• Asian-Australasian Journal of Animal Sciences
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• 제31권11호
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• pp.1721-1728
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• 2018

Objective: The use of genetic markers can help to enhance reproduction in cattle, which is a very important trait for profitability in dairy production systems. This study evaluated the association between genotypes of leptin (LEP), toll-like receptor 4 (TLR4), and chemokine receptor of interleukin 8 C-X-C motif (CXCR1) genes and fertility traits in Czech Fleckvieh cattle. Methods: Phenotypic data from 786 Czech Fleckvieh cows raised on 5 farms in the Czech Republic were used, along with information from the 1st three parities. To determine genotype, the polymerase chain reaction-restriction fragment length polymorphism method was used. Results: Except for LEP g.-963C>T, all studied genotype frequencies of single nucleotide polymorphisms (SNPs) were distributed according to the Hardy-Weinberg equilibrium. Two LEP SNPs (g.-963C>T and c.357C>T) were associated with the age at the 1st calving, days open (DO), pregnancy rate after 1st service (PR), and calving interval (CLI). In LEP g.-963C>T the TT genotype heifers firstly calved 24 days earlier than CC genotype and the CT genotype cow showed a tendency for shorter DO and higher PR. In LEP c.357C>T we observed longer CLI and DO period in TT cows. In general, we can propose the TT genotype of g.-963C>T as favorable and the TT genotype of c.357C>T as unfavorable for a cow's fertility. Heterozygotes in TLR4 c.-226C>G were significantly associated with shorter CLI, and presented a nonsignificant tendency to be associated with higher PR. In CXCR1 c.777 C>G, we did not observe any relationship of this SNP with reproduction. Conclusion: Overall, the results showed that LEP could be an effective marker for improving reproduction in Czech Fleckvieh cattle. This study also provides novel insights into the relationship between TLR4 and CXCR1 SNPs and reproduction in dual-purpose cattle.

• 농업과학연구
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• 제40권2호
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• pp.155-162
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• 2013

Genome-wide association study was performed on data from 266 Hanwoo steers derived from 66 sire using bovine 10K mapping chip in Hanwoo (Korean Cattle). SNPs were excluded from the analysis if they failed in over 5% of the genotypes, had median GC scores below 0.6, had GC scores under 0.6 in less than 90% of the samples, deviated in heterozygosity more than 3 standard deviations from the other SNPs and were out of Hardy-Weinberg equilibrium for a cutoff p-value of $1^{-15}$. Unmapped and SNPs on sex chromosomes were also excluded. A total of 4,522 SNPs were included in the analysis. To test an association between SNP and QTL, GWAS for five genetic mode (additive, dominant, overdominant, recessive and codominant) was implemented in this study. Three SNPs (rs29018694, ss46526851 and rs29018222) at a threshold p< $1.11{\times}10^{-5}$ were detected on BTA12 and BTA21 for dressing percentages in codominant and recessive genetic mode. The G allele for rs29018694 has 4.9% higher dressing percentage than A allele, while the T allele for ss46526851 has 2.57 % higher dressing percentage than C allele. Therefore, rs29018694 SNP showed a bigger effect than the other two SNPs (ss46526851 and rs29018222) in this study. In conclusion, this study identifies three loci with moderate effects and many loci with infinitesimally small effect across genome in Hanwoo.

• Journal of the Korean Academy of Child and Adolescent Psychiatry
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• 제22권4호
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• pp.287-293
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• 2011

Objectives : The region of chromosome 5p14 is known to be associated with autism spectrum disorder (ASD). The cadherin9 (CDH9) and cadherin10 (CDH10) genes are located in the region of chromosome 5p14 and reported to be associated with ASD in the Caucasian population. We performed an association study to identify if single nucleotide polymorphisms (SNPs) located on the CDH9 and CDH10 genes are associated in the Korean population. Methods : Genomic DNA was extracted from the blood of 214 patients with ASD and 258 controls. SNPs selected from two genes were genotyped using an Illumina Golden-Gate Genotyping assay with VeraCode technology. Statistical analysis was performed using SAS and Plink software. Results : All controls and ASD patients were in Hardy-Weinberg equilibrium. In the results of logistic regression analyses for the genotype model and the chi-square test for the allele model, we found that SNPs on the CDH9 and CDH10 genes were not associated with ASD. Conclusion : Our data suggests that the CDH9 and CDH10 genes are not associated with ASD in the Korean population.

