• 한국균학회지
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• 제45권2호
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• pp.114-120
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• 2017

표고버섯은 주로 아시아 국가에서 재배되는 식용 버섯이다. 표고버섯은 최근 국내에서 신품종의 개발이 활발히 이루어지고 있으며, 국내외적으로 품종의 보호가 중요해짐에 따라 표고의 품종을 구분할 수 있는 효율적인 마커 개발이 요구되고 있다. 본 연구에서는 산마루1호와 천장3호를 구분할 수 있는 CAPS (cleaved amplified polymorphic sequence) 마커를 개발하였다. 이 연구에서 개발된 CAPS 마커는 단핵균주인 B17의 표준유전체 정보와 연구에 사용된 10개 균주의 resequencing 정보를 바탕으로 개발되었다. 산마루1호는 scaffold9번, 1630048의 염기서열 G가 T로 변한 SNP를 포함하여 PCR 후 제한효소 TspR I을, 천장3호는 scaffold13번, 920681의 염기서열 G가 A로 변한 single nucleotide polymorphism (SNP)를 포함하여 PCR 후, 제한효소 Xho I을 처리하였을 때 다른 균주들과 구분되었다. 따라서 이를 마커로 개발하였다.

• 생명과학회지
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• 제28권10호
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• pp.1233-1243
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• 2018

SREBPs는 지질의 항상성 및 대사를 조절하는 전사 인자이다. 이들은 내인성 콜레스테롤, 지방산(FA), 트리아실글리세롤(TG) 및 인지질 합성에 필요한 효소의 발현을 정밀하게 조절한다. 3종류의 SREBP 단백질은 2개의 다른 유전자에 의해 암호화 된다. SREBP1 유전자는 SREBP-1a와 SREBP-1c를 만든다. 이는 RNA의 alternative splicing에 의한 대체 프로모터의 이용으로부터 유도된다. SREBP-2는 별도의 유전자에서 유래한다. 또한, SREBPs는 ER 스트레스, 염증, 자가포식 및 세포사멸과 같은 수많은 병인과정에 관여하며, 비만, 이상 지질혈증, 당뇨병 및 비알콜성 지방간 질환 등을 유발하는 것으로 알려져 있다. 유전체의 분석은 SREBPs가 생물학적 신호 전달, 세포 신진 대사, 및 성장을 조절하는 중요한 연결고리임을 보여 주었다. 이 과정에서 SREBP는 PI3K-Akt-mTOR 경로를 통해 활성화 된다고 알려져 있다. 하지만 정확한 분자 메커니즘은 좀더 밝혀져야 한다. 이 리뷰에서는 세포, 기관 및 생물개체 수준의 생리학 및 병태 생리학 영역에서 SREBP의 역할에 대한 포괄적인 이해를 넓혀 줄 것이다.

• Molecules and Cells
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• 제25권3호
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• pp.407-416
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• 2008

Thirteen near-isogenic lines (NILs) of japonica rice were developed via a backcross method using the recurrent parent Chucheong, which is of good eating quality but is susceptible to Magnaporthe grisea, and three blast resistant japonica donors, Seolak, Daeseong and Bongkwang. The agro-morphological traits of these NILs, such as heading date, culm length, and panicle length, were similar to those of Chucheong. In a genome-wide scan using 158 SSR markers, chromosome segments of Chucheong were identified in most polymorphic regions of the 13 NIL plants, and only a few chromosome segments were found to have been substituted by donor alleles. The genetic similarities of the 13 NILs to the recurrent parent Chucheong averaged 0.961, with a range of 0.932-0.984. Analysis of 13 major blast resistance (R) genes in these lines using specific DNA markers showed that each NIL appeared to contain some combination of the four R genes, Pib, Pii, Pik-m and Pita-2, with the first three genes being present in each line. Screening of nine M. grisea isolates revealed that one NIL M7 was resistant to all nine isolates; the remaining NILs were each resistant to between three and seven isolates, except for NIL M106, which was resistant to only two isolates. In a blast nursery experiment, all the NILs proved to be more resistant than Chucheong. These newly developed NILs have potential as commercial rice varieties because of their increased resistance to M. grisea combined with the desirable agronomic traits of Chucheong. They also provide material for studying the genetic basis of blast resistance.

