J. H. Lee

Investigation of Coat Color Candidate Genes in Korean Cattle(Hanwoo)

본 연구는 한우의 모색발현에 정확히 어떤 유전자가 어떤 유전기작에 의해 관여하고 있는가를 규명하고자 황갈색의 모색을 지닌 한우와 검정모색을 지닌 홀스타인과의 교배를 통해 만든 F2집단의 DNA를 이용하여, MC1R, ASIP 및 TYRP1 유전자형과 한우모색 발현양상을 연관분석 하였으며, 또 한우 집단내에서의 이들 유전자형 빈도를 조사하여 황갈색 한우모색 다양성과 후보유전자 변이의 연관성연구에 필요한 정보를 제공하고자 하였다. MC1R 유전자의 경우 황갈색을 지닌 3두의 유전자형은 모두 e/e 형으로 밝혀졌으며, 검정모색을 지니고 태어난 나머지 3두의 두 좌위에서의 유전자형은 ED/e임을 확인하였는데 황갈색과 검정모색의 비율이 1:1로 나온다는 것은 MC1R 단일유전자가 한우의 모색에 중요한 영향을 미치는 것으로 사료된다. MC1R 이외의 모색발현에 영향을 줄 수 있는 ASIP와 TYRP1 유전자들은 F2 집단에서 염기서열을 분석한 결과 이들 유전자들이 한우 황갈색모색에 주된 영향을 미치지 않는 것으로 나타났다. 하지만 TYRP1 유전자에서 발견된 329번 (Glu329Lys) 아미노산 변이는 TYRP1 단백질의 구조와 화학적 성질에 영향을 줄 수 있는 것으로 사료되어 한우집단에서 황갈색바탕의 모색변이에 영향을 줄 수 있는지에 대한 추가적인 연구가 이루어져야 할 것이다. 【Most cattle breeds have a coat color pattern that is characteristic for the breed. Korean cattle(Hanwoo) has a coat color ranging from yellowish brown to dark brown including a red coat color. Variation in the Hanwoo coat color is likely to be the effects of modified genes segregating within the Hanwoo breed. MC1R encoded by the Extension(E) locus was almost fixed with recessive red e allele in the Hanwoo, but other gene(s) might be affecting the variation of the Hanwoo coat color into yellowish to red brown. We have analyzed a segregation of coat color in the F2 families generated from two Hanwoo bulls(yellowish brown) mated to six F1 dams(black) derived from Hanwoo and Holstein crosses. Segregation of coat color in the offspring found a ratio of 1(yellowish brown) : 1(black) and this ratio indicates that a single gene may play a major role for the Hanwoo coat color. We further investigated SNPs in MC1R, ASIP and TYRP1 loci to determine genetic cause of the Hanwoo coat color. Several polymorphisms within ASIP intron 2 and TYRP1 exons were found but not conserved within the Hanwoo population. However, the segregation of the MC1R e allele was completely associated with the Hanwoo coat color. Based on this information, it is clear that the MC1R e allele is mainly responsible for the yellowish red Hanwoo coat color. Further study is warrant to identify possible genetic interaction between MC1R e allele and other coat color related gene(s) for the variation of Hanwoo coat color from yellowish brown to dark brown. (Key words : Hanwoo, Coat color, SNP, MC1R, ASIP, TYRP1)】

Meta-analysis of factors affecting milk component yields in dairy cattle

The objectives of this study were thus to identify most significant factors that determine milk component yield (MCY) using a meta-analysis and, if possible, to develop equations to predict MCY using variables that can be easily measured in the field. A literature database was constructed based on the research articles published in the Journal of Dairy Science from Oct., 2007 till May, 2010. The database consisted of a total of 442 observed means for MCY from 118 studies. The candidate factors that determine MCY were those which can be routinely measured in the field (e.g. DMI, BW, dietary forage content, chemical composition of diets). Using a simple linear regression, the best equations for predicting milk fat yield(MFY) and milk protein yield (MPY) were MFYu2009=u20090.351 (±0.068)u2009+u20090.038 (±0.003) DMI (R2u2009=u20090.27), and MPYu2009=u20090.552 (±0.071)u2009+u20090.031 (±0.002) DMI - 0.004 (±0.001) FpDM (%, forage as a percentage of dietary DM) (R2u2009=u20090.38), respectively. The best equation for predicting milk fat content (%) explained only 12% of variations in milk fat content, and none of a single variable can explain more than 5% of variations in milk protein content. We concluded that among the tested variables, DMI was the only significant factor that affects MFY and both DMI and FpDM significantly affect MPY. However, predictability of linear equations was relatively low. Further studies are needed to identify other variables that can predict milk component yield more accurately.

