Hong-Sik Kong

Whole transcriptome analyses of six thoroughbred horses before and after exercise using RNA-Seq.

BackgroundThoroughbred horses are the most expensive domestic animals, and their running ability and knowledge about their muscle-related diseases are important in animal genetics. While the horse reference genome is available, there has been no large-scale functional annotation of the genome using expressed genes derived from transcriptomes.ResultsWe present a large-scale analysis of whole transcriptome data. We sequenced the whole mRNA from the blood and muscle tissues of six thoroughbred horses before and after exercise. By comparing current genome annotations, we identified 32,361 unigene clusters spanning 51.83 Mb that contained 11,933 (36.87%) annotated genes. More than 60% (20,428) of the unigene clusters did not match any current equine gene model. We also identified 189,973 single nucleotide variations (SNVs) from the sequences aligned against the horse reference genome. Most SNVs (171,558 SNVs; 90.31%) were novel when compared with over 1.1 million equine SNPs from two SNP databases. Using differential expression analysis, we further identified a number of exercise-regulated genes: 62 up-regulated and 80 down-regulated genes in the blood, and 878 up-regulated and 285 down-regulated genes in the muscle. Six of 28 previously-known exercise-related genes were over-expressed in the muscle after exercise. Among the differentially expressed genes, there were 91 transcription factor-encoding genes, which included 56 functionally unknown transcription factor candidates that are probably associated with an early regulatory exercise mechanism. In addition, we found interesting RNA expression patterns where different alternative splicing forms of the same gene showed reversed expressions before and after exercising.ConclusionThe first sequencing-based horse transcriptome data, extensive analyses results, deferentially expressed genes before and after exercise, and candidate genes that are related to the exercise are provided in this study.

Peeling Back the Evolutionary Layers of Molecular Mechanisms Responsive to Exercise-Stress in the Skeletal Muscle of the Racing Horse

The modern horse (Equus caballus) is the product of over 50 million yrs of evolution. The athletic abilities of the horse have been enhanced during the past 6000 yrs under domestication. Therefore, the horse serves as a valuable model to understand the physiology and molecular mechanisms of adaptive responses to exercise. The structure and function of skeletal muscle show remarkable plasticity to the physical and metabolic challenges following exercise. Here, we reveal an evolutionary layer of responsiveness to exercise-stress in the skeletal muscle of the racing horse. We analysed differentially expressed genes and their co-expression networks in a large-scale RNA-sequence dataset comparing expression before and after exercise. By estimating genome-wide dN/dS ratios using six mammalian genomes, and FST and iHS using re-sequencing data derived from 20 horses, we were able to peel back the evolutionary layers of adaptations to exercise-stress in the horse. We found that the oldest and thickest layer (dN/dS) consists of system-wide tissue and organ adaptations. We further find that, during the period of horse domestication, the older layer (FST) is mainly responsible for adaptations to inflammation and energy metabolism, and the most recent layer (iHS) for neurological system process, cell adhesion, and proteolysis.

Genetic Traceability of Black Pig Meats Using Microsatellite Markers

Pork from Jeju black pig (population J) and Berkshire (population B) has a unique market share in Korea because of their high meat quality. Due to the high demand of this pork, traceability of the pork to its origin is becoming an important part of the consumer demand. To examine the feasibility of such a system, we aim to provide basic genetic information of the two black pig populations and assess the possibility of genetically distinguishing between the two breeds. Muscle samples were collected from slaughter houses in Jeju Island and Namwon, Chonbuk province, Korea, for populations J and B, respectively. In total 800 Jeju black pigs and 351 Berkshires were genotyped at thirteen microsatellite (MS) markers. Analyses on the genetic diversity of the two populations were carried out in the programs MS toolkit and FSTAT. The population structure of the two breeds was determined by a Bayesian clustering method implemented in structure and by a phylogenetic analysis in Phylip. Population J exhibited higher mean number of alleles, expected heterozygosity and observed heterozygosity value, and polymorphism information content, compared to population B. The FIS values of population J and population B were 0.03 and −0.005, respectively, indicating that little or no inbreeding has occurred. In addition, genetic structure analysis revealed the possibility of gene flow from population B to population J. The expected probability of identify value of the 13 MS markers was 9.87×10−14 in population J, 3.17×10−9 in population B, and 1.03×10−12 in the two populations. The results of this study are useful in distinguishing between the two black pig breeds and can be used as a foundation for further development of DNA markers.

