• Asian-Australasian Journal of Animal Sciences
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• 제30권12호
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• pp.1689-1695
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• 2017

Objective: The cytokine inducible SH2-containing protein (CISH), which might play a role in porcine intestine immune responses, was one of the promising candidate genes for piglet anti-disease traits. An experiment was conducted to characterize the porcine CISH (pCISH) gene and to evaluate its genetic effects on pig anti-disease breeding. Methods: Both reverse transcription polymerase chain reaction (RT-PCR) and PCR were performed to obtain the sequence of pCISH gene. A pEGFP-C1-CISH vector was constructed and transfected into PK-15 cells to analysis the distribution of pCISH. The sequences of individuals were compared with each other to find the polymorphisms in pCISH gene. The association analysis was performed in Min pigs and Landrace pigs to evaluate the genetic effects on piglet diarrhea traits. Results: In the present research, the coding sequence and genomic sequence of pCISH gene was obtained. Porcine CISH was mainly localized in cytoplasm. TaqI and HaeIII PCR restriction fragment length polymorphism (RFLP) assays were established to detect single nucleotide polymorphisms (SNPs); A-1575G in promoter region and A2497C in Intron1, respectively. Association studies indicated that SNP A-1575G was significantly associated with diarrhea index of Min piglets (p<0.05) and SNP A2497C was significantly associated with the diarrhea trait of both Min pig and Landrace piglets (p<0.05). Conclusion: This study suggested that the pCISH gene might be a novel candidate gene for pig anti-disease traits, and further studies are needed to confirm the results of this preliminary research.

• Asian-Australasian Journal of Animal Sciences
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• 제23권12호
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• pp.1543-1551
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• 2010

A major aim of cattle genome research is to identify candidate genes associated with meat quantity and quality through QTL analysis for application in the livestock industry. Therefore, this study focused on discovery of useful SNPs within the LOC534614 gene, containing 12273_165 SNP which is located on the same site as the QTL on chromosome 6, and evaluation of the association between SNP and body weight and cold carcass weight in Hanwoo (Korean cattle) As a result of a BLAST search of the NCBI web site, we discovered that the mRNA sequence of the LOC534614 gene was similar to that of the coiled-coil domain containing 158 (CCDC158) for dog and human. According to the direct DNA sequence from the CCDC158 gene, we identified 19 polymorphic SNPs within exons and their flanking regions. Among them, 17 polymorphic SNPs were selected for genotyping in Hanwoo (n = 476) and seventeen marker haplotypes containing 12273_165 SNP (frequency >0.1) were identified. As a result of the association between 17 polymorphic SNPs and Hanwoo (n = 476), g.8778G>A SNP in exon 6 was found to be a non-synonymous SNP, and was significantly associated with body weight and cold carcass weight (p<0.05). We discovered 19 polymorphic SNPs in the CCDC158 gene on the QTL region of BTA 6 in Hanwoo and identified that the g.8778G>A SNP was significantly associated with body weight and cold carcass weight (p<0.05), which causes an amino acid variation from valine to methionine. Furthermore, statistical analysis demonstrated that the CCDC158 gene is strongly associated with body weight and cold carcass weight in Hanwoo. In this regard, the g.8778G>A SNP in the CCDC158 gene can be useful as a positional candidate for body weight and cold carcass weight for marker-assisted selection in Hanwoo.

• Animal Bioscience
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• 제37권3호
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• pp.451-460
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• 2024

Objective: The objective is to identify genomic regions and candidate genes associated with age to 105 kg (AGE), average daily gain (ADG), backfat thickness (BF), and eye muscle area (EMA) in Yorkshire pig. Methods: This study used a total of 104,380 records and 11,854 single nucleotide polymorphism (SNP) data obtained from Illumina porcine 60K chip. The estimated genomic breeding values (GEBVs) and SNP effects were estimated by single-step genomic best linear unbiased prediction (ssGBLUP). Results: The heritabilities of AGE, ADG, BF, and EMA were 0.50, 0.49, 0.49, and 0.23, respectively. We identified significant SNP markers surpassing the Bonferroni correction threshold (1.68×10^-6), with a total of 9 markers associated with both AGE and ADG, and 4 markers associated with BF and EMA. Genome-wide association study (GWAS) analyses revealed notable chromosomal regions linked to AGE and ADG on Sus scrofa chromosome (SSC) 1, 6, 8, and 16; BF on SSC 2, 5, and 8; and EMA on SSC 1. Additionally, we observed strong linkage disequilibrium on SSC 1. Finally, we performed enrichment analyses using gene ontology and Kyoto encyclopedia of genes and genomes (KEGG), which revealed significant enrichments in eight biological processes, one cellular component, one molecular function, and one KEGG pathway. Conclusion: The identified SNP markers for productive traits are expected to provide valuable information for genetic improvement as an understanding of their expression.

