• The Plant Pathology Journal
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• 제40권2호
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• pp.171-191
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• 2024

Identification of Helicotylenchus species is very challenging due to phenotypic plasticity and existence of cryptic species complexes. Recently, the use of rDNA barcodes has proven to be useful for identification of Helicotylenchus. Molecular markers are a quick diagnostic tool and are crucial for discriminating related species and resolving cryptic species complexes within this speciose genus. However, DNA barcoding is not an error-free approach. The public databases appear to be marred by incorrect sequences, arising from sequencing errors, mislabeling, and misidentifications. Herein, we provide a comprehensive analysis of the newly obtained, and published DNA sequences of Helicotylenchus, revealing the potential faults in the available DNA barcodes. A total of 97 sequences (25 nearly full-length 18S-rRNA, 12 partial 28S-rRNA, 16 partial internal transcribed spacer [ITS]-rRNA, and 44 partial cytochrome c oxidase subunit I [COI] gene sequences) were newly obtained in the present study. Phylogenetic relationships between species are given as inferred from the analyses of 103 sequences of 18S-rRNA, 469 sequences of 28S-rRNA, 183 sequences of ITS-rRNA, and 63 sequences of COI. Remarks on suggested corrections of published accessions in GenBank database are given. Additionally, COI gene sequences of H. dihystera, H. asiaticus and the contentious H. microlobus are provided herein for the first time. Similar to rDNA gene analyses, the COI sequences support the genetic distinctness and validity of H. microlobus. DNA barcodes from type material are needed for resolving the taxonomic status of the unresolved taxonomic groups within the genus.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2000년도 International Symposium on Bioinformatics
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• pp.17-20
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• 2000

Structural genomics aims to provide a good experimental structure or computational model of every tractable protein in a complete genome. Underlying this goal is the immense value of protein structure, especially in permitting recognition of distant evolutionary relationships for proteins whose sequence analysis has failed to find any significant homolog. A considerable fraction of the genes in all sequenced genomes have no known function, and structure determination provides a direct means of revealing homology that may be used to infer their putative molecular function. The solved structures will be similarly useful for elucidating the biochemical or biophysical role of proteins that have been previously ascribed only phenotypic functions. More generally, knowledge of an increasingly complete repertoire of protein structures will aid structure prediction methods, improve understanding of protein structure, and ultimately lend insight into molecular interactions and pathways. We use computational methods to select families whose structures cannot be predicted and which are likely to be amenable to experimental characterization. Methods to be employed included modern sequence analysis and clustering algorithms. A critical component is consultation of the presage database for structural genomics, which records the community's experimental work underway and computational predictions. The protein families are ranked according to several criteria including taxonomic diversity and known functional information. Individual proteins, often homologs from hyperthermophiles, are selected from these families as targets for structure determination. The solved structures are examined for structural similarity to other proteins of known structure. Homologous proteins in sequence databases are computationally modeled, to provide a resource of protein structure models complementing the experimentally solved protein structures.

• 한국가금학회지
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• 제22권1호
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• pp.15-31
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• 1995

This study was carried out to develop a computer software system for poultry breeding by using microcomputer(PC). Through this study, SPPB(Statistical Package for Poultry Breeding) was designed and developed, which can help poultry breeder collect and analyse the chick records. A main feature of the system was the application of user-oriented procedure, for example, choice of the flock file, selection of the family size and the desired traits. Creation of the data files and the breeding files. calculation of the elementary statistics, estimation of the heritability and the genetic and phenotypic correlation coefficients can be obtained by user's choice of the sire and dam family size. Also, it is possible to estimate the various selection indices through this system. Easiness of using this system and the flexibility of the file management could help increasing the efficiency of related practical poultry breeding jobs. Correctness and relationships between the unit programs in the system were proved through the run-test of the SPPB using sample data. Because it wasn't able to collect breeding records at the commercial breeding farm, effectiveness of the system was not proved totally. Also. it will be necessary to develop the integrated software system which make possible to computerize the general works at breeding farm and the genetic analyses of the records from chick breeders.