• 한국자원식물학회지
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• 제28권2호
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• pp.279-289
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• 2015

소나무의 유전다양성과 유전구조를 추정하기 위해 9개의 ESTP 표지를 13개 소나무 집단에 적용하였다. 소나무 집단의 유전다양성은 관찰된 대립유전자 수(A)가 2.2개, 유효 대립유전자 수(A_e)가 1.8개, 다형적 유전자좌 비율(P)이 98.8%, 이형접합도 관찰치(H_o)가 0.391, 이형접합도 기대치(H_e)가 0.402로 나타났다. 안강과 강릉 집단을 제외한 11개 집단이 하디-바인베르그 평형을 만족하였다. 집단간 유전분화도(F_ST)는 0.057으로, 동위효소나 nSSR 표지분석 결과보다 강하게 나타났다. 군집분석에서 집단의 유전적 거리와 지리적 분포간에 뚜렷한 연관성은 확인할 수 없었으며, 집단의 유전분화와 지리적 인접성도 상관이 없는 것으로 나타났다(Mantel 검증, r = 0.017, P = 0.344). 유전자좌에 대한 F_ST-outlier 분석을 실시한 결과, 빈도주의 방법에서는 F_ST 값이 신뢰하한 이하인 3개 유전자좌와 신뢰상한 이상인 3개 유전자좌가 특이값으로 추정되었고, 베이즈 방법에서는 3개 유전자좌들만 특이값으로 확인되었다. 두 방법에서 공히 특이값으로 판정된 3개 유전자좌(sams2+AluⅠ, sams2+RsaⅠ, PtNCS_p14A9+HaeⅢ)중 sams2 표지에서 유래된 2개 유전자좌는 balancing selection의 영향을 받는 것으로 추정되었다.

• Asian-Australasian Journal of Animal Sciences
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• 제32권8호
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• pp.1104-1111
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• 2019

Objective: The aim of this study was to detect single nucleotide polymorphisms (SNP) of G protein-coupled receptor 54 (GPR54) gene and explore association of this candidate gene with reproductive traits in Jiaxing Black sows. Methods: Six pairs of primers of the gene were designed to amplify all exons thus sequences of which were detected by means of direct sequencing and then SNP loci were scanned. The effects of SNPs on total number of piglets born (TNB), number of piglets born alive (NBA), number of still born piglets (NSB), and litter weight at birth (LWB) of Jiaxing Black sows were analyzed. Results: Three SNP loci, including T3739C, C3878T and T6789C, were identified via comparison of sequencing and two genotypes (AB, BB) at each SNP site were observed. T3739C resulted in the change of amino acid ($Leu{\rightarrow}Pro$) in corresponding protein, and C3878T resulted in synonymous mutation ($Ile{\rightarrow}Ile$). Statistical results demonstrated that allele B was the preponderant allele at the three SNP loci and Genotype BB was the preponderant genotype. Meanwhile, Chi-Square test of these three SNPs indicated that all mutation sites fitted in Hardy-Weinberg equilibrium (p>0.05). For GPR54-T3739C locus, Jiaxing Black sows with genotype BB had 1.23 TNB and 1.28 NBA (p<0.01) that were more than those with genotype AB, respectively. Jiaxing Black sows that had the first two parities with genotype BB had additional 2.23 TNB, 2.27 NBA (p<0.01), and 1.94 LWB (p<0.05) compared to those with genotype AB, respectively. However, for other two loci, no significant difference was found between TNB, NBA, NSB, and LWB, and different genotypes of Jiaxing Black sows. Conclusion: In conclusion, the polymorphisms of GPR54-T3739C locus were significantly associated to TNB, NBA, and LWB and could be used as a potential genetic marker to improve reproductive function of Jiaxing black sows.

