Genetic diversity in oocyte donors used in in vitro bovine embryo production programs in Brazil / Diversidad genética en donadoras de ovocitos utilizadas en programas de producción de embriones bovinos in vitro en Brasil / Diversidade genética em doadoras de oócitos utilizadas em programas de produção de embriões bovinos in vitro no Brasil

Abstract Background: Current reproductive management of bovine elite populations involves the use of assisted reproductive technologies (ARTs), aiming to obtain the greatest genetic gain. However, inadequate use of ARTs may lead to loss of genetic diversity in the offspring. Objective: To assess the genetic diversity in elite female cattle populations used in commercial in vitro embryo production. Methods: Using genetic and ecological approaches for the study of populations based on microsatellite markers, we assessed the genetic diversity between and within populations of cows used in commercial in vitro embryo production programs in Brazil. Results: Endogamy within populations varied from zero to 9.1%, while heterozygosity between populations (FST) was <0.05 in the different population interactions. AMOVA showed 1% variation between populations, 8% between individuals and 91% within individuals. The dimensionality reduction method utilized indicated a lack of structure in the populations analyzed, identifying two main clusters in the three populations. Conclusions: Low genetic diversity between cow populations associated with commercial programs of in vitro embryo production in Brazil was evidenced. Variable levels of endogamy within the populations were observed. Approaches of population genetics as well as ecological diversity can be implemented to more thoroughly estimate genetic diversity in livestock populations.

Resumen Antecedentes: El actual manejo reproductivo en poblaciones de bovinos de élite incluye la utilización de tecnologías de reproducción asistida (ARTs) con el fin de obtener mayor ganancia genética. Sin embargo, el uso inadecuado de las ART puede llevar a la pérdida de diversidad genética en los descendientes. Objetivo: Evaluar la diversidad genética en poblaciones de vacas de élite utilizadas en la producción comercial de embriones bovinos in vitro. Métodos: Utilizando abordajes de la genética y ecología de poblaciones basados en marcadores microsatélites, evaluamos la diversidad genética entre y dentro de poblaciones de vacas participantes de programas comerciales de producción de embriones in vitro en Brasil. Resultados: La endogamia dentro de las poblaciones varió de cero a 9,1%, mientras que la heterocigosidad entre poblaciones (FST) fue <0,05 en las diferentes interacciones de la población. El AMOVA mostró variación del 1% entre poblaciones, 8% entre individuos y 91% dentro de individuos. El método de reducción de dimensionalidad utilizado indicó una falta de estructura en las poblaciones analizadas, identificando dos grupos principales en las tres poblaciones. Conclusiones: Se evidenció una baja diversidad genética entre las poblaciones de vacas asociadas a programas comerciales de producción de embriones in vitro en Brasil. Se evidenciaron niveles variables de endogamia entre las poblaciones. Abordajes de la genética poblacional, así como de diversidad ecológica pueden ser implementados para estimar de manera más amplia la diversidad genética en poblaciones animales de interés pecuario.

Resumo Antecedentes: O atual manejo reprodutivo das populações de elite em bovinos envolve o uso de tecnologias de reprodução assistida (ARTs), visando obter o maior ganho genético. No entanto, o uso inadequado de ARTs pode levar à perda de diversidade genética na prole. Objetivo: Avaliar a diversidade genética em populações de vacas de elite utilizadas na produção comercial de embriões bovinos in vitro. Métodos: Utilizando abordagens da genética e ecologia de populações baseadas em marcadores microssatélites, foi avaliada a diversidade genética entre e dentro das populações de vacas participantes de programas comercias de produção in vitro de embriões. Resultados: A endogamia dentro das populações variou de zero a 9,1%, enquanto a heterozigosidade entre populações (FST) foi <0,05 nas diferentes interações populacionais. AMOVA mostrou variação de 1% entre populações, 8% entre indivíduos e 91% dentro de indivíduos. O método de redução de dimensionalidade utilizado indicou uma falta de estrutura nas populações analisadas, identificando dois clusters principais nas três populações. Conclusões: Baixa diversidade genética entre populações de vacas associadas a programas de produção in vitro de embriões foi evidenciada. Níveis de endogamia variáveis dentro das populações foram observados. Abordagens da genética populacional assim como de diversidade ecológica podem ser implementadas na tentativa de estimar de maneira mais abrangente a diversidade genética em populações animais de interesse pecuário.

Determining of JK*A and JK*B Allele Frequency Distribution among Muslim Blood Donors from Southern Thailand

