• Animal Bioscience
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• 제35권9호
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• pp.1303-1313
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• 2022

Objective: The current study aimed to perform whole-genome resequencing of Chinese indigenous Mongolian sheep breeds including Ujimqin, Sunit, and Wu Ranke sheep breeds (UJMQ, SNT, WRK) and deeply analyze genetic variation, population structure, domestication, and selection for domestication traits among these Mongolian sheep breeds. Methods: Blood samples were collected from a total of 60 individuals comprising 20 WRK, 20 UJMQ, and 20 SNT. For genome sequencing, about 1.5 ㎍ of genomic DNA was used for library construction with an insert size of about 350 bp. Pair-end sequencing were performed on Illumina NovaSeq platform, with the read length of 150 bp at each end. We then investigated the domestication and signatures of selection in these sheep breeds. Results: According to the population and demographic analyses, WRK and SNT populations were very similar, which were different from UJMQ populations. Genome wide association study identified 468 and 779 significant loci from SNT vs UJMQ, and UJMQ vs WRK, respectively. However, only 3 loci were identified from SNT vs WRK. Genomic comparison and selective sweep analysis among these sheep breeds suggested that genes associated with regulation of secretion, metabolic pathways including estrogen metabolism and amino acid metabolism, and neuron development have undergone strong selection during domestication. Conclusion: Our findings will facilitate the understanding of Chinese indigenous Mongolian sheep breeds domestication and selection for complex traits and provide a valuable genomic resource for future studies of sheep and other domestic animal breeding.

• Animal Bioscience
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• 제35권9호
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• pp.1340-1350
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• 2022

Objective: Luxi Black Head sheep (LBH) is the first crossbreed specialized for meat production and was developed by crossbreeding Black Head Dorper sheep (DP) and Small Tailed Han sheep (STH) in the farming areas of northern China. Research on the genomic variations and selection signatures of LBH caused by continuous artificial selection is of great significance for identifying the genetic mechanisms of important traits of sheep and for the continuous breeding of LBH. Methods: We explored the genetic relationships of LBH, DP, and several Mongolian sheep breeds by constructing phylogenetic tree, principal component analysis and linkage disequilibrium analysis. In addition, we analysed 29 whole genomes of sheep. The genome-wide selection signatures have been scanned with four methods: heterozygosity (H_P), fixation index (F_ST), cross-population extended haplotype homozygosity (XP-EHH) and the nucleotide diversity (𝜃_π) ratio. Results: The genetic relationships analysis showed that LBH appeared to be an independent cluster closer to DP. The candidate signatures of positive selection in sheep genome revealed candidate genes for developmental process (HoxA gene cluster, BCL2L11, TSHR), immunity (CXCL6, CXCL1, SKAP2, PTK6, MST1R), growth (PDGFD, FGF18, SRF, SOCS2), and reproduction (BCAS3, TRIM24, ASTL, FNDC3A). Moreover, two signalling pathways closely related to reproduction, the thyroid hormone signalling pathway and the oxytocin signalling pathway, were detected. Conclusion: The selective sweep analysis of LBH genome revealed candidate genes and signalling pathways associated with developmental process, immunity, growth, and reproduction. Our findings provide a valuable resource for sheep breeding and insight into the mechanisms of artificial selection.

• Genomics & Informatics
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• 제8권3호
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• pp.131-137
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• 2010

Genome-wide association studies (GWASs) have greatly contributed to the identification of common variants responsible for numerous complex traits. There are, however, unavoidable limitations in detecting causal and/or rare variants for traits in this approach, which depends on an LD-based tagging SNP microarray chip. In an effort to detect potential casual and/or rare variants for complex traits, such as type 2 diabetes (T2D) and triglycerides (TGs), we conducted a targeted resequencing of loci identified by the Korea Association REsource (KARE) GWAS. The target regions for resequencing comprised whole exons, exon-intron boundaries, and regulatory regions of genes that appeared within 1 Mb of the GWA signal boundary. From 124 individuals selected in population-based cohorts, a total of 0.7 Mb target regions were captured by the NimbleGen sequence capture 385K array. Subsequent sequencing, carried out by the Roche 454 Genome Sequencer FLX, generated about 110,000 sequence reads per individual. Mapping of sequence reads to the human reference genome was performed using the SSAHA2 program. An average of 62.2% of total reads was mapped to targets with an average 22X-fold coverage. A total of 5,983 SNPs (average 846 SNPs per individual) were called and annotated by GATK software, with 96.5% accuracy that was estimated by comparison with Affymetrix 5.0 genotyped data in identical individuals. About 51% of total SNPs were singletons that can be considered possible rare variants in the population. Among SNPs that appeared in exons, which occupies about 20% of total SNPs, 304 nonsynonymous singletons were tested with Polyphen to predict the protein damage caused by mutation. In total, we were able to detect 9 and 6 potentially functional rare SNPs for T2D and triglycerides, respectively, evoking a further step of replication genotyping in independent populations to prove their bona fide relevance to traits.

