Moon-Suck Ko

QTL analysis of white blood cell, platelet and red blood cell-related traits in an F2 intercross between Landrace and Korean native pigs

Haematological traits play important roles in disease resistance and defence functions. The objective of this study was to locate quantitative trait loci (QTL) and the associated positional candidate genes influencing haematological traits in an F(2) intercross between Landrace and Korean native pigs. Eight blood-related traits (six erythrocyte traits, one leucocyte trait and one platelet trait) were measured in 816 F(2) progeny. All experimental animals were genotyped with 173 informative microsatellite markers located throughout the pig genome. We report that nine chromosomes harboured QTL for the baseline blood parameters: genomic regions on SSC 1, 4, 5, 6, 8, 9, 11, 13 and 17. Eight of twenty identified QTL reached genome-wide significance. In addition, we evaluated the KIT locus, an obvious candidate gene locus affecting variation in blood-related traits. Using dense single nucleotide polymorphism marker data on SSC 8 and the marker-assisted association test, the strong association of the KIT locus with blood phenotypes was confirmed. In conclusion, our study identified both previously reported and novel QTL affecting baseline haematological parameters in pigs. Additionally, the positional candidate genes identified here could play an important role in elucidating the genetic architecture of haematological phenotype variation in swine and in humans.

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.

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.

Nutritional characteristics of horsemeat in comparison with those of beef and pork.

This study was conducted to determine the nutritional characteristics of horsemeat and bone meal in comparison with those of beef and pork presented by Dietary Reference Intakes For Koreans. Longissimus muscle and large metacarpal bone samples were collected from 20 fattened Jeju horses. Muscle samples were subjected to proximate analysis, assays for fatty acid profile and minerals, and bone samples to mineral assays. Horsemeat had similar levels of protein (21.1 vs 21.0 or 21.1%) and lower levels of fat (6.0 vs 14.1 or 16.1%) compared with beef or pork, respectively. Horsemeat had much higher levels of palmitoleic (8.2 vs 4.4 or 3.3%) and α-linolenic (1.4 vs 0.1 or 0.6%) acids than beef or pork, respectively. Linoleic acid was much higher in horsemeat (11.1%) and pork (10.1%) than in beef (1.6%). PUFA:SFA and n-6:n-3 ratios in horsemeat were 0.29 and 10.2, respectively. There were no big differences in mineral contents between horsemeat, beef and pork. For daily recommended mineral intakes of male adults (Dietary Reference Intakes For Koreans), phosphorus, sodium, potassium, iron, zinc and copper can be provided up to 24, 2.5, 6.7, 21, 26 and 40%, respectively, by 100 g raw horsemeat, but calcium and manganese levels are negligible. Horse cannon bone had much higher mineral contents especially in calcium (10,193 mg/100 g), phosphorus (5,874 mg/100 g) and copper (0.79 mg/100 g). Thiamin, riboflavin, niacin and retinol contents were 0.20, 0.21, 1.65 mg/100 g and 30 µg/100 g, respectively. But ascorbic acid and beta-carotene were not detected. Our data demonstrated that higher levels of palmitoleic and α-linolenic acid in horsemeat than in beef and pork may be beneficial for human health. Horsemeat and bone meal are a good source of some minerals and vitamins.

QTL analysis of body weight and carcass body length traits in an F2 intercross between Landrace and Korean native pigs

Growth traits, such as body weight and carcass body length, directly affect productivity and economic efficiency in the livestock industry. We performed a genome-wide linkage analysis to detect the quantitative trait loci (QTL) that affect body weight, growth curve parameters and carcass body length in an F2 intercross between Landrace and Korean native pigs. Eight phenotypes related to growth were measured in approximately 1000 F2 progeny. All experimental animals were subjected to genotypic analysis using 173 microsatellite markers located throughout the pig genome. The least squares regression approach was used to conduct the QTL analysis. For body weight traits, we mapped 16 genome-wide significant QTL on SSC1, 3, 5, 6, 8, 9 and 12 as well as 22 suggestive QTL on SSC2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16 and 17. On SSC12, we identified a major QTL affecting body weight at 140 days of age that accounted for 4.3% of the phenotypic variance, which was the highest test statistic (F-ratio = 45.6 under the additive model, nominal P = 2.4 × 10(-11) ) observed in this study. We also showed that there were significant QTL on SSC2, 5, 7, 8, 9 and 12 affecting carcass body length and growth curve parameters. Interestingly, the QTL on SSC2, 3, 5, 6, 8, 9, 10, 12 and 17 influencing the growth-related traits showed an obvious trend for co-localization. In conclusion, the identified QTL may play an important role in investigating the genetic structure underlying the phenotypic variation of growth in pigs.

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.

Whole-genome association study for the roan coat color in an intercrossed pig population between Landrace and Korean native pig

The roan coat color is characterized by white hairs intermingled with colored hairs. Candidate genes based on comparative phenotypes in horses and cattle involve the KIT and KIT ligand (MGF) genes. Here, we report the result of the whole genome scanning to detect genomic regions responsible for the roan coat color, using a three-generation pedigree of 62 pigs in an intercross between Landrace and Korean native pig. These pigs were genotyped using the PorcineSNP 60 BeadChip (Illumina, USA). The whole genome scan indicated that three genomic regions, 35∼36 Mb, 38∼39 Mb, and 58∼59 Mb on SSC8, were commonly and highly associated/linked with the roan phenotype in the case/control, sib-pair, and linkage test, respectively. The porcine KIT was selected as a candidate gene, because it is located in one of the three significant regions and its function is related to coat color formation. SNPs and Indels within coding sequence (CDS), promoter, and 3′-UTR of KIT were surveyed. Twenty-two SNPs in the CDS reported previously, as well as nine variations in promoter (2 SNPs) and 3′-UTR (5 SNPs and 2 Indels) were detected. Although no causative mutations were identified, these results will help to elucidate the genetic mechanisms involved in the expression of the roan phenotype and will aid in identifying key mutations responsible for the roan phenotype in further studies.

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