• Asian-Australasian Journal of Animal Sciences
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• v.32 no.9
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• pp.1340-1348
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• 2019

Objective: The objectives were to compare variance components, genetic parameters, prediction accuracies, and genomic-polygenic estimated breeding value (EBV) rankings for milk yield (MY) and fat yield (FY) in the Thai multibreed dairy population using five single nucleotide polymorphism (SNP) sets from GeneSeek GGP80K chip. Methods: The dataset contained monthly MY and FY of 8,361 first-lactation cows from 810 farms. Variance components, genetic parameters, and EBV for five SNP sets from the GeneSeek GGP80K chip were obtained using a 2-trait single-step average-information restricted maximum likelihood procedure. The SNP sets were the complete SNP set (all available SNP; SNP100), top 75% set (SNP75), top 50% set (SNP50), top 25% set (SNP25), and top 5% set (SNP5). The 2-trait models included herd-year-season, heterozygosity and age at first calving as fixed effects, and animal additive genetic and residual as random effects. Results: The estimates of additive genetic variances for MY and FY from SNP subsets were mostly higher than those of the complete set. The SNP25 MY and FY heritability estimates (0.276 and 0.183) were higher than those from SNP75 (0.265 and 0.168), SNP50 (0.275 and 0.179), SNP5 (0.231 and 0.169), and SNP100 (0.251and 0.159). The SNP25 EBV accuracies for MY and FY (39.76% and 33.82%) were higher than for SNP75 (35.01% and 32.60%), SNP50 (39.64% and 33.38%), SNP5 (38.61% and 29.70%), and SNP100 (34.43% and 31.61%). All rank correlations between SNP100 and SNP subsets were above 0.98 for both traits, except for SNP100 and SNP5 (0.93 for MY; 0.92 for FY). Conclusion: The high SNP25 estimates of genetic variances, heritabilities, EBV accuracies, and rank correlations between SNP100 and SNP25 for MY and FY indicated that genotyping animals with SNP25 dedicated chip would be a suitable to maintain genotyping costs low while speeding up genetic progress for MY and FY in the Thai dairy population.

• Genomics & Informatics
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• v.12 no.4
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• pp.254-260
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• 2014

Best linear unbiased prediction (BLUP) has been used to estimate the fixed effects and random effects of complex traits. Traditionally, genomic relationship matrix-based (GRM) and random marker-based BLUP analyses are prevalent to estimate the genetic values of complex traits. We used three methods: GRM-based prediction (G-BLUP), random marker-based prediction using an identity matrix (so-called single-nucleotide polymorphism [SNP]-BLUP), and SNP-SNP variance-covariance matrix (so-called SNP-GBLUP). We used 35,675 SNPs and R package "rrBLUP" for the BLUP analysis. The SNP-SNP relationship matrix was calculated using the GRM and Sherman-Morrison-Woodbury lemma. The SNP-GBLUP result was very similar to G-BLUP in the prediction of genetic values. However, there were many discrepancies between SNP-BLUP and the other two BLUPs. SNP-GBLUP has the merit to be able to predict genetic values through SNP effects.

• The KIPS Transactions:PartA
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• v.13A no.1 s.98
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• pp.79-86
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• 2006

Recently the tagSNP selection problem has been researched for reducing the cost of association studies between human's diversities and SNPs. General approach for this problem is that all of SNPs are separated into appropriate blocks and then tagSNPs are chosen in each block. Marsel in this paper is the system that involved the concept of linkage disequilibrium for overcoming the problem that the existing block partitioning approaches have short of biological meanings. In most approaches, the contiguous regions, which recombinations have LD coefficient |D'| and then tagSNP selection step is performed. And MarSel guarantees the minimum tagSNP selection using entropy-based optimal selection algorithm when tagSNPs are chosen in each block, and enables chromosome-level association studies using efficient memory management technique when input is very large-scale dataset that is impossible to be processed in the existing systems.

• The Korean Journal of Applied Statistics
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• v.21 no.1
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• pp.53-63
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• 2008

It is commonly believed that disease of human or economic traits of livestock are caused not by single gene acting alone, but by multiple genes interacting with one an-other. This issue is difficult due to the limitations of parametric statistical method like as logistic regression for detection of gene effects that are dependent solely on interactions with other genes and with environmental exposures. Multifactor dimensionality reduction (MDR) nonparametric statistical method, to improve the identification of single nucleotide polymorphism (SNP) associated with the Hanwoo(Korean cattle) carcass cold weight, is applied and compared with ANOVA results.