• Genomics & Informatics
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• 제21권3호
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• pp.34.1-34.10
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• 2023

Nosocomial infections, commonly referred to as healthcare-associated infections, are illnesses that patients get while hospitalized and are typically either not yet manifest or may develop. One of the most prevalent nosocomial diseases in hospitalized patients is pneumonia, among the leading causes of mortality and morbidity. Viral, bacterial, and fungal pathogens cause pneumonia. More severe introductions commonly included Staphylococcus aureus, which is at the top of bacterial infections, per World Health Organization reports. The staphylococci, S. aureus, strain RMI-014804, mesophile, on-sporulating, and non-motile bacterium, was isolated from the sputum of a pulmonary patient in Pakistan. Many characteristics of S. aureus strain RMI-014804 have been revealed in this paper, with complete genome sequence and annotation. Our findings indicate that the genome is a single circular 2.82 Mbp long genome with 1,962 protein-coding genes, 15 rRNA, 49 tRNA, 62 pseudogenes, and a GC content of 28.76%. As a result of this genome sequencing analysis, researchers will fully understand the genetic and molecular basis of the virulence of the S. aureus bacteria, which could help prevent the spread of nosocomial infections like pneumonia. Genome analysis of this strain was necessary to identify the specific genes and molecular mechanisms that contribute to its pathogenicity, antibiotic resistance, and genetic diversity, allowing for a more in-depth investigation of its pathogenesis to develop new treatments and preventive measures against infections caused by this bacterium.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2022년도 추계학술대회
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• pp.30-30
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• 2022

Philippines is the second world supplier of coconut by-products. As its first major genomics project, the Philippine Genome Center program for Agriculture (PGC-Agriculture) took the challenge to sequence and assemble the whole coconut genome. The project aims to provide advance genetics tools for our collaborating coconut researchers while taking the opportunity to initiate local capacity. Combination of different NGS platforms was explored and the Philippine 'Catigan Green Dwarf' (CATD) variety was selected with the breeders to be the crop's reference genome. A high quality genome assembly of CATD was generated and used to characterize important genes of coconut towards the development of resilient and outstanding varieties especially for added high-value traits. The talk will present the significant results of the project as published in various papers including the first report of whole genome sequence of a dwarf coconut variety. Updates will include the challenges hurdled and specific applications such as gene mining for host insect resistance and screening for least damaged coconuts (thus potentially insect resistant varieties). Genome-wide DNA markers as published and genes related to coconut oil qualitative/quantitative traits will also be presented, including initial molecular/biochemical studies that support nutritional and medicinal claims. A web-based genome database is currently built for ease access and wider utility of these genomics tools. Indeed, a major milestone accomplished by the coconut genomics research team, which was facilitated with the all-out government support and strong collaboration among multidisciplinary experts and partnership with advance research institutes.

• Journal of Plant Biotechnology
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• 제33권3호
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• pp.153-160
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• 2006

