-specific primers (PCR-SSP) at the allele group resolution. A total of seven SLA haplotypes (Lr-5.34, Lr-7.23, Lr-31.13, Lr-56.23, Lr-56.30, Lr-59.1, Lr-65.34), comprising six unique class I and five unique class II haplotypes, were characterized in the founding animals. Class I haplotype Lr-65.0 and class II haplotype Lr-0.34 were novel; and together with Lr-56.0 these haplotypes appeared to be breed-specific. In the progeny population, Lr-7.23 and Lr-56.30 appeared to be the most prevalent haplotypes with frequencies of 34.7% and 31.6%, respectively; the overall homozygosity was 27.4%. This resource population of SLA-defined Korean native pigs will be useful as large animal models for various transplantation and xenotransplantation experiments, as well as for dissecting the roles of SLA proteins in swine disease resistance and production traits.

Coat Color Patterns and Genotypes of Extension and Agouti in Hanwoo and Jeju Black Cattle

To understand the relationship between coat color inheritance patterns and genotypes of Extension( E) and Agouti( A) loci in cattle, the genotypes for melanocortin-1 receptor( MC1R) and agouti signaling protein ( ASIP) were analyzed in Hanwoo, Jeju black cattle (JBC), and their crossbred progeny. Three MC1R alleles ( E D , E?, and e) were found in the black-colored JBC population. JBC had no recessive homoygotes (e/e), but this genotype was predominant in the Hanwoo breed. However, MC1R E?/eHanwoo did not produce a black coat color as they appeared either as brown or solid red. For ASIP, three genotypes ( A/A, A/A Br , and A Br /A Br ) were determined by insertion/deletion of an L1-BT element in Hanwoo. The ASIP A Br allele was rarely observed, and no ASIP A Br /A Br homozygotes were detected in the JBC population. Cattle carrying ASIP ABr did not show any agouti-like brindle pigmentation patterns in either breed or their progeny. The coat colors of the crossbred progeny were discriminated by two colors, yellowish-brown versus dark-brown or black, and their coat colors were directly related to the genotypes of the Extensionlocus, yellowish-brown (e/e) and dark-brown or black (E?/e), but not to the Agouti locus. ASIP genotypes probably did not affect coat color development in the Hanwoo or crossbred progeny. Our results suggest that the ASIP genotypes do not play key roles in coat color variation, but the MC1R genotypes do direct the phenotypes of Hanwoo, JBC, and their progeny.

Effects of ADCYP1R1, FABP3, FABP4, MC4R, MYL2 Genotypes on Growth Traits in F 2 Population Between Landrace and Jeju Native Black Pig

Genetic polymorphisms was investigated at five single nucleotide polymorphisms (SNP) sites in four porcine genes (ADCYAP1R1, FABP3, MC4R, and MYL2) and analyzed their statistical association with growth traits in F2 reciprocal-crossbred population between Landrace and Jeju native black pig (JNP). All populations, JNP, Landrace and their F2 were polymorphic for all five SNP loci tested, however, the homozygote T/T of FABP3 g.-158T>C and the homozygote G/G of ADCYAP1R1 intron 2 337A>G were not found in JNP and Landrace, respectively. The genotypes of ADCYAP1R1 were significantly associated with body weights (BW) at 3 weeks and at 20 weeks (P G were associated with body weights during late growth period such as, BW20 and LADG (P<0.01). Those of MC4R were also significantly associated with BW10 suggesting by the difference of early average daily gain (EADG) (P<0.05), and with LADG (P<0.01). The body length of F2 animals was affected by the genotypes of ADCYAP1R1, MC4R, and MYL2 (P<0.05), respectively. Among these, MC4R A/A homozygotes showed over 3 cm longer in body length than those of other genotypes. As the useful basic information, these results suggested that SNP markers showing statistical association with growth traits and the results help to select the sires of JNP for improving the productivity in JNP-related crossbreeding system in pig

QTL analysis of clinical-chemical traits in an F2 intercross between Landrace and Korean native pigs

Clinical-chemical traits are essential when examining the health status of individuals. The aim of this study was to identify quantitative trait loci (QTL) and the associated positional candidate genes affecting clinical-chemical traits in a reciprocal F(2) intercross between Landrace and Korean native pigs. Following an overnight fast, 25 serum phenotypes related to clinical-chemical traits (e.g., hepatic function parameters, renal function parameters, electrolyte, lipids) were measured in >970 F(2) progeny. All experimental samples were subjected to genotyping analysis using 165 microsatellite markers located across the genome. We identified eleven genome-wide significant QTL in six chromosomal regions (SSC 2, 7, 8, 13, 14, and 15) and 59 suggestive QTL in 17 chromosomal regions (SSC 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, and 18). We also observed significant effects of reciprocal crosses on some of the traits, which would seem to result from maternal effect, QTL on sex chromosomes, imprinted genes, or genetic difference in mitochondrial DNA. The role of genomic imprinting in clinical-chemical traits also was investigated. Genome-wide analysis revealed a significant evidence for an imprinted QTL in SSC4 affecting serum amylase levels. Additionally, a series of bivariate linkage analysis provided strong evidence that QTL in SSC 2, 13, 15, and 18 have a pleiotropic effect on clinical-chemical traits. In conclusion, our study detected both novel and previously reported QTL influencing clinical-chemical traits in pigs. The identified QTL together with the positional candidate genes identified here could play an important role in elucidating the genetic structure of clinical-chemical phenotype variation in humans and swine.

Relationship between Monounsaturated Fatty Acid Composition and Stearoyl-CoA Desaturase mRNA Level in Hanwoo Liver and Loin Muscle

The Stearoyl-CoA Desaturase(SCD) is a key enzyme, which converting palmitic acid(16:0) and stearic acid (18:0) to pahnitoleic acid(16:1) and oleic acid(l8:1), respectively. The concentration of oleic acid(18:1) in meat of beef cattle could influence both palatability and perception of meat. This experiment has conducted to determine relationship between the compositions of monounsaturated fatty acids and the SCD mRNA level in bovine liver and loin muscle tissue. The compositions of palmitoleic acid(16:1) and oleic acid(18:1) in loin muscle were 5% and 46% of total lipid and in liver were 2% and 20% of total lipid, respectively. On the other hand, the compositions of palmitic acid(16:0) and stearic acid(18:0) in loin muscle were 25% and 45% of total lipid and in liver were 14% and 43% of total lipid, respectively. The ratio of monounsaturated to saturated fatty acids(the desaturation index) was used as a measure of SCD activity in tissues. The average desaturation index in loin muscle was higher about 3.6-fold than that in liver. The desaturation index of oleate/stearate and palmitoleatelpalmitate in loin muscle were higher 8-fold and 1.8-fold than those in liver, respectively, showing that the substrate specificity of SCD enzyme was very different between liver and muscle tissues. To determine whether the composition of monounsaturated fatty acids in liver and muscle are dependent on SCD expression, SCD mRNA level was examined by RT-PCR analysis. The SCD mRNA level in loin muscle was higher about 3-fold than that in liver. Thus, the quantitative relationship between the desaturation index of fatty acid and SCD mRNA was observed in liver and muscle. The difference in the compositions of monounsaturated fatty acids between bovine liver and muscle tissues may be due to different level of Stearoyl-CoA Desaturase mRNA.