• Asian-Australasian Journal of Animal Sciences
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• 제32권7호
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• pp.949-955
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• 2019

Objective: The present study was to investigate the association of polymorphisms in exon-9 of the bone morphogenetic protein receptor-1B (BMPR-1B) gene (C864T) with litter size in 240 Dorset, 232 Mongolian, and 124 Small Tail Han ewes. Methods: Blood samples were collected from 596 ewes and genomic DNA was extracted using the phenol: chloroform extraction method. The 304-bp amplified polymerase chain reaction product was analyzed for polymorphism by single-strand conformation polymorphism method. The genotypic frequency and allele frequency of BMPR-1B gene exon-9 were computed after sequence alignment. The ${\chi}^2$ independence test was used to analyze the association of genotypic frequency and litter size traits with in each ewe breed, where the phenotype was directly treated as category. Results: The results indicated two different banding patterns AA and AB for this fragment, with the most frequent genotype and allele of AA and A. Calculated Chi-square test for BMPR-1B gene exon-9 was found to be more than that of p value at the 5% level of significance, indicating that the population under study was in Hardy-Weinberg equilibrium for all ewes. The ${\chi}^2$ independence test analyses indicated litter size differences between genotypes was not the same for each breed. The 304-bp nucleotide sequence was subjected to BLAST analysis, and the C864T mutation significantly affected litter size in singletons, twins and multiples. The heterozygosity in exon-9 of BMPR-1B gene could increase litter size for all the studied ewes. Conclusion: Consequently, it appears that the polymorphism BMPR-1B gene exon-9 detected in this study may have potential use in marker assisted selection for litter size in Dorset, Mongolian, and Small Tail Han ewes.

• Genomics & Informatics
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• 제21권3호
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• pp.33.1-33.11
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• 2023

Type 2 diabetes mellitus (T2DM) is a multifactorial, polygenic, and metabolically complicated disease. A large number of genes are responsible for the biogenesis of T2DM and calpain10 (CAPN10) is one of them. The association of numerous CAPN10 genetic polymorphisms in the development of T2DM has been widely studied in different populations and noticed inconclusive results. The present study is an attempt to evaluate the plausible association of CAPN10 polymorphism SNP-19 (rs3842570) with T2DM and T2DM-related anthropometric and metabolic traits in the Noakhali region of Bangladesh. This case-control study included 202 T2DM patients and 75 healthy individuals from different places in Noakhali. A significant association (p < 0.05) of SNP-19 with T2DM in co-dominant 2R/3R vs. 3R/3R (odds ratio [OR], 2.7; p=0.0014) and dominant (2R/3R) + (2R/2R) vs. 3R/3R (OR, 2.47; p=0.0011) genetic models was observed. High-risk allele 2R also showed a significant association with T2DM in the allelic model (OR, 1.67; p=0.0109). The genotypic frequency of SNP-19 variants showed consistency with Hardy-Weinberg equilibrium (p > 0.05). Additionally, SNP-19 genetic variants showed potential associations with the anthropometric and metabolic traits of T2DM patients in terms of body mass index, systolic blood pressure, diastolic blood pressure, total cholesterol, and triglycerides. Our approach identifies the 2R/3R genotype of SNP-19 as a significant risk factor for biogenesis of T2DM in the Noakhali population. Furthermore, a large-scale study could be instrumental to correlate this finding in overall Bangladeshi population.

• 한국산림과학회지
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• 제78권4호
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• pp.345-359
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• 1989