유전체 연구란 목적하는 유전체의 구조를 밝히고 가지고 있는 모든 유전자의 기능 및 진화과정을 망라하여 이해하고자 하는 것이다. 계통발생학상 애기장대와 연관되어 있는 Brassica rapa는 채소, 유지 및 사료로 이용되는 중요한 작물의 하나이다. Brassica rapa의 유전체 연구를 착수하는 데는 적합한 유전학적 재료 및 유전체 재료가 있어야 한다. 우리는 배추 (Brassica rapa spp. pekinensis)를 재료로 하여 표준 mapping 집단을 개발하여, 78계통으로 구성된 DH집단과 약 250 계통으로 구성된 RI집단을 개발하였다. 2가지 제한효소 (HintIII, BamHI)를 이용해 세균인공염색체 (BAC) library (KBrH, KBrB)를 만들었고, 이들은 각각 56,592개와 50,688개의 클론으로 구성되어 있다. 또한 배추의 각기 다른 부위를 이용하여 만든 22가지의 cDNA library를 이용하여 평균 575bp의 길이를 가지는 104,914개의 EST 분석을 실시 하였다. 세계적으로 'Multinational Brassica Genome Project (MBGP)' 조직이 구성되었고 배추의 전 염기서열 분석을 하기로 2003년 결정되었다. 그 첫 단계로 104,914개의 BAC 클론의 BAC-end 염기서열분석이 제안되어 2006년 9월 5개국 공동 프로젝트로 추진하여 완성하게 되었다. 이러한 BAC-end 염기서열분석의 결과는 유전자의 염기서열 해석, 및 풍부하게 존재하는 반복염기서열 DNA를 분석함으로써 배추의 유전체 구조를 이해할 수 있는 실마리를 주었다. BAC 클론의 전체 염기서열분석은, 비록 단편 내에 유전자의 결실이 변화무쌍하게 일어나지만 배추 DNA 단편이 유전체에서 광범위하게 삼중복으로 존재함을 나타냈다. 이러한 BAC-end 염기서열을 아기장대 염기서열에 비교하여 629개의 종자 BAC을 선정하게 되었고, 이들의 염기서열 분석을 완성하였다. MBGP에서는2단계로서 배추의 전 유전체 염기서열 분석을 추진하게 되었고, 유전자지도에 위치한 종자 BAC을 이용하여 인접한 BAC 클론을 찾아 염기서열 분석하는 BAC-to-BAC 방법을 추진하고 있으며 8개국에서 참여하여 현재 염기서열 분석을 추진 중 이다. 최근에 각 국에서는 생물정보학기법을 활용한 염기서열 분석 기반에 대하여 많은 토론이 진행되고 있다. 앞으로 다양한 유전체 정보가 축적됨에 따라 배추의 유전체 구조를 이해하고 농업적으로 적용하고자 하는데 기여를 할 것이다.

• Journal of Plant Biotechnology
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• 제3권1호
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• pp.39-44
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• 2001

Plastid transformation was attempted with soybean [Glycine max (L.) Merr.] leaves and photoautotrophic and embryogenic cultures by particle bombardment using the transforming vector pZVII that carries the coding sequences for both subunits of Chlamydomonas reinhardtii Rubisco and a spectinomycin resistance gene (aadA). Spectinomycin resistant calli were selected from the bombarded leaves but the transgene was not present, indicating that the resistance was due to mutations. The Chlamydomonas rbcL and rbcS genes were shown to be site-specifically integrated into the plastid genome of the embryogenic cells with a very low transformation efficiency. None of the transformed embryogenic lines survived the plant regeneration process so no whole plants were recovered. This result does indicate that it should be possible to insert genes into the plastid genome of the important crop soybean if the overall methods are improved.

• 한국유전체학회:학술대회논문집
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• 한국유전체학회 2004년도 The 13th Korea Genome Conference
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• pp.47.2-47.2
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• 2004

• 한국자원식물학회:학술대회논문집
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• 한국자원식물학회 2018년도 춘계학술발표회
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• pp.43-43
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• 2018

Dumortiera hirsuta (Sw.) Nees (Dumortieraceae) is a thallose liverwort distributed in tropics and subtropics. It is the only species in family Dumortieraceae, which is the second basal family in order Marchantiales. D. hirsuta is characterized by hairy receptacles and lacking air chamber. The complete chloroplast genome of D. hirsuta was successfully rescued from raw reads generated by HiSeq4000. Its total length is 122,050 bp consisting of four regions: large single copy (LSC) region (81,697 bp), small single copy (SSC) region (20,061 bp), and two inverted repeats (IRs; 10,146 bp per each). It contained 129 genes (84 coding DNA sequence (CDS), eight rRNAs, and 37 tRNAs); 18 genes including four rRNAs, and five tRNAs are duplicated in the IR regions. The overall GC content of D. hirsuta is 28.7%, which is almost same to that of Marchantia paleacea. Phylogenetic tree based on all genes from whole chloroplast genomes will provides phylogenetic position of D. hirstua. This sequence will be an fundamental resources for further researches of order Marchantiales.

• Journal of Preventive Medicine and Public Health
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• 제40권2호
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• pp.102-107
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• 2007

Human Genome Project (HGP) could unveil the secrets of human being by a long script of genetic codes, which enabled us to get access to mine the cause of diseases more efficiently. Two wheels for HGP, bioinformatics and high throughput technology are essential techniques for the genomic medicine. While microarray platforms are still evolving, we can screen more than 500,000 genotypes at once. Even we can sequence the whole genome of an organism within a day. Because the future medicne will focus on the genetic susceptibility of individuals, we need to find genetic variations of each person by efficient genotyping methods.