• Clinical and Experimental Pediatrics
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• 제55권1호
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• pp.18-23
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• 2012

Purpose: Transforming growth factor beta receptor 2 ($TGFBR2$) is a tumor suppressor gene that plays a role in the differentiation of striated cells and remodeling of coronary arteries. Single nucleotide polymorphisms (SNPs) of this gene are associated with Marfan syndrome and sudden death in patients with coronary artery disease. Cardiovascular remodeling and T cell activation of $TGFBR2$ gene suggest that the $TGFBR2$ gene SNPs are related to the pathogenesis of Kawasaki disease (KD) and coronary artery lesion (CAL). Methods: The subjects were 105 patients with KD and 500 healthy adults as controls. Mean age of KD group was 32 months age and 26.6% of those had CAL. We selected $TGFBR2$ gene SNPs from serum and performed direct sequencing. Results: The sequences of the eleven SNPs in the $TGFBR2$ gene were compared between the KD group and controls. Three SNPs (rs1495592, rs6550004, rs795430) were associated with development of KD ($P$=0.019, $P$=0.026, $P$=0.016, respectively). One SNP (rs1495592) was associated with CAL in KD group ($P$=0.022). Conclusion: Eleven SNPs in $TGFBR2$ gene were identified at that time the genome wide association. But, with the change of the data base, only six SNPs remained associated with the $TGFBR2$ gene. One of the six SNPs (rs6550004) was associated with development of KD. One SNP associated with CAL (rs1495592) was disassociated from the $TGFBR2$ gene. The other five SNPs were not functionally identified, but these SNPs are notable because the data base is changing. Further studies involving larger group of patients with KD are needed.

• 한국자원식물학회지
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• 제27권6호
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• pp.687-700
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• 2014

Rice blast (Magnaporthe oryza B.) is one of the most important diseases in rice that causing great yield losses every year around the world. It is important to screen valuable genetic resources for improving blast resistance. This study was conducted to identify the blast resistance in 279 Korean rice landraces using blast nursery tests and isolate inoculum screening. The results showed that 11 landrace accessions found to be resistant to rice blast in blast nursery and inoculation screening tests and the degree of lesions in most accessions showed that they were susceptible to reactions. In order to find the distribution of blast resistant genes, a molecular survey was conducted to identify the presence of major blast resistance (R) gene in 279 Korean landraces. The results revealed that their frequency distribution was Pik-m (36.2%), Piz (25.4%), Pit (13.6%), and Pik (10%). Besides, the frequency distribution of Piz-t, Pii, Pik-m/Pik-p, Pi-39(t), Pib, Pi-d(t)2, Pita/Pita-2 and Pi-ta genes were identified as less than 10%. The results did not consist with the reactions against blast diseases between genotypes and phenotypic part of the nursery tests and isolate inoculation. For concluding these results, we used genome-wide SSR markers that have closely been located with resistance genes. The PCoA analysis showed that the landrace accessions formed largely two distinct groups according to their degree of blast resistance. By comparing genetic diversities using polymorphic information contents (PIC) value among the resistant, total and susceptible landraces, we found that PIC values decreased in four SSR markers and increased in six markers in the resistant accessions, which showed contrary to total and susceptible groups. These regions might be linked to resistance alleles. In this study, we evaluated the degree of blast resistance and the information about the distribution of rice blast resistant genes in Korean rice landraces. This study might be the basis for association analysis of blast resistance in rice.

