This study was conducted to analyze the effect of single nucleotide polymorphisms (SNPs) on the equine chromosomes (ECA) 3 for the body conformations of 12 month of age in Jeju crossbred (Jeju horses × Thoroughbred). A total of 199 Jeju crossbred horse samples were obtained from the National Institute of Subtropical Livestock Research Institute for this study. To correctly estimate the body conformations, we measured thirteen elements relevant to the body conformation such as body weight, wither height, body length for all the 199 horses at 12 month of age. Furthermore, all the horses were genotyped using four SNPs including the BIEC2-808466, BIEC2-808543, BIEC2-808967, BIEC2-809370, of which genomic coordinates range approximately from 105.1Mbp to 110 Mbp in the ECA3. For the phenotypic data sets, the average body weight was 193.7 ± 24.5㎏ and the height was 124.5 ± 4.0㎝. As for the genotypic data, the miner allele frequencies of the SNPs were shown to be varied from 0.01 to 0.291. Using the phenotypic and genotypic data sets, analysis of covariance was performed to find any association between those SNP genotypes and body conformations, using year of birth, month of birth, sex, and parity as the covariance components. The result showed that alternative genotypes in the BIEC2-808967 and BIEC2-809370 SNPs were significantly associated with the body length (P<0.05) and the wither height (P<0.05) respectively in the Jeju crossbred horses. Therefore, it is estimated that there are significant associations in the body conformation of 12 month of age of Jeju crossbred for those two SNPs used in this study.

The ANK1 (Ankyrin-1) gene, located on the bovine chromosome 27, encodes a structural protein which forms an important component of the cytoskeleton. Ankyrin belongs to a protein family that links membrane proteins to the underlying spectrin-actin cytoskeleton. Many studies on gene expression regulation have revealed that RNA polymerase binds to the ANK1 gene promoter region. The purpose of the present study was to investigate the relationship between the SNP of the ANK1 promoter region and economic traits in Hanwoo cattle. A total of seven SNPs (C-944T, C-733T, C-687G, A-672G, C-307T, A-104G, C-24T), found in 119 animals, were correlated to economic traits. One of these SNPs, A-104G, was reported for the first time in the present study. Three newly discovered haplotypes were not associated with economic traits. Significant (p<0.05) relationships were found between C-944T and carcass weight, backfat thickeness, loin muscle area and between C-733T, A-672G and intramuscular fat. These results suggest that the SNPs of ANK1 gene may be useful molecular markers for selection of meat yield and quality traits in Hanwoo

One of the major problems in the modern pig industry is infectious disease. Susceptibility to infectious diseases is influenced by both constitutional (e.g. genotype, age, gender, and reproductive status) and environmental factors (e.g. nutrition, management, infections, and other forms of stress). Genetic variations within individual animals or herds can cause differences in the execution of immune functions against infectious agents in domestic pigs. The objectives of the present study were to identify genetic factor(s) responsible for piglet survival and mortality under commercial field conditions with infectious diseases as well as determine QTL regions for immune capacity in a pig reference family. Sex ratio was examined between normal grown and presumed dead groups of F2 animals generated by Korean native pigs (KNP) and Yorkshire (YS) breeds. The ratio of males was significantly higher in the presumed dead group than in the normal grown group. In order to study genetic factors associated with presumed mortality under disease outbreak, allelic frequencies of 239 single nucleotide polymorphisms (SNPs) were compared between normal grown and presumed dead groups. Exactly 22 SNPs showed significant differences in their allelic frequencies between the two groups, and four of them were validated with another commercial population divided by normal and emaciated pigs. Furthermore, the relationships between 239 SNPs and immune-related traits were studied. These results demonstrate that identification of genetic components of animal immune systems and susceptibility to infectious diseases is possible and will be useful to improve disease resistance in individuals as well as in breeding programs.

Single nucleotide polymorphisms (SNPs), that usually occurs with a modification in single nucleotide among the population of 1000 nucleotides. Such changes in nucleotides have been investigated and been associated by meat scientist for economically important traits and to increase economical profits in stock breeding. Pluralities in the study have correlated SNPs of potential candidate gene with economically important traits in domestic animals have been put forward. In chickens, INS, IGF1, IGF1R, IGFBP, CAPN1, CAPN3, GHSR, FATP1, FGFBP1, FGFBP2, apoVlDL-Ⅱ, PB1, miR-1614-3p, DAAM1, Wnt3A, LRP5, CHP, RHOA, MAPK9, SFRP1, ATGL, PGC-1α, NPY, GnRHR, PRL, TGFβ2, CASR. UCP, ADSL, STAT5b, LRP2 and CTSD genes have been found to have significant effects on body weight, breast muscle weight, carcass weight and egg number. For the similar reasons, SNPs of these genes have been considered useful DNA markers for the improvement economic value of poultry. Although further studies on different breeds of chickens would be required to segregate such dataset for different breeds of chickens.