Comparison for genetic diversity between Korean native commercial chicken brand groups using microsatellite markers.

To estimate the genetic characteristics within two brands of Korean native commercial chicken, we used a total of 302 genomic DNAs from two groups (Woorichicken: 152, Hanhyup3chicken: 150). Sizes of 10 microsatellite markers were decided using GeneMapper Software (v.4.0) after analyzing ABI 3130. Genetic diversity indices including expected heterozygosity (Ex H), observed heterozygosity (Ob H) and polymorphism information content (PIC). Frequencies of microsatellites markers were used to estimate heterozygosities and genetic distances. LEI0073 showed the highest value in all genetic diversity (Ex H, Ob H and PIC). On the other hand, MCW322 showed the lowest value in all genetic diversity. The calculated genetic distance of the two brand groups is 0.199 (standard genetic distance) and 0.132 (DA distance). Genetic distances of the two groups were relatively

Estimation of genetic characteristic and cumulative power of discrimination using the microsatellite markers in Korean Native Chicken.

To estimate the genetic characteristics and cumulative power of discrimination (CPD) Korean Native Chicken. We used a total of 195 genomic DNAs from four breeds population (Korean Native Red chicken: R, Korean Native Yellow chicken: Y, Korean Native Black chicken: L, Ogal chicken: S). Frequencies of microsatellites markers were used to estimate heterozygosities and genetic distances. The lowest distance (0.05) was observed between the R and L strains and the highest distance (0.158) between the L and S strains. Korean native chicken strains (R, Y, K) have each other comparatively near genetic distance. Cumulative power of discriminate (CPD) was 99.999% by including the 10 microsatellites loci individual identification system. And then matching probability in that two different individuals incidentally have same genotype was estimated to 0.36×10 -7 . The system employing

Identification of Polymorphisms in CAST Gene Associated with Economic Traits in Hanwoo (Bos taurus coreanae)

A number of studies have shown that the calpain system is important in normal skeletal muscle growth. An increased rate of skeletal muscle growth can result from a decreased rate of muscle protein degradation, and this is associated with a decrease in activity of the calpain system, due principally to a large increase in calpastatin (CAST) activity. The CAST gene, mapped to BTA 7, is considered a candidate gene for beef tenderness and muscle growth. The present study used comparative sequencing of five novel polymorphisms located within exon 20 and 22 of the bovine CAST gene in Hanwoo: exon20- 109737G/A, 109749T/C, 109823T/C, exon22- 116151G/A, intron- 109926G/A. The association of the CAST SNPs with economic traits was studied. The 109926G/A showed a significant effect only on the longissimus muscle area (LMA, p

Genetic diversity of Halla horses using microsatellite markers

BackgroundCurrently about 26,000 horses are breeding in Korea and 57.2% (14,776 horses) of them are breeding in Jeju island. According to the statistics published in 2010, the horses breeding in Jeju island are subdivided into Jeju horse (6.1%), Thoroughbred (18.8%) and Halla horse (75.1%). Halla horses are defined as a crossbreed between Jeju and Thoroughbred horses and are used for horse racing, horse riding and horse meat production. However, little research has been conducted on Halla horses because of the perception of crossbreed and people’s weighted interest toward Jeju horses.MethodUsing 17 Microsatellite (MS) Markers recommended by International Society for Animal Genetics (ISAG), genomic DNAs were extracted from the hair roots of 3,880 Halla horses breeding in Korea and genetic diversity was identified by genotyping after PCR was performed.Results and conclusionIn average, 10.41 alleles (from 6 alleles in HTG7 to 17 alleles in ASB17) were identified after the analysis using 17 MS Markers. The mean value of Hobs was 0.749 with a range from 0.612(HMS1) to 0.857(ASB2). Also, it was found that Hexp and PIC values were lowest in HMS1 (0.607 and 0.548, respectively), and highest in LEX3(0.859 and 0.843, respectively), and the mean value of Hexp was 0.760 and that of PIC was 0.728. 17 MS markers used in this studies were considered as appropriate markers for the polymorphism analysis of Halla horses. The frequency for the appearance of identical individuals was 5.90 × 10−20 when assumed as random mating population and when assumed as half-sib and full-sib population, frequencies were 4.08 × 10−15 and 3.56 × 10−8, respectively. Based on these results, the 17 MS markers can be used adequately for the Individual Identification and Parentage Verification of Halla horses. Remarkably, allele M and Q of ASB23 marker, G of HMS2 marker, H and L of HTG6 marker, L of HTG7 marker, E of LEX3 marker were the specific alleles unique to Halla horses.