• Communications for Statistical Applications and Methods
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• v.16 no.1
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• pp.67-74
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• 2009

In order to make the high quality Korean cattle, it has been identified the gene markers which influence to various economic traits. To identify statistically significances among SNP markers, Lee et. al. (2008b) identified SNP(19_1)$^*$SNP(28_2) marker was an important marker in LMA(longissimus muscle dorsi area). In addition, CWT(carcass cold weight) and ADG(average daily gain) are applied for expanded multifactor dimensionality reduction (expanded MDR) method from the comprehensive economic traits. The results showed that SNP(19_1)$^*$SNP(28_2) interaction marker was good and a very meaningful for economic traits.

• Journal of applied mathematics & informatics
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• v.26 no.3_4
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• pp.493-500
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• 2008

In this paper, we first construct a mathematical model for tagSNP selection based on LD measure $r^2$, then aiming at this kind of model, we develop an efficient algorithm, which is called approximate greedy algorithm. This algorithm is able to make up the disadvantage of the greedy algorithm for tagSNP selection. The key improvement of our approximate algorithm over greedy algorithm lies in that it adds local replacement(or local search) into the greedy search, tagSNP is replaced with the other SNP having greater similarity degree with it, and the local replacement is performed several times for a tagSNP so that it can improve the tagSNP set of the local precinct, thereby improve tagSNP set of whole precinct. The computational results prove that our approximate greedy algorithm can always find more efficient solutions than greedy algorithm, and improve the tagSNP set of whole precinct indeed.

• Proceedings of the Korean Information Science Society Conference
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• 2006.06a
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• pp.19-21
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• 2006

Single Nucleotide Polymorphism(SNP)는 인간 유전자 서열의 0.1%에 해당하는 부분으로 이는 각 개인의 체질 및 각종 유전질환과 밀접한 관련이 있다고 알려져 있다. 최근 이 SNP정보의 패턴을 이용 질병의 진단 및 치료에 연관지으려는 노력이 시도되고 있다. 그러나 아직 SNP를 이용한 효율적인 분석방법에 대한 전산학적 연구는 많지 않다. 본 논문에서는 대표적인 패턴인식기 중 하나인 Support Vector Machine(SVM)을 이용 한국인의 대표적인 유전질환으로 알려진 만성간염에 대해서 관련된 SNP에 대한 패턴 인식율 측정을 실험하였다. 실험 데이터는 간 및 소화기 질환 유전체 센터에서 얻어진 만성간염 환자와 관련 SNP정보를 사용하였으며, 실험 결과 전체 SNP 정보를 모두 가지는 환자그룹에 대한 학습인식율이 66.46%로 나타났으며, 부분그룹에서는 72.91%로 높은 인식율을 보였다. 이 결과는 SNP 정보를 이용한 만성간염의 초기진단예측에 SVM을 효율적으로 사용할 수 있음을 보인다.

• Reproductive and Developmental Biology
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• v.28 no.2
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• pp.83-87
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• 2004