닭의 7번 염색체에 위치하고 있는 NRAMP-1(Natural Resistance Associated Macrophage Protein1) 유전자는 면역 반응에서 작용하는 유전자로서 대식세포의 초기 활성화 과정에 영향을 주는 것으로 알려져 있으며, 유전자의 변이에 따라 살모넬라균에 감염되었을 시에 비장의 변화에 영향을 주는 것으로 보고되어져 있다. 본 연구는 3개의 품종(로드아일랜드 레드, 코니쉬, 재래닭)을 대상으로 유전자 변이 지역 중 하나인 C3229T 지역의 유전자형을 확인하고, 경제형질간의 연관성을 분석하기 위하여 실시하였다. 분석결과 C3229T 지역은 변이에 의해 Serine에서 phenyl-alanine으로 변하는 missence mutation으로 확인 되었으며, 로드아일랜드 레드에서 변이지역과 경제형질간의 연관성 분석 결과 150일령 체중에서 유의적인 연관성이 확인 되었다. 본 연구를 통하여 확인된 C3229T 지역의 SNP를 활용하여 추후 닭의 선발 및 육종을 위한 기초자료로 활용 가능할 것으로 사료된다.

The purpose of the livestock industry is to pursuit economic profits by increasing the economic productivity of livestock. Single nucleotide polymorphisms (SNPs), that is characterized by one variation out of every 1000 polymorphisms, to increase economical benefits in stock breeding has been extensively studied. Particularly, replete number of investigations have been put forward that has associated SNPs of candidate genes with economically important traits such as carcass weight (CW), longissimus muscle area (LMA), backfat thickness (BFT) and marbling score (MS) in beef cattle. Bovine genome sequencing and HapMap projects have provided, millions of SNPs in the cattle genome. However, till date studies related to the association of the SNPs with economic traits in beef cattles are meager. Discovering of SNPs bovine whole genome would certainly be useful genetic assets for the development of SNP marker for economically important traits in beef cattle.

The aim of this study is to investigate the genetic interrelationships between economic or meat quality traits (birth weight, weaning weight, average daily gain, market weight, carcass weight, backfat thickness, water, ash, fat, protein, water holding capacity and pH) and 6 SNPs located on six selected candidate genes (MC4R, PGK2, TNNI1, TNNI2, PIK3C3, and CTSK) in Korean native pigs. The genotypes were identified in the 6 SNPs by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) procedure, and association of the genotype on economically important traits was analyzed by general liner model. According to the analyzed results, the MC4R c.1426A>G was correlated with birth weight (p=0.032) and the PGK2 g.122T>G was associated with pH (p=0.026). These findings obtained in the present revealed that the each SNPs of MC4R and PGK2 could be useful as potential genetic markers for birth weight and pH in Korean native pigs, respectively.

In order to provide information of genetic variants for Haptoglobin (Hp) gene, which may be related to weight traits in pig, a total of 235 animals from National Institute of Animal Science (NIAS) were screened with 3 primers. The primer sequences were selected using the porcine cDNA sequences based on NM_214000, and the exon boundaries were estimated. Genetic variants were observed using direct sequencing analysis, and there were 9 SNPs detected at nucleotide positions 503 (A/G), 509 (A/G), 709 (C/T), 734 (C/A), 742 (G/A), 769 (A/G), 840 (C/T), 876 (C/T) and 882 (C/A). All the SNPs were located in coding regions, and mutations caused amino acid changes at nucleotide positions 503, 509, 734, 742 and 769. Allele frequencies of SNPs were estimated for all segments. The SNPs at nucleotide position 509 (p<0.0001) and 734 (p<0.05) were significantly associated with average daily gain, but no significance was observed with other SNPs. From the results, the identified SNPs may be a useful candidate marker for the porcine weight gain traits.