• Genomics & Informatics
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• 제9권2호
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• pp.64-68
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• 2011

Monomelic amyotrophy (MA), also known as Hirayama disease, occurs mainly in young men and manifests as weakness and wasting of the muscles of the distal upper limbs. Here, we sought to identify a genetic basis for MA. Given the predominance of MA in males, we focused on candidate neurological disease genes located on the X chromosome, selecting two X-linked candidate genes, androgen receptor (AR ) and ubiquitin-like modifier activating enzyme 1 (UBA1). Screening for genetic variants using patients' genomic DNA revealed three known genetic variants in the coding region of the AR gene: one nonsynonymous single-nucleotide polymorphism (SNP; rs78686797) encoding Leu57Gln, and two variants of polymorphic trinucleotide repeat segments that encode polyglutamine (CAG repeat; rs5902610) and polyglycine (GGC repeat; rs3138869) tracts. Notably, the Leu57Gln polymorphism was found in two patients with MA from 24 MA patients, whereas no variants were found in 142 healthy male controls. However, the numbers of CAG and GGC repeats in the AR gene were within the normal range. These data suggest that the Leu57Gln polymorphism encoded by the X-linked AR gene may contribute to the development of MA.

• 생물정신의학
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• 제16권2호
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• pp.121-126
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• 2009

Objectives : The serotonin transporter gene(SLC6A4) is one of the most widely studied candidate genes in autism spectrum disorder(ASD), but there have been conflicting results from studies into the association between SLC6A4 and ASD. The aim of this study was to evaluate the association between single nucleotide polymorphisms(SNPs) in the SLC6A4 gene and ASD in the Korean population. Methods : We selected 12 SNPs in SLC6A4 and observed the genotype of 151 Korean ASD trios. We tested the family-based association for each individual polymorphism and haplotype by using the standard TDT method in Haploview(http://www.broad.mit.edu/mpg/haploview/). Results : Through transmission-disequilibrium testing and haplotype analysis, we could not find any statistically significant transmitted allele or haplotype. In addition, a case-control association test with Korean HapMap data did not reveal any statistical significance. Conclusion : Although serotonin-related genes must be considered candidate genes for ASD, we suggest that common SNPs of SLC6A4 are not important markers for associations with Korean ASD.

• Journal of Plant Biotechnology
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• 제45권1호
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• pp.17-29
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• 2018

본 연구에서는 국내외에서 수집한 벼 294개 유전자원 핵심집단을 대상으로 벼의 지엽각 특성에 대한 조사를 수행하였고, GWAS를 이용하여 지엽각 연관 유전자를 추출 및 분석하였다. 표현형 데이터를 이용한 GWAS의 Manhattan plot 결과 분석을 통해, 각 집단에서 염색체를 대상으로 표현형과 통계적 유의성을 나타내 연관성을 보이는 SNP를 발굴하였다. 지엽각 관련 특성에 대하여 선행 연구된 QTL region과의 비교를 통하여 본 연구에서 발굴된 SNP간의 유의성을 조사한 결과, 지엽각과 유의성이 있는 SNP (S8-19815442)가 이미 확인된 QTL region에 위치하는 것으로 나타났으며, 후보유전자 Os08g31950 대해 연관 유전자 변이를 관찰하기 위해서 형질 특이적 품종군 간의 염기서열을 비교한 결과 1개의 지역에서 단일염기변이가 검출되었다. Os08g31950의 조직별 RNA의 상대적 발현량 수준을 비교한 결과, Os08g31950 유전자는 모든 조직에서 높은 발현량을 확인할 수 있었으며 조직별로 다양한 발현 양상을 관찰할 수 있었다. 또한, 모두 직립형 품종군에서 상대적으로 발현량이 높게 나타났으며 뿌리보다 잎에서의 발현율이 높게 나타났다. 본 연구를 통해 동정된 지엽각 연관 후보유전자 Os08g31950는 벼 생육 및 수량 증대에 이용할 수 있는 마커제작 및 육종의 기초자료가 될 것으로 기대된다.