The objective of this study was performed to establish the in vitro culture system of porcine in vitro maturation and in vitro fertilization(IVM/IVF) embryo. These studies was to determine the effects of melatonin, nitric oxide donor(SNP), and the combination effects of SNP and melatonin in porcine IVM/IVF embryos. In routine porcine IVM/IVF procedure, oocytes were cultured for 40∼44h incubation, and the zygotes were cultured for 40∼44h in NCSU 23 medium. Then 2 to 8 cell embryos were removed cumulus cell and were allotted randomly to NCSU 23 containing different concentration of melatonin, SNP and SNP plus melatonin in 5% $O_2$, 5% $CO_2$ and 90% $N_2$ at 38.5$^{\circ}C$. Cell numbers of blastocyst were also counted using double fluorescence stain method. In NCSU 23 medium treated with melatonin 0, 1, 5 and 10 nM, the developmental rate of morula plus blastocysts were 33.3%, 39.1%, 33.3% and 27.9%, respectivly. This result show that the developmental rate of morula and blascytocys treated with 1 nM melatonin was higher than in any other groups(P<0.05). The developmental rates of morula plus blastocysts were 41.9% in 0 uM SNP, 25.6% in 50 uM and 28.4% in 100 uM, respectively. The developmental rate of morula plus blastocysts were decreased treated with SNP in NCSU 23. In combined effects of SNP plus melatonin (0, SNP 50 uM, SNP 50 uM plus melatonin 1 nM, SNP 50 uM plus melatonin 5 nM and SNP 50 uM plus melatonin 10 nM), the developmental rates beyond morula stage of porcine embryos were 31.3%, 34.1%, 39.5%, 29.4% and 39.5%, respectively. The addition of SNP 50 uM plus maltonin 1 nM, developmental rates of blastocyst was higher rate than in any other groups. Cell numbers of blastocyst in NCSU 23 treated with melatonin 0, 1, 5 and 10 nM were 41.0, 42.6, 39.6 and 33.0, respectively. In combined effects of SNP plus melatonin (0, SNP 50 uM, SNP 50 uM plus melatonin 1 nM , SNP 50 uM plus melatonin 5 nM and SNP 50 uM plus melatonin 10 nM), cell numbers of developed blastocyst were 36.3, 34.6, 39.0, 39.9 and 39.0, respectively. These result show that the cell numbers of blastocyst treated with 0, 1 and 5 nM melatonin were higher than in 10 nM group(P<0.05), but cell numbers of blatocyst produced by SNP plus melatonin were not significantly difference in all experimental groups.

• The Korean Journal of Physiology and Pharmacology
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• v.1 no.6
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• pp.797-808
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• 1997

Nitric oxide (NO) has been 3mown as a mediator of nonadrenergic, noncholinergic inhibitory neurotransmitter in intestinal smooth muscles. It has been suggested that NO donor such as sodium nitroprusside (SNP) produces relaxation of smooth muscle via activation of guanylate cyclase and elevation of cGMP levels. We have therefore investigated the effects of NO, using SNP, on muscle tension in the longitudinal smooth muscle of guinea-pig ileum. The possible role of cGMP was also investigated as well as the involvement of $K^+$ channel on SNP-induced inhibitory effect. The results are summarized as follows; high KCI-or CCh-activated contractions were inhibited by SNP in a concentration-dependent manner. 8-Br-cGMP also showed a similar effect in that of SNP TEA (1 mM) significantly reduced the SNP-induced inhibitory effect. SNP-induced effect was forther reduced by the presence of 10 mM TEA. On the other hand, 4-AP (0.1 mM), glibenclamide $(10\;{\mu}M)$ and apinain $(0.1\;{\mu}M)$ showed little effects on SNP-induced relaxation. Zaprinast significantly potentiated the SNP-induced inhibitory effect in all ranges. ODQ also significantly decreased the SNP-induced inhibitory effect. Pretreatment with CPA $(10\;{\mu}M)$ slightly reduced the SNP-induced inhibitory effect. From the above results, both effect mediated by NO and cGMP might be responsible for the activation of $Ca^{2+}$-activated $K^+$ channel by SNP in guinea-rig ileum. And this $K^+$ channel activation by SNP also contributes to the SNP-induced membrane hyperpolarization and relaxation.

• Journal of The Korean Society of Grassland and Forage Science
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• v.37 no.2
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• pp.168-175
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• 2017

Single nucleotide polymorphisms (SNP) markers allow rapid screening of crop varieties in early growth stages. We developed a modified SNP PCR procedure for assaying SNPs in maize. For SNP marker development, we chosen 200 SNP sites from MaizeGDB database, and designed two base pair mismatch primers based on putative SNP site of B73 genome sequence. PCR products size was from 200 to 500 bp or was not shown in the case of SNP site existing in Korean silage corns. Using previously discovered 16 primer sets, we investigated distinctness of 50 silage F1 hybrid corns including 10 Korean silage corns developed by RDA such as Gangdaok, Kwangpyeongok, Dapyeongok, Andaok, Yanganok, Singwangok, Jangdaok, Cheongdaok, Pyeonggangok, and Pyeonganok as well as 40 foreign commercial silage corns. From cluster analysis, we confirmed that 10 Korean silage F1 hybrid corns were clearly distinguished except for Singwangok, P1395, and several foreign commercial corns, and selected minimum SNP primer combination for Gangdaok, Jangdaok, Pyeonggangok, and Pyeonganok. Therefore, development of SNP marker sets might be faster, cheaper, and feasible breed discrimination method through simple PCR and agarose gel electrophoresis.