• Journal of Dairy Science and Biotechnology
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• 제18권1호
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• pp.47-60
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• 2000

Over decades of work, the probiotic research has grown rapidly with a number of new cultures, which is claimed a variety of benefit. However, many of the specific effects attributed to the ingestion of probiotics remain convoluted and scientifically unsubstantiated. Accordingly, the scientific community faces a greater challenge and must objectively seek cause and effect relationships for many potential and currently investigated probiotic species. Rational selection and design of probiotics remains an important challenge and will require a solid information about the physiology and genetics of candidate strains relevant to their intestinal roles, functional activities, and interaction of with other resident micro flora. As far as beneficial culture of lactic acid bacteria (LAB) is concerned, simple, cost-effective, and exact identification of candidate strains is of foremost importance among others. Until recently, the relatedness of bacterial isolates has been determined sorely by testing for one or several phenotyphic markers, using methods such as serotyping, phage-typing, biotyping, and so forth. However, there are problems in the use of many of these phenotype-based methods. In contrast, some of newer molecular typing methods involving the analysis of DNA offer many advantages over traditional techniques. These DNA-based methods have the greater discriminatory power than that of phenotypic procedures. This review focuses on the importance and the basis of molecular typing methods along with some considerations on de-sign and selection of probiotic culture for human consumption.

• Journal of Animal Science and Technology
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• 제46권1호
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• pp.31-38
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• 2004

본 연구는 산차, 계절, 영양상태, 번식주기에 따라 변화하는 한우 빈우의 몸 상태(Body Condition)를 주기적으로 등급화 하여 조사한 값과 동일한 시기에 조사된 한우 번식우의 발육 및 번식형질과의 상관관계를 추정하고, 한우 빈우에서 측정된 몽상태 점수(Body Condition Score, BCS)를 번식 및 사양관리의 수단으로 적용할 수 있는 범위의 기초자료로 제공하고자 실시하였다. 각 형질별 최소자승평균을 추정하였는 바, 분만간격은 406.7일, 임신기간은 287.7일, 분만후 첫종부 일수는 66.2일, 수태당 종부횟수는 1.78회였다. 송아지 생시체중은 23.3kg, 이유시 체중은 70.7kg 이었다. 종부시 BCS와 분만시 BCS의 평균은 4.55, 5.29 이었으며, 수태당 종부횟수를 BCS 점수에 따라 추정한 바, 종부시 BCS가 5 이하에서는 1.50${\sim}$1.74회였으나, 6 이상에서는 2.00${\sim}$3.00회 로 나타났다. 종부시와 분만시 BCS의 분포는 종부시에는 BCS 4${\sim}$5에 서 57%를, 분만시 BCS 5${\sim}$6에 서 46%로 나타내었다. 주요 번식형질의 표현형 상관은 종부시 BCS와 분만시 BCS, 분만간격, 임신기간, 수태당 종부횟수 사이에는 0.16, 0.26, 0.08, 0.06으로 정의 상관을 보였고, 분만시 BCS와 분만간격, 임신기간, 수태당 종부횟수 사이에는 0.10, 0.13, 0.10으로 역시 정의 상관관계를 보였으나, 분만간격과 임신기간, 임신기간과 수태당 종부횟수간에는 -0.11, - 0.13으로 부의 상관을 보였다.

• Animal Bioscience
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• 제36권7호
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• pp.991-1002
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• 2023