As a first step of mapping genes conferring resistance to the brown planthopper, Nilaparvata lugens Stål, in Gayabyeo using a population derived from a cross between Gayabyeo and Taebaegbyeo, we performed the whole genome resequencing of these two Tongil-type rice varieties. The amount of raw sequence data was about 18.5X109 bp and 17.9X109 bp in Gayabyeo and Taebaegbyeo, respectively. After quality trimming and read mapping onto Nipponbare reference genome sequence, 9.3X109 bp was mapped in Gayabyeo with mapping depth of 25.0X, and 9.5X109 bp was mapped in Taebaegbyeo with mapping depth of 25.5X. Between Gayabyeo and Nipponbare, 1,585,880 SNPs were detected, while 1,416,898 SNPs were detected between Taebaegbyeo and Nipponbare. Between Gayabyeo and Taebaegbyeo, 284,501 SNPs were detected. Among the SNPs between Gayabyeo and Taebaegbyeo, 21.2% were in genic region and 78.8% were in intergenic region. In CDS region, 15,924 SNPs were detected, among which synonymous SNPs covered 47.3% and non-synonymous SNPs covered 52.7%. We designed Cleaved Amplified Polymorphic Sequences (CAPS) markers with SNPs in the restriction enzyme recognition sites, and 20 CAPS markers were tested. Of the 20 markers, 19 markers showed polymorphism and one marker showed monomorphism between Gayabyeo and Taebaegbyeo. It is expected that sufficient DNA markers for mapping genes with a population derived from a cross between Gayabyeo and Taebaegbyeo can be developed based on the results of the study.

The newly developed varieties, Jayoung (violet flesh color) and Hongyoung (red flesh color) that harboring various anthocyanins and flavonoids in flesh colored potato are highly increase their interesting not only for food but also functional characteristics such as anti-inflammatory effects. Up to date, most of the molecular markers developed in potato are linked to disease resistance including late blight and PVY, nematode. A few markers linked to economically important functional materials such as anthocyanin biosynthesis are published. With the low cost and high throughput of NGS (Next Generation Sequencing) technology, numerous molecular markers are highly increased in may crops. Among the molecular markers, SNPs (Single nucleotide Polymorphisms) are most useful markers owing to their large numbers in inter and intra varieties in potato. Here we reported SNPs discovery from transcriptome sequencing data acquired from colored flesh potato cultivars, Jayoung and Hongyoung with white flesh color Atlantic. Total RNA was isolated from shoot in tuber after breaking dormancy about 2cm length. Short read sequence data were obtained form Illumina Hiseq2000 and the raw dat set were trimmed with Q socore over 20. Sequencing data were align to reference genome (Solanum tuberosum v4.03, http://potatogeomics.plantbiolgy.msu.edu). About 70% of sequence read were mapped int to reference genome. 139,050, 140,976 and 146,429 total SNPs were discovered in Hongyoung, Jayoung and Atlantic, respectively. All SNPs are mapped into the psedomolecules in reference genome by chromosome. SNPs are also analyzed with homozygous and heterozygous SNPs and genic and intergenic region. SNPs are compared with Potato Infinium 8K Chip data. SNPs found in candidate genes of anthocyanin biosynthesis were discovered. These SNPs information of flesh colored potato will be further analyzed for the allele mining for anthocyanin syhthesis and control region

Bacterial spot of tomato (Solanum lycopersicum L.) is caused by at least four species of Xanthomonas with multiple physiological races. In this study, we developed a mapping population for association analysis of bacterial spot resistance. For this population, six advanced breeding lines with distinct sources of resistance were first crossed in all combinations and their F1 hybrids were intercrossed. The 1,100 segregating progeny from these crosses were evaluated in the field against T1 strains. Based on this individual evaluation, we selected 5% of the most resistant and 5% of the most susceptible progeny for evaluation as plots in two subsequent replicate field trials inoculated with T1 and T3 strains. A total of 461 markers across 12 chromosomes were used for genotyping these selections. Of these markers, an optimized subset of 384 SNPs was derived from the 7,720 SNP Infinium array developed by the Solanaceae Coordinated Agricultural Project (SolCAP). For association analysis to detect known resistance loci and additional novel loci, we used the mixed models with correction for population structure, and found that accounting for kinship appeared to be sufficient. Detection of known loci was not improved by adding a correction for structure using either a Q matrix from model-based clustering or covariate matrix from Principal Component Analysis. Both single-point and haplotype analyses identified strong associations in the region of the genome known to carry Rx-3 (chromosome 5) and Rx-4/Xv3 (chromosome 11). Additional QTL associated with resistance were detected on chromosomes 1, 3, 4, 6 and 7 for T1 resistance and chromosomes 2, 4, and 6 for T3 resistance. Haplotype analysis improved our ability to trace the origin of positive alleles. These results demonstrate that both known and novel associations can be identified using complex breeding populations that have experienced directional selection.