• Journal of the Korean Data and Information Science Society
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• 제25권5호
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• pp.1057-1067
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• 2014

인간게놈 프로젝트 이후 질병과 연관된 변이유전자를 탐색하기 위해 유전형질의 차이에 영향을 주는 단일 유전자를 중심으로 전장유전체 연관성 연구가 활발하게 진행되어왔다. 그러나 전장유전체 연관성 연구에서 접근한 단일유전자 분석방법에 한계점이 발견되면서 최근에는 다중유전자 분석방법이나 유전자-유전자간의 상호작용에 대한 연구들이 활발하게 진행 중이다. 이 중 다중차원축소방법은 유전자-유전자간의 상호작용의 연관성을 찾아내기 위하여 고차원을 일차원으로 축소하는 방법으로 이진형 반응변수를 기반으로 크게 활용되고 있다. 본 논문에서는 이 방법을 생존시간으로 확장하여 생존시간과 연관된 유전자-유전자간의 상호작용을 찾아내는 방법을 제안하고자 한다. 구체적으로 가속화 고장시간 회귀모형 하에서 표준화잔차 스코어를 분류기준으로 사용하여 다중차원축소방법을 적용하는 방법으로 AFT-MDR이라고 지칭하였다. 시뮬레이션 연구를 통하여 기존에 제안된 Surv-MDR과 Cox-MDR과의 검정력을 비교하였으며 국내의 백혈병환자 자료분석에 적용하였다. 시뮬레이션 결과로부터 AFT-MDR은 유전율이 높을수록 검정력이 커지며 회귀모형에 기반하여 공변량의 효과를 고려할 수 있다는 장점이 있으나 센서링 비율이 높아지면서 검정력이 매우 떨어진다는 단점이 발견되었다. 따라서 이를 보완하기 위한 추후연구의 필요성이 요구된다.

• 화훼연구
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• 제18권3호
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• pp.193-200
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• 2010

현재 재배되고 있는 장미 재배종은 오랜 기간 동안 종간교잡과 종내교잡을 통해 선발되어 온 것으로서 대부분이 이형잡종의 게놈으로 구성되어 있어 발아율이 저조한 편이다. 따라서, 효율적인 교배를 위해서는 화분의 활력 검정이 선행되어야 한다. 이에 본 연구에서는 염색액과 발아배지를 이용하여 7품종의 화분 임성율과 발아율 검정하고 이들 결과를 토대로 화분의 크기, 배수성 및 교배조합과의 상관관계를 알아보고자 실시하였다. 화분 임성율은 '스칼렛미미'가 82%로 가장 높았으며 '피노키오'가 39%로 가장 낮았다. 발아율 관찰 결과 '스칼렛미미'가 41%로 가장 높았으며 '미니로사'가 1%로 가장 낮았다. 화분의 크기를 관찰한 결과 화분은 큰 화분과 작은 화분으로 구분되었으며 화분의 직경은 각각 $41.3-45.4{\mu}m$과 $30.7-37.4{\mu}m$로 관찰되었으며 화분의 크기는 10-40% 정도 차이가 있는 것으로 나타났다. 화분의 크기와 염색체 전체 길이의 합을 비교한 결과 염색체 크기와 화분의 크기는 정의 상관관계가 있음을 알 수 있었다. 교배조합 검정 결과 착과율과 발아율은 화분 발아율, 임성률 및 배수성과 상관관계가 있음을 확인하였다.

• Genes and Genomics
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• 제40권11호
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• pp.1181-1197
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• 2018