Objective: This study aimed to elucidate the underlying gene regions responsible for productive, phenotypic or adaptive traits in different ecological types of Tibetan sheep and the discovery of important genes encoding valuable traits. Methods: We used whole-genome resequencing to explore the genetic relationships, phylogenetic tree, and population genetic structure analysis. In addition, we identified 28 representative Tibetan sheep single-nucleotide polymorphisms (SNPs) and genomic selective sweep regions with different traits in Tibetan sheep by fixation index (Fst) and the nucleotide diversity (θπ) ratio. Results: The genetic relationships analysis showed that each breed partitioned into its own clades and had close genetic relationships. We also identified many potential breed-specific selective sweep regions, including genes associated with hypoxic adaptability (MTOR, TRHDE, PDK1, PTPN9, TMTC2, SOX9, EPAS1, PDGFD, SOCS3, TGFBR3), coat color (MITF, MC1R, ERCC2, TCF25, ITCH, TYR, RALY, KIT), wool traits (COL4A2, ERC2, NOTCH2, ROCK1, FGF5, SOX9), and horn phenotypes (RXFP2). In particular, a horn-related gene, RXFP2, showed the four most significantly associated SNP loci (g. 29481646 A>G, g. 29469024 T>C, g. 29462010 C>T, g. 29461968 C>T) and haplotypes. Conclusion: This finding demonstrates the potential for genetic markers in future molecular breeding programs to improve selection for horn phenotypes. The results will facilitate the understanding of the genetic basis of production and adaptive unique traits in Chinese indigenous Tibetan sheep taxa and offer a reference for the molecular breeding of Tibetan sheep.

• 한국균학회지
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• 제23권3호통권74호
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• pp.246-256
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• 1995

잿빛곰팡이병균(Botrytis cinerea) 51균주를 국내 여러곳에서 분리 또는 확보하여 이들 균주의 기주, 형태적 특성, 약제저항성 및 polygalacturonase 활성을 조사하였으며, 분리 기주별로 병원성을 포함한 이들 특성의 상호관계를 조사하였다. 분리된 균주들은 모두 흰색, 엷은 회색 또는 짙은 회색의 균총색을 보였고, 균주에 따라 균핵과 포자형성량이 달랐다. 병원성 검정에서는 토마토, 오이, 딸기로부터 분리된 균주들의 오이잎 괴사병반 지름이 평균 3.2 cm로 감귤, 양다래, 배 등 다른 기주로부터 분리된 균주의 1.8 cm보다 훨씬 컸다. 각 균주들의 살균제 저항성은 토마토 분리균주들의 benomyl 저항성이 $EC_{50}$ 562 ppm으로 다른 균주에 비해 훨씬 높았으며, 딸기 분리균주의 경우 사용된지 얼마되지 않은 diethofencarb에 대하여 $EC_{50}$ 210 ppm으로 높은 저항성을 나타내었다. Polygalacturonase 활성은 균주간에 변이가 심하여 specific activity가 최저 0 unit부터 103 unit까지 걸쳐 있었으며, 토마토, 오이, 딸기 등 주요 기주로부터 분리된 균주가 그렇지 않은 균주에 비해 약간 낮은 경향을 보였다. 균주들의 효소활성, 살균제 저항성과 병원성간에는 직접적인 상관관계가 없었다. 그러나, 병원성이 강한 균주와 약한 균주의 polygalacturonase 동위효소 pattern은 배양시 탄소원에 따라 서로 약간의 차이가 있었다.

• 한국작물학회지
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• 제56권4호
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• pp.322-328
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• 2011

우리나라에서 수집한 재래종 조 26계통들에 대하여 9개의 AFLP primer조합을 사용하여 유전적 다양성 및 계통유연관계를 분석한 결과는 다음과 같다. 1. 분석에 이용한 9개의 AFLP primer조합들은 국내에서 수집한 조 26계통들에서 총 170개의 DNA단편을 나타내었고, 이중에서 145개의 단편(85.3%)들은 다형성을 나타내었다. 9개의 AFLP primer조합들에서 측정된 유전적 다양성 값(Hs)은 1.84에서 6.80의 범위로 나타나, 평균 3.85값을 나타내었다. 강원지역에서 수집한 조 계통(Group 1)들은 평균 3.39의 유전적 다양성 값을 나타내었고, 경기도 등 타 지역에서 수집한 조 계통들(Group 2)은 평균 2.99의 유전적 다양성 값을 나타내었다. 2. 국내에서 수집된 재래종 조 26계통들은 유전적 유사성 73% 수준에서 크게 두 개의 그룹으로 구분되었다. Group I은 유전적 유사성 76.8% 수준에서 강원도에서 수집한 13계통들과 경기도에서 수집한 1계통을 포함하고 있었으며, Group II는 유전적 유사성 78.9% 수준에서 강원도에서 수집한 2계통들과 타 지역에서 수집한 10계통들을 포함하고 있었다. 본 연구결과는 우리나라에서 수집한 재래종 조 계통들에 대한 유전적 다양성 및 계통유연관계 이해 그리고 이들 자원의 수집 및 보존 등에 유용한 정보를 제공할 것으로 기대된다.