@#Background: The Kidd (JK) blood group system is of clinical importance in transfusion medicine. JK*A and JK*B allele detections are useful in genetic anthropological studies. This study aimed to determine the frequencies of JK*A and JK*B alleles among Muslim blood donors from Southern Thailand and to compare how they differ from those of other populations that have been recently studied. Methods: A cross-sectional study was used. Totally, 427 samples of dissimilar Thai- Muslim healthy blood donors living in three southern border provinces were selected via simple random sampling (aged 17–65 years old) and donors found to be positive for infectious markers were excluded. All samples were analysed for JK*A and JK*B alleles using PCR-SSP. The Pearson’s chi-squared and Fisher exact tests were used to compare the JK frequencies among southern Thai- Muslim with those among other populations previously reported. Results: A total of 427 donors—315 males and 112 females, with a median age of 29 years (interquartile range: 18 years)—were analysed. A JK*A/JK*B genotype was the most common, and the JK*A and JK*B allele frequencies among the southern Thai-Muslims were 55.2% and 44.8%, respectively. Their frequencies significantly differed from those of the central Thai, Korean, Japanese, Brazilian–Japanese, Chinese, Filipino, Africans and American Natives populations (P < 0.05). Predicted JK phenotypes were compared with different groups of Malaysians. The Jk(a+b+) phenotype frequency among southern Thai-Muslims was significantly higher than that of Malaysian Malays and Indians (P < 0.05). Conclusions: The JK*A and JK*B allele frequencies in a southern Thai-Muslim population were determined, which can be applied not only to solve problems in transfusion medicine but also to provide tools for genetic anthropology and population studies.

Diversidad genética de palomas domésticas (Columba livia) en Ciénaga de Oro (Colombia), utilizando genes del plumaje / Genetic diversity of domestic pigeons (Columba livia) in Ciénaga de Oro, Colombia, using plumage genes / Diversidade genética de pombos domésticos (Columba livia) em Ciénaga de Oro (Colômbia), utilizando genes da plumagem

Resumen El objetivo de este trabajo fue evaluar la diversidad genética de las poblaciones de palomas domésticas (Columba livia) por medio del uso de genes que codifican la coloración y diseño del plumaje, en Ciénaga de Oro (Córdoba, Colombia). Se realizaron muestreos aleatorios en cinco colonias de Ciénaga de Oro, en el periodo comprendido entre junio y agosto de 2015. Mediante excursiones urbanas, observación directa y registros fotográficos, se estudiaron 325 palomas. Se utilizaron los marcadores autosómicos que codifican la coloración y diseño del plumaje: Grizzle (G), Spread (S), Checker (C) y el locus ligado al sexo Ash-Red (B). Los parámetros genéticos -frecuencia alélica, diversidad genética, equilibrio Hardy-Weinberg y estructura poblacional- fueron calculados con el programa PopGene 1.31. La estructura genética y la distancia genética se evaluaron mediante el programa FSTAT v. 2.9.3.2. La elaboración del dendrograma se realizó con el programa MEGA 5.2. El marcador de mayor frecuencia alélica fue Spread, mientras que el marcador Ash-Red presentó los valores más bajos. Se obtuvo escasa diferenciación genética entre las poblaciones y un elevado flujo génico. Se observó un exceso de heterocigotos; a esto se le suma la ausencia de equilibrio Hardy-Weinberg. Se evidenció posible selección natural para el marcador Spread.

Abstract This study aimed to evaluate the genetic diversity of domestic pigeon populations (Columba livia), using genes that are responsible for encoding plumage color and design, in Ciénaga de Oro (Córdoba, Colombia). Random samplings were performed in 5 colonies of Ciénaga de Oro from June to August 2015. By means of urban excursions, direct observation and photographic records, 325 pigeons were studied. Autosomal markers encoding plumage color and design were used: Grizzle (G), Spread (S), Checker (C), and the sex-linked Ash-Red locus (B). Genetic parameters-allele frequency, genetic diversity, Hardy-Weinberg equilibrium, and population structure-were calculated using the PopGene 1.31 program. Genetic structure and genetic distance were evaluated using the FSTAT v. 2.9.3.2 program. A dendrogram was elaborated using the MEGA 5.2 program. The marker with the highest allele frequency was Spread, while the Ash-Red marker showed the lowest values. Little genetic differentiation between populations and high gene flow were obtained. An excess of heterozygotes was observed, in addition to the absence of Hardy-Weinberg equilibrium. A possible natural selection for the Spread marker was evidenced.

Resumo O objetivo deste trabalho foi avaliar a diversidade genética das populações de pombos domésticos (Columba livia) por meio do uso de genes que codificam a coloração e desenho da plumagem, em Ciénaga de Oro (Córdoba, Colômbia). Se realizaram amostragens aleatórias em 5 colônias de Ciénaga de Oro, no periodo compreendido entre junho e agosto de 2015. Mediante excursões urbanas, observação direta e registros fotográficos, se estudaram 325 pombos. Se utilizaram os marcadores autossômicos que codificam a coloração e desenho da plumagem: Grizzle (G), Spread (S), Checker (C) e o locus ligado ao sexo Ash-Red (B). Os parâmetros genéticos - frequência alélica, diversidade gené tica, equilíbrio Hardy-Weinberg e estrutura populacional - foram calculados com o programa PopGene 1.31. A estrutura genética e a distância genética foram avaliadas mediante o programa FSTAT v. 2.9.3.2. A elaboração do dendrograma se realizou com o programa MEGA 5.2. O marcador de maior frequência alélica foi Spread, em quanto que o marcador Ash-Red apresentou os valores mais baixos. Obteve-se escassa diferenciação genética entre as populações e um elevado fluxo génico. Pôde-se observar um excesso de heterozigotos; a isto soma-se a ausência de equilíbrio Hardy-Weinberg. Constatou-se possível seleção natural para o marcador Spread.

Population Difference Analysis of Allele