Tropical plant rubber tree (Hevea brasiliensis) is the sole source of commercial natural rubber and low-temperature stress is the most important limiting factor for its cultivation. To characterize the gene expression profiles of H. brasiliensis under the cold stress and discover the key cold stress-induced genes. Three cDNA libraries, CT (control), LT2 (cold treatment at $4^{\circ}C$ for 2 h) and LT24 (cold treatment at $4^{\circ}C$ for 24 h) were constructed for RNA sequencing (RNA-Seq) and gene expression profiling. Quantitative real time PCR (qRT-PCR) was conducted to validate the RNA-Seq and gene differentially expression results. A total of 1457 and 2328 differentially expressed genes (DEGs) in LT2 and LT24 compared with CT were respectively detected. Most significantly enriched KEGG pathways included flavonoid biosynthesis, phenylpropanoid biosynthesis, plant hormone signal transduction, cutin, suberine and wax biosynthesis, Pentose and glucuronate interconversions, phenylalanine metabolism and starch and sucrose metabolism. A total of 239 transcription factors (TFs) were differentially expressed following 2 h or/and 24 h of cold treatment. Cold-response transcription factor families included ARR-B, B3, BES1, bHLH, C2H, CO-like, Dof, ERF, FAR1, G2-like, GRAS, GRF, HD-ZIP, HSF, LBD, MIKC-MADS, M-type MADS, MYB, MYB-related, NAC, RAV, SRS, TALE, TCP, Trihelix, WOX, WRKY, YABBY and ZF-HD. The genome-wide transcriptional response of rubber tree to the cold treatments were determined and a large number of DEGs were characterized including 239 transcription factors, providing important clues for further elucidation of the mechanisms of cold stress responses in rubber tree.

• Molecules and Cells
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• 제41권12호
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• pp.1061-1071
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• 2018

From Xenopus embryo studies, the BMP4/Smad1-targeted gene circuit is a key signaling pathway for specifying the cell fate between the ectoderm and neuro-ectoderm as well as the ventral and dorsal mesoderm. In this context, several BMP4/Smad1 target transcriptional factors have been identified as repressors of the neuro-ectoderm. However, none of these direct target transcription factors in this pathway, including GATA1b, Msx1 and Ventx1.1 have yet been proven as direct repressors of early neuro-ectodermal gene expression. In order to demonstrate that Ventx1.1 is a direct repressor of neuro-ectoderm genes, a genome-wide Xenopus ChIP-Seq of Ventx1.1 was performed. In this study, we demonstrated that Ventx1.1 bound to the Ventx1.1 response cis-acting element 1 and 2 (VRE1 and VRE2) on the promoter for zic3, which is a key early neuro-ectoderm gene, and this Ventx1.1 binding led to repression of zic3 transcription. Site-directed mutagenesis of VRE1 and VRE2 within zic3 promoter completely abolished the repression caused by Ventx1.1. In addition, we found both the positive and negative regulation of zic3 promoter activity by FoxD5b and Xcad2, respectively, and that these occur through the VREs and via modulation of Ventx1.1 levels. Taken together, the results demonstrate that the BMP4/Smad1 target gene, Ventx1.1, is a direct repressor of neuro-ectodermal gene zic3 during early Xenopus embryogenesis.

• Clinical and Experimental Pediatrics
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• 제61권12호
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• pp.403-406
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• 2018

Floating-Harbor syndrome is a rare autosomal dominant genetic disorder associated with SRCAP mutation. To date, approximately 50 cases of Floating-Harbor syndrome have been reported, but none have been reported in Korea yet. Floating-Harbor syndrome is characterized by delayed bony maturation, unique facial features, and language impairment. Here, we present a 6-year-old boy with a triangular face, deep-set protruding eyes, low-set ears, wide nose with narrow nasal bridge, short philtrum, long thin lips, clinodactyly, and developmental delay that was transferred to our pediatric clinic for genetic evaluation. He showed progressive delay in the area of language and cognition-adaption as he grew. He had previously undergone chromosomal analysis at another hospital due to his language delay, but his karyotype was normal. We performed targeted exome sequencing, considering several syndromes with similar phenotypes. Library preparation was performed with the TruSight One sequencing panel, which enriches the sample for about 4,800 genes of clinical relevance. Massively parallel sequencing was conducted with NextSeq. An identified variant was confirmed by Sanger sequencing of the patient and his parents. Finally, the patient was confirmed as the first Korean case of Floating-Harbor syndrome with a novel SRCAP (Snf2 related CREBBP activator protein) mutation (c.7732dupT, p.Ser2578Phefs*6), resulting in early termination of the protein; it was not found in either of his healthy parents or a control population. To our knowledge, this is the first study to describe a boy with Floating-Harbor syndrome with a novel SRCAP mutation diagnosed by targeted exome sequencing in Korea.