• Asian-Australasian Journal of Animal Sciences
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• 제28권9호
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• pp.1259-1265
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• 2015

The present study was performed to study the genetic relationship of productive life with production and type traits of Korean Holsteins at first three lactations. The data for the analysis from 56,054, 28,997, and 11,816 animals of first, second and third parity cows which were born from 2006 to 2011 were collected by Dairy Cattle Improvement Center, National Agricultural Co-operative Federation. Milk, protein and fat yields adjusted for 305 days and average somatic cell score considered as production traits and analyzed type traits were stature, strength, body depth, dairy form, rump angle, rump width, rear leg side view, foot angle, front attachment placement, rear attachment height, rear attachment width, udder cleft, udder depth, front teat placement and front teat length. A multi trait genetic analysis was performed using Wombat program with restricted maximum likelihood animal model composed of fixed effect of birth year, farm and the random effect of animal and random residual effect according to the traits. Heritability estimates of productive life were between 0.06 and 0.13. Genetic and phenotypic correlations between production and productive life traits ranged from 0.35 to 0.04 for milk, 0.16 to 0.05 for protein and 0.18 to 0.02 f 15-0034 (2nd) 150520 or fat. Somatic cells score showed a negative genetic and phenotypic correlation with productive life and also udder type traits, indicating that the selection for higher udder traits will likely to improve resistance to mastitis and persistence in the herd. Among all dairy form type traits, udder characters such as udder cleft showed a significant relationship with productive life. However, a specific change of heritabilities or correlations were not observed with the change of parity. Moreover, further studies are needed to further confirm the significance of the above traits and the effect of parity on above relationships in order to minimize both voluntary and involuntary culling rates while improving herd health and maintaining high yielding dairy cows.

• Asian-Australasian Journal of Animal Sciences
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• 제19권12호
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• pp.1678-1684
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• 2006

The objectives of this study were to estimate genetic parameters and sire breeding values for average daily gain (ADG) and carcass traits using sire-maternal grandsire model with REML approach, sire model with REML approach, sire model without relationships among sires and with REML and ANOVA approach, and to investigate advantages and disadvantages of these methods. Data were collected from 42,325 Japanese Black steers and heifers finished and slaughtered from 1991 to 2004. Traits analyzed in this study were average daily gain (ADG) during the fattening period, live weight at slaughter (LW), cold carcass weight (CW), estimated lean yield percentage (LYE), longissimus muscle area (LMA), subcutaneous fat thickness (SFT), rib thickness (RT), and marbling score (BMS). Bivariate analyses were also performed to obtain genetic and phenotypic correlation coefficients among traits. Estimated breeding values were obtained from each model, and simple and rank correlations among breeding values from each model were calculated. Estimates of heritability using the four models ranged from 0.25 to 0.31 in ADG, from 0.21 to 0.24 in LW, from 0.23 to 0.27 in CW, from 0.10 to 0.17 in DP, from 0.40 to 0.42 in LYE, from 0.19 to 0.31 in LMA, from 0.31 to 0.34 in SFT, from 0.26 to 0.33 in RT, and from 0.18 to 0.44 in BMS. The differences in heritability estimates using the four models seemed to be feasible in ADG, CW, DP, LMA, RT, and BMS. Genetic correlation coefficients of ADG with CW, SFT, RT and BMS were moderate to high and positive while the genetic correlation coefficients between ADG and LYE was low and negative. Correlation coefficients of BMS with SFT were negligible for both genetic and phenotypic correlations. The correlations of estimates evaluated from sire models with those from sire-maternal grandsire model were not large enough to convincing that breeding values using a sire model were corresponding to those using a sire-maternal grand sire model. If information of maternal grand sires are not available, the sire model with incomplete pedigree information included only sire of sire (Model 2) is optimal among the sire models evaluated in this study.