• 농업생명과학연구
• /
• 제50권3호
• /
• pp.99-117
• /
• 2016

ssGBLUP을 이용한 전장 유전체 연관분석(ssGWAS)을 수행하기 위하여 이용한 표현형 자료는 2010년도부터 2015년까지 농협중앙회 한우개량사업소에서 후대 검정한 한우 거세우 총 1,829두의 부분육수율자료를 이용하였다. 유전체 자료는 Illumina Bovine 50K Beadchip을 활용하였으며 표현형 자료와 매칭이 되는 개체는 674두였다. 먼저 안심, 등심, 채끝 및 갈비수율의 유전체 육종가(GEBV)를 구하고 이를 통해 SNP 표지인자에 대한 효과와 SNP 표지인자의 분산을 계산하여 형질별 전체 유전분산 대비 SNP 표지인자의 효과를 추정한 후, QTL일 가능성이 있는 효과가 높은 SNP 좌위에 대한 결과를 주요하게 조사하였다. 안심수율의 경우, 상위 20개의 전체 유전분산 대비 SNP 표지인자의 효과에서 10번 염색체에서의 효과가 가장 높았는데 12,812,193 ~ 12,922,313bp 영역에서 전체 유전분산 대비 7.32 ~ 7.34%의 효과를 나타냈다. 채끝수율은 전체 유전분산에 대한 설명력이 가장 높은 SNP 표지인자를 포함하는 염색체는 24번 염색체로 38,158,543 ~ 38,347,278bp 영역이 약 8.36 ~ 8.56%의 전체 유전분산 대비 효과를 나타내었다. 등심수율은 다른 부분육 조사형질보다 낮은 SNP 표지인자의 효과를 나타내었다. 따라서 등심의 경우 보통 크기의 효과와 작은 효과를 갖는 많은 유전자들에 의해서 형질이 발현되는 것으로 사료된다.

• Journal of Microbiology and Biotechnology
• /
• 제26권1호
• /
• pp.207-212
• /
• 2016

PacBio's long-read sequencing technologies can be successfully used for a complete bacterial genome assembly using recently developed non-hybrid assemblers in the absence of second-generation, high-quality short reads. However, standardized procedures that take into account multiple pre-existing second-generation sequencing platforms are scarce. In addition to Illumina HiSeq and Ion Torrent PGM-based genome sequencing results derived from previous studies, we generated further sequencing data, including from the PacBio RS II platform, and applied various bioinformatics tools to obtain complete genome assemblies for five bacterial strains. Our approach revealed that the hierarchical genome assembly process (HGAP) non-hybrid assembler resulted in nearly complete assemblies at a moderate coverage of ~75x, but that different versions produced non-compatible results requiring post processing. The other two platforms further improved the PacBio assembly through scaffolding and a final error correction.

• 한국가금학회지
• /
• 제42권1호
• /
• pp.27-32
• /
• 2015

In this study, we used two breeds of chicken to identify genomic regions corresponding to necrotic enteritis (NE) resistance. We scanned the genomes of a resistant and susceptible line of Fayoumi and White Leghorn chickens (20 birds/line) using a chicken 60 K Illumina SNP panel. A total of 235 loci with divergently fixed alleles were identified across the genome in both breeds; particularly, several clusters of multiple loci with fixed alleles were found in five narrow regions. Moreover, consensus 15-SNP haplotypes that were shared by the resistant lines of both breeds were identified on chromosomes 3, 7 and 9. Genes responsible for NE resistance were identified in chicken lines selected for resistance and susceptibility. Annotation of the regions spanning clustered divergently fixed regions revealed a set of interesting candidate genes such as phosphoinositide-3-kinase, regulatory subunit 5, p101 (PIK3R5) and inositol 1,4,5-trisphosphate receptor 1 (ITPR1), which participate in immune response. Consensus haplotypes were found in regions containing possibly relevant genes, such as myostatin and myosin, which play important roles in muscle development. Thus, genome scans of divergent selection in multiple chicken lines and breeds can be used to identify genomic regions associated with NE resistance.

• Genomics & Informatics
• /
• 제14권4호
• /
• pp.187-195
• /
• 2016

In genetic association studies with high-dimensional genomic data, multiple group testing procedures are often required in order to identify disease/trait-related genes or genetic regions, where multiple genetic sites or variants are located within the same gene or genetic region. However, statistical testing procedures based on an individual test suffer from multiple testing issues such as the control of family-wise error rate and dependent tests. Moreover, detecting only a few of genes associated with a phenotype outcome among tens of thousands of genes is of main interest in genetic association studies. In this reason regularization procedures, where a phenotype outcome regresses on all genomic markers and then regression coefficients are estimated based on a penalized likelihood, have been considered as a good alternative approach to analysis of high-dimensional genomic data. But, selection performance of regularization procedures has been rarely compared with that of statistical group testing procedures. In this article, we performed extensive simulation studies where commonly used group testing procedures such as principal component analysis, Hotelling's $T^2$ test, and permutation test are compared with group lasso (least absolute selection and shrinkage operator) in terms of true positive selection. Also, we applied all methods considered in simulation studies to identify genes associated with ovarian cancer from over 20,000 genetic sites generated from Illumina Infinium HumanMethylation27K Beadchip. We found a big discrepancy of selected genes between multiple group testing procedures and group lasso.

• Genomics & Informatics
• /
• 제5권4호
• /
• pp.152-160
• /
• 2007

Most common diseases are caused by multiple genetic and environmental factors. Among the genetic factors, single nucleotide polymorphisms (SNPs) are common DNA sequence variations in individuals and can serve as important genetic markers. Recently, investigations of gene-based and whole genome-based SNPs have been applied to association studies for marker discovery. However, SNPs are so population-specific that the association needs to be verified. Fifty-five genes and 384 SNPs were selected based on association with disease. Genotypes of 337 SNPs in candidate genes were determined using Illumina Sentrix Array Matrix (SAM) chips by an allele-specific extension method in 364 unrelated Korean individuals. Allelic frequencies of SNPs were compared with those of other populations obtained from the International HapMap database. Minor allele frequencies, linkage disequilibrium blocks, tagSNPs, and haplotypes of functional candidate SNPs in 55 genetic disease-associated genes were provided. Our data may provide useful information for the selection of genetic markers for gene-based genetic disease-association studies of the Korean population.

• 식물분류학회지
• /
• 제50권3호
• /
• pp.327-332
• /
• 2020

Microsatellite markers were developed as a tool for phylogeographic studies of Hosta capitata. We also assessed cross-amplification in species closely related to Hosta capitata. We produced 28 polymorphic microsatellite markers by mapping 300 bp paired-end reads obtained from Illumina MiSeq data of H. capitata. In H. capitata, the number of alleles per locus ranged from 1 to 13. Observed and expected heterozygosity ranged from 0.000 to 0.844 and 0.000 to 0.832, respectively. Additionally, 13 loci were successfully transferable to the related species of H. minor and H. venusta. These markers will provide a powerful genetic tool not only for elucidating the phylogeographic patterns of H. capitata populations but also for studying the genetic delimitation of H. capitata from its related species.

• International Journal of Industrial Entomology and Biomaterials
• /
• 제35권1호
• /
• pp.30-38
• /
• 2017

The red-spotted apollo butterfly, Parnassius bremeri Bremer, 1864 (Lepidoptera: Papilionidae), is an endangered species in South Korea. Development and application of molecular markers to assess population genetics perspectives can be used as a basis to establish effective conservation strategies. In this study, we developed 12 microsatellite markers specific to P. bremeri using Illumina paired-end sequencing and applied the markers to South Korean populations to understand population characteristics. Genotyping of 40 P. bremeri individuals from three localities showed that at each locus, the observed number of alleles ranged from 6 to 22 and the observed and expected heterozygosities were 0.500-1.00 and 0.465 to 0.851, respectively. Significant deviation from the Hardy-Weinberg equilibrium was not observed in all loci studied. The population based $F_{ST}$ and $R_{ST}$ collectively suggest that at least the Samcheok population in northernmost Gangwon Province has a significant divergence from the remaining two populations (P < 0.01), and this result is also reflected in the forewing length. Further studies with an increased sample size will be necessary to draw robust conclusions and devise conservation strategies.

• Asian-Australasian Journal of Animal Sciences
• /
• 제28권2호
• /
• pp.158-165
• /
• 2015

Marbling is an important trait regarding the quality of beef. Analysis of beef cattle transcriptome and its expression profile data are essential to extend the genetic information resources and would support further studies on beef cattle. RNA sequencing was performed in beef cattle using the Illumina High-Seq2000 platform. Approximately 251.58 million clean reads were generated from a high marbling (H) group and low marbling (L) group. Approximately 80.12% of the 19,994 bovine genes (protein coding) were detected in all samples, and 749 genes exhibited differential expression between the H and L groups based on fold change (>1.5-fold, p<0.05). Multiple gene ontology terms and biological pathways were found significantly enriched among the differentially expressed genes. The transcriptome data will facilitate future functional studies on marbling formation in beef cattle and may be applied to improve breeding programs for cattle and closely related mammals.

• 한국동물위생학회지
• /
• 제42권4호
• /
• pp.217-225
• /
• 2019

To detect Single nucleotide polymorphisms (SNP) markers associated with Bovine viral diarrhea virus (BVDV) and Bovine respiratory syncytial virus (BRSV) S/P ratio in Korean Holstein dairy cattle, Genome-wide association study (GWAS) was performed using Illumina BovineSNP50 Beadchip. The number of phenotype data and genotype data were 107, and 294. respectively. Phenotype data were collected for four periods (0 week, 1 week, 4 week, 24 week) after having vaccinated (0 week no vaccinated period). A total of 36,257 SNPs was remained after quality control had been done by PLINK. The result of GWAS showed 6 SNP markers (BTB-01704243, BTB-01594395, ARS-BFGL-NGS-118070, ARS-BFGL-NGS-111365, BTA-65410-no-rs, Hapmap38331-BTA-61256) under BVDV and 4 SNP markers (ARS-BFGL-NGS-109861, Hapmap53701-rs29017064, ARS-BFGL-NGS-71055, BTA-11232-no-rs) under BRSV. And also, 10 candidate genes found through 10 SNP markers (TBX18, CEP162, PAFAH1B1, METTL16, BRCA1, RND2, POLK, ENSBTAG00000051724, ADAM18, NRG3).

• Asian-Australasian Journal of Animal Sciences
• /
• 제27권10호
• /
• pp.1406-1410
• /
• 2014

Age at first calving is an important trait for achieving earlier reproductive performance. To detect quantitative trait loci (QTL) for reproductive traits, a genome wide association study was conducted on the 96 Hanwoo cows that were born between 2008 and 2010 from 13 sires in a local farm (Juk-Am Hanwoo farm, Suncheon, Korea) and genotyped with the Illumina 50K bovine single nucleotide polymorphism (SNP) chips. Phenotypes were regressed on additive and dominance effects for each SNP using a simple linear regression model after the effects of birth-year-month and polygenes were considered. A forward regression procedure was applied to determine the best set of SNPs for age at first calving. A total of 15 QTL were detected at the comparison-wise 0.001 level. Two QTL with strong statistical evidence were found at 128.9 Mb and 111.1 Mb on bovine chromosomes (BTA) 2 and 7, respectively, each of which accounted for 22% of the phenotypic variance. Also, five significant SNPs were detected on BTAs 10, 16, 20, 26, and 29. Multiple QTL were found on BTAs 1, 2, 7, and 14. The significant QTLs may be applied via marker assisted selection to increase rate of genetic gain for the trait, after validation tests in other Hanwoo cow populations.