경북북부(慶北北部)와 남부지방(南部地方)소나무는 외부형태적(外部形態的)으로 차이(差異)가 있으므로 소나무 16개집단(個集團)과 곰솔 5개집단(個集團)의 동위효소(同位酵素) IDH, ME, PGI, ADH, GOT 및 LAP에 의한 종자(種子)의 megagametophyte tissue로 집단간(集團間)의 변이(變異)를 조사(調査)하였다.1. 6개(個)의 동위효소(同位酵素)에서 소나무는 13개(個)의 유전자좌중(遺傳子座中) 변이(變異)가 있는 8개(個) 유전자좌(遺傳子座)에서 24개(個)의 대립유전자(對立遺傳子) 변이(變異)가 있었고, 곰솔은 13개(個) 유전자좌중(遺傳子座中) 변이(變異)가 있는 6개(個) 유전자좌(遺傳子座)에서 18개(個)의 대립유전자(對立遺傳子)가 변이(變異)를 나타냈다. 2. 소나무의 유전자형(遺傳子型) 빈도(頻度)는 동위효소(同位酵素)에 따라 다소 차이(差異)는 있으나 대체로 Hardy-Weinberg의 평형법칙(平衡法則)을 따르고 있으며, 평형법칙(平衡法則)을 따르지 않는 일부집단(一部集團)은 fixation index 값이 높고 동형접합체(同型接合體)의 발생빈도(發生頻度)가 기대치(期待値)보다 높게 나타났다. 3. 소나무에서 상주(尙州), 영주(榮州) 및 봉화집단(奉化集團)을 제외(除外)하고 genetic distance에 의한 집단간(集團間)의 차이(差異)가 없었으나, 경북(慶北)의 북부지방(北部地方)과 태백산맥(太白山脈)의 소나무가 같은 group에 속하고 내륙지방(內l陸地方)인 성주(星州), 의성(義城) 및 금능(金陵)같은 group에 속하며, 경주(慶州)와 백암(白巖)은 각각(各各) 다른 group으로 구분(區分)되었다. 4. 외부형태적(外部形態的)으로 차이(差異)가 있는 경북(慶北) 북부지방(北部地方)과 남부지방(南都地方)의 소나무는 동위효소(同位酵素)에 의한 변이(變異)로서는 뚜렷한 차이점(差異點)을 찾아 볼 수가 없었다. 5. 소나무에서 한 개체당(個體當) 이형접합체(異型接合體)의 유전자좌(遺傳子座) 빈도(頻度)는 ME-A 및 ADH-B locus에서, 곰솔에서는 ADH-B, LAP-B 및 PGI-B에서 가장 높게 나타났으며, 그외(外) locus에서는 동형접합체(同型接合體)의 빈도(頻度)가 높게 나타났다.

• Journal of Animal Science and Technology
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• 제54권5호
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• pp.323-329
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• 2012

본 연구는 한우 거세우 266두에서 유전자형 결정이 완료된 4,522개의 SNP를 이용하여 한우 성장형질 (6, 12, 18 및 24개월령 체중)에 대한 양적형질좌위 (QTL)을 탐색 하였다. 각 SNP와 성장형질과의 연관성 분석은 회귀분석 (single marker regression)을 이용하여 수행하였으며, 통계적 유의성은 P-value (P<0.001)로 설정하였다. 그 결과, 6개월체중에서 3개 좌위, 12개월 체중에서는 5개 좌위, 18개월체중에서 5개좌위 그리고 24개월체중에서 4개 좌위가 통계적 유의차를 보였다. 통계적 유의차를 보인 SNP의 상가적 유전분산을 분석한 결과, 몇몇 SNP에서는 6~11% 정도의 상가적 유전효과를 보였으며, 대부분의 SNP들은 2~5%로 매우 작은 효과를 보였다.

• 대한한방내과학회지
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• 제36권4호
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• pp.547-561
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• 2015

Objectives In this study, we divided Korean asthma patients into excess syndrome or deficiency syndrome groups according to clinical phenotype. Genetic analysis was conducted to investigate the association of exonic SNPs in the CD46 gene polymorphism with the clinical phenotype based on the differentiation syndrome of the bronchial asthma patients.Methods There were 95 healthy patients (control group) and 53 asthma patients. (The deficiency syndrome group included 24 and the excess syndrome group 29). We searched the exonic areas of the CD46 gene in the NCBI website SNPs with <0.01 minor allele frequency (MAF) and <0.01 heterozygosity. We finally selected two SNPs: rs138843816, Ser13Phe and rs7144, 3’-UTR. Hardy-Weinberg equilibrium was calculated using SNPStats.Results There were significant differences in the codominant 1 model and the dominant model between the healthy group and the asthma group. There were significant differences between deficiency syndrome group and the excess syndrome group in the genotype frequencies and in the codominant 1 model, the dominant model, and the log-additive model. The allele frequency of rs7144C showed a significant difference between the deficiency syndrome group and the excess syndrome group. Two-SNP haplotype analysis showed a significant difference in frequency in the deficiency syndrome group and in the excess syndrome group. There were significant differences between the healthy group and the excess syndrome group in the codominant 1 model, the dominant model, and the log-additive model. The frequency of the rs7144 C allele exhibited a significant difference in the demonstration. SNP haplotype analysis between the healthy group and the excess syndrome group showed a significant difference in the frequency of the CT haplotype and the CC haplotype.Conclusions The results indicate that two CD46 SNPs (rs138843816, Ser13Phe and rs7144, 3′–UTR) might be associated with the symptomatic excess syndrome in Korean asthma patients.