Novel alternative splicing by exon skipping in KIT associated with whole-body roan in an intercrossed population of Landrace and Korean Native pigs

The KIT locus has been suggested to be a strong candidate region linked with whole-body roan in the F(2) population produced by intercrosses between Landrace and Korean Native pigs. In this manuscript, we report the finding of a novel alternative splicing event in the porcine KIT gene that results in the skipping of exon 5 in the I(Rn) allele. KIT mRNAs that lack exon 5 were identified in the large intestine and skin, suggesting that the mechanism responsible for the skipping of exon 5 may be tissue specific. A U(26) repeat in intron 5 showed complete linkage (LOD = 11.8) with the roan phenotype and absolute association with the black phenotype of the Korean Native pig (KNP) population samples, inferring that the repeat pattern may alter the complementary base-pairing-mediated looping-out of introns 4 and 5, which may mediate the exon 5-skipping event. Although the sample size in our study was relatively small, we speculate that the R3 allele containing the U(26) repeat is a causative element for the roan phenotype via alternative control of the exon skipping in our roan pedigree.

Quantitative trait loci and candidate genes for the economic traits in meat-type chicken

Recent progress has been achieved in the identification of quantitative trait loci (QTLs) and candidate genes, and they have been found to be very important for the production of chickens with more desirable meat characteristics. The major economic traits of chicken meat production were divided into two major categories, namely growth and carcass condition. In this paper, the QTL locations and candidate genes for the above mentioned traits are reviewed. The results presented here will provide guidelines for the selection of high quality and highly productive chickens through the marker assisted selection (MAS), which should be extensively used by poultry breeders and companies.

Effect of vaccination against foot-and-mouth disease on growth performance of Korean native goat (Capra hircus coreanae).

The objectives of this study were 1) to evaluate the effects of vaccination against foot-and-mouth disease (FMD) on growth performance, nutrient digestibility, hematological parameters, and behavior in a ruminant animal and 2) to investigate a possible strategy for reducing its adverse effect. A total of 12 Korean native goats (Capra hircus coreanae; 19.8 ± 2.9 kg) were used in a crossover design with 3 experimental periods and 3 treatments, randomized and balanced for counteracting possible carry-over effects. The treatments were 1) control, 2) co-injection with a commercially available dipyrone (CADI), and 3) supplementation with γ-amino butyric acid (GABA) at 10 g/kg in concentrate mix. Each period lasted 4 wk, and the vaccination against FMD was performed at 2 wk after the start of each period. The goats were individually housed in a metabolic cage and fed ad libitum with a diet consisting of bermuda grass and commercial concentrate mix (6:4, wt/wt). Dry matter intake, ADG, nutrients digestibility, hematological parameters, and behavioral activities of the goats were measured before and after vaccination. Although DMI was not decreased (P > 0.05), ADG was decreased by the vaccination to the goats (P < 0.01). The total number of leukocytes was increased while that of erythrocytes was decreased by the FMD vaccination (P < 0.01). The vaccination shortened standing time while extended lying time and the time spent in drinking (P < 0.05). The treatment by CADI reduced the adverse effect of vaccination on ADG and goat behavior compared with control and GABA treatment (P < 0.05). We concluded that the FMD vaccination decreased ADG of the goats without depression of diet intake, and CADI may attenuate the adverse effect of the FMD vaccination.

The breeding history and commercial development of the Korean native chicken

The Korean native chicken (KNC) is believed to have existed in the Korean Peninsula more than 1,400 years ago. Since then, KNC have been bred only by private farmers in rural areas of Korea. In 1994, a KNC conservation program was established by the Korean government and, as a result, five lines were restored. KNC are considered to have a unique taste and texture that is more attractive to Korean consumers than meat from commercial broilers. However, the price of KNC is relatively high, which is mainly due to the breeds low growth rate, hence the limitations for industrial applications. In addition, their unique taste and texture in comparison with that of other broilers has been evaluated by scientists over the past few years. The general composition, physiochemical traits, content of taste-active and endogenous bioactive compounds and sensory quality of KNC meat, as well as breeding history are reviewed in this paper. The information from this review can be used for the development of commercial KNC breeds and can be applied to models for the commercialisation of native chicken breeds in developing countries.

Genome-wide linkage disequilibrium and past effective population size in three Korean cattle breeds.

The routine collection and use of genomic data are useful for effectively managing breeding programs for endangered populations. Linkage disequilibrium (LD) using high-density DNA markers has been widely used to determine population structures and predict the genomic regions that are associated with economic traits in beef cattle. The extent of LD also provides information about historical events, including past effective population size (Ne ), and it allows inferences on the genetic diversity of breeds. The objective of this study was to estimate the LD and Ne in three Korean cattle breeds that are genetically similar but have different coat colors (Brown, Brindle and Jeju Black Hanwoo). Brindle and Jeju Black are endangered breeds with small populations, whereas Brown Hanwoo is the main breeding population in Korea. DNA samples from these cattle breeds were genotyped using the Illumina BovineSNP50 Bead Chip. We examined 13 cattle breeds, including European taurines, African taurines and indicines, and hybrids to compare their LD values. Brown Hanwoo consistently had the lowest mean LD compared to Jeju Black, Brindle and the other 13 cattle breeds (0.13, 0.19, 0.21 and 0.15-0.22 respectively). The high LD values of Brindle and Jeju Black contributed to small Ne values (53 and 60 respectively), which were distinct from that of Brown Hanwoo (531) for 11 generations ago. The differences in LD and Ne for each breed reflect the breeding strategy applied. The Ne for these endangered cattle breeds remain low; thus, effort is needed to bring them back to a sustainable tract.

Genetic Diversity and Phylogenetic Analysis of South-East Asian Duck Populations Based on the mtDNA D-loop Sequences

The maternally inherited mitochondrial DNA (mtDNA) D–loop region is widely used for exploring genetic relationships and for investigating the origin of various animal species. Currently, domestic ducks play an important role in animal protein supply. In this study, partial mtDNA D–loop sequences were obtained from 145 samples belonging to six South-East Asian duck populations and commercial duck population. All these populations were closely related to the mallard duck (Anas platyrhynchos), as indicated by their mean overall genetic distance. Sixteen nucleotide substitutions were identified in sequence analyses allowing the distinction of 28 haplotypes. Around 42.76% of the duck sequences were classified as Hap_02, which completely matched with Anas platyrhynchos duck species. The neighbor-joining phylogenetic tree also revealed that South-East Asian duck populations were closely related to Anas platyrhynchos. Network profiles were also traced using the 28 haplotypes. Overall, results showed that those duck populations D-loop haplotypes were shared between several duck breeds from Korea and Bangladesh sub continental regions. Therefore, these results confirmed that South-East Asian domestic duck populations have been domesticated from Anas platyrhynchos duck as the maternal origins.

Sequence-based characterization of five SLA loci in Asian wild boars.

Two swine leucocyte antigen (SLA) class I (SLA‐1 and SLA‐2) and three class II (DRB1, DQB1 and DQA) genes were investigated for their diversity in Asian wild boars using a sequence‐based typing method. A total of 15 alleles were detected at these loci, with eleven being novel. The findings provide one of the first glimpses of the SLA allelic diversity and architecture in the wild boar populations.

An allelic ladder for eleven short tandem repeat loci for use in the cattle identity test

Comments: The set of 15 STR markers is suitable for parentage testing of Arabian horses but some markers show very low PE values. Because of problems in genotyping, HMS3, included in the kit, should be interpreted with caution. The minimum standard set of core loci recommended by the Horse Genetic Committee of ISAG (http://www.isag.org.uk/. Accessed: September 15, 2008) should be extended by additional markers, because 9 STR loci are not always enough to determine parentage. For human parentage testing, the minimum PI and POP are required for all inclusion cases (Morling et al. 2002). Similarly, the final interpretation for horse parentage verification should also take the PI and POP values into consideration to avoid false inclusions. The first set of guidelines has already been published (Budowle et al. 2005). The minimum value of the POP for an inclusion should be discussed, and if we cannot achieve the appropriate level of certainty, additional markers should be tested to support a decision for such an inclusion.