Effects of Change of Body Weight on Racing Time in Thoroughbred Racehorses

본 연구는 한국마사회로부터 수집한 8,197두의 경주기록 총 155,656개를 이용하여 더러브렛 경주마의 체중변화가 주파기록에 미치는 효과를 구명하기 위하여 수행되었다. 국내 더러브렛 경주마의 평균 체중은 449 kg 이었으며, 거세말, 수말과 암말의 평균 체중은 각각 460 kg, 454 kg과 441 kg으로 수말의 체중이 가장 높게 나타났다. 암말의 경우 체중의 감소는 3월, 4월과 5월사이에 가장 크게 나타나며, 수말과 거세마의 경우 5월, 6월과 7월에 체중의 감소가 가장 크게 나타났다. 전반적으로 경주마의 체중은 봄과 여름에 감소하며, 가을과 겨울에 증가하는 현상을 나타내었다. 주파기록에 대한 유전력과 반복력은 각각 0.237과 0.525였으며, 체중에 대한 유전력은 0.612로 추정되었다. 직전 경주 대비 체중의 변화가 ±10 kg 이상일 때 주파기록은 현저히 증가하였으며, 직전 경주 대비 체중의 변화가 ±20 kg인 경우는 ±5 kg인 경우와 비교했을 때 주파기록의 차이가 0.3초 정도 증가하였다. 체중의 변화가 체중에 비례하여 ±0.5% 정도 변화하였을 때 주파기록이 가장 우수하였으며, 체중의 변화가 체중 대비 ±2.5% 이상이 되면 경주능력은 현저히 감소하였다.(

Estimation of Genetic Parameters for Economic Traits of Hanwoo Cows Using Ultrasound

This experiment was conducted to estimate the genetic parameters and breeding values of the economic traits measured from the cows (aged 15 months or older) using ultrasound and to use them as the information for the selection of stock animals at the farm level. The means and standard deviations of longissimus muscle area, backfat thickness and marbling score were 54.11 cm 2 ± 9.06, 3.57 mm ± 2.45 and 2.65 ± 2.88, respectively. While the linear regression coefficients of longissimus muscle area, backfat thickness and marbling score for age (in months) were all positive (0.3532, 0.0868 and 0.0833), the quadratic regression coefficients of them for age (in months) were all negative ( 0.0023, 0.0005 and 0.0006), and as the body condition score increased longissimus muscle area, backfat thickness and marbling score increased collectively. The heritability estimates for the longissimus muscle area, backfat thickness and marbling score were 0.39, 0.48 and 0.13, respectively and the estimated annual genetic gains for the longissimus muscle area, backfat thickness and marbling score were 0.00334 cm 2 , 0.0073 mm and 0.0043

Effect of Sequence Variation in Bovine Mitochondrial DNA D-loop Region on Economic Traits for Hanwoo.

ABSTRACT This study was performed to analyse the sequences of variations of mtDNA D-loop and their effects oncarcass traits in Hnawoo(Korean cattle). The resulting sequences were compared with previously publishedsequences for other cattle breeds(GenBank J01394). The PCR was used to amplify a total of 964 bp betweennucleotide 15758 and 383 within D-loop region of mtDNA using specific primers. Twenty five polymorphicsites by nucleotide substitution were found in mtDNA of Hanwoo. The frequencies of positions at 169, 16042,16093, 16119, 16255 and 16302 nt with high levels of sequence polymorphism were 0.891, 0.117, 0.109,0.182, 0.197 and 0.117, respectively. The substitution effect at 169 and 16119 nt was found significant onmarbling score. Also substitution effect at 169 and 16042 nt was highly significant(p 0.01) on backfat.thickness. Polymorphism of mtDNA sequence in D-loop region could be useful for the analysis of cytoplasmicgenetic variation and associations with the other economically important traits and maternal lineage analysis inHanwoo.(