• 한국환경성돌연변이발암원학회지
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• 제22권3호
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• pp.183-186
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• 2002

Hypertension is a multifactorial disease. Both genetic and environmental factors have been implicated in its etiology. Since the impairment of nitric oxide (NOS) production plays an important role in the pathogenesis of hypertension, endothelial nitric oxide synthase (ecNOS) gene is supposed to be a candidate gene of hypertension. Our study group investigated the 27 bp insertion/deletion (Ins/Del) polymorphism of ecNOS gene in 99 Korean normotensives and 98 hypertensives, respectively. There was no significant association with any cardiovascular risk factors as well as hypertension in Koreans. The Ins/Del polymorphism of the ecNOS gene indicated the similar allele distribution among ethnic groups studied. Further studies using larger sample size and subject information is required to describe the general picture of the association between the ecNOS gene polymorphic loci and hypertension

• 약학회지
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• 제48권1호
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• pp.75-81
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• 2004

Bone mineral density (BMD) is influenced by genetic and environmental factors. Among genetic study; calcitonin receptor (CTR) gene is a good candidate influencing the inter-individual difference in BMD because CTR is involved in calcium and bone metabolism. Thus, we investigated the distribution of C1377T polymorphism in the CTR gene among male Korean elite athletic and control groups, respectively and also an association with BMD in lumbar spine and femoral neck. Our results suggested that this polymorphism of CTR gene was not significantly associated with lumbar spine or femoral neck BMDs in the both groups, respectively. However, we found that there was the racial difference in genotype distribution of this polymorphism between Caucasian and Asian populations. Though we could not detect the significant association between C1377T polymorphism of CTR gene and lumbar spine or femoral neck BMDs, further studies using other ethnic groups are necessary to clarify the precise role in BMD of CTR gene.

• Asian-Australasian Journal of Animal Sciences
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• 제30권8호
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• pp.1066-1073
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• 2017

Objective: Growth-related traits are important economic traits in the swine industry. However, the genetic mechanism of growth-related traits is little known. The aim of this study was to screen the candidate genes and molecular markers associated with body dimension and body weight traits in pigs. Methods: A genome-wide association study (GWAS) on body dimension and body weight traits was performed in a White $Duroc{\times}Erhualian$ $F_2$ intercross by the illumina PorcineSNP60K Beadchip. A mixed linear model was used to assess the association between single nucleotide polymorphisms (SNPs) and the phenotypes. Results: In total, 611 and 79 SNPs were identified significantly associated with body dimension traits and body weight respectively. All SNPs but 62 were located into 23 genomic regions (quantitative trait loci, QTLs) on 14 autosomal and X chromosomes in Sus scrofa Build 10.2 assembly. Out of the 23 QTLs with the suggestive significance level ($5{\times}10^{-4}$), three QTLs exceeded the genome-wide significance threshold ($1.15{\times}10^{-6}$). Except the one on Sus scrofa chromosome (SSC) 7 which was reported previously all the QTLs are novel. In addition, we identified 5 promising candidate genes, including cell division cycle 7 for abdominal circumference, pleiomorphic adenoma gene 1 and neuropeptides B/W receptor 1 for both body weight and cannon bone circumference on SSC4, phosphoenolpyruvate carboxykinase 1, and bone morphogenetic protein 7 for hip circumference on SSC17. Conclusion: The results have not only demonstrated a number of potential genes/loci associated with the growth-related traits in pigs, but also laid a foundation for studying the genes' role and further identifying causative variants underlying these loci.

• 농업과학연구
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• 제45권2호
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• pp.238-247
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• 2018

The overall consumption of meat is increasing as the level of national income increases. The end weight is a trait closely associated with dressed meat. Genome-wide association study (GWAS) is an effective method of analyzing genetic variation and gene identification associated with a number of natural alternative traits because it can detect variations. So this paper did a GWAS analysis to identity the location on the genome related to the end weight in purebred landrace pigs and to explore the relevant candidate gene. This study identified a significant single nucleotide poly morphism (SNP) marker in chromosome 6 (ASGA0029422, $p=1.22{\times}10^{-6}$). Adhesion G protein-coupled receptor L2 (ADGRL2) was found to be the candidate gene at the identified SNP marker location. ADGRL2 genes have been found to be associated with cell development in relation to the external and internal environment of a cell. In addition, genotype and statistical analyses were done on nine variations on the exon of ADGRL2. The results show that the SNP marker (ASGA0029422, $p=1.32{\times}10^{-6}$) was significant, but the significance of the nine variations on the ADGRL2 exon was not verified. However, by performing further experiments and functional studies on other SNPs showing possible genetic ADGRL-Exon mutations, objects with high associations of high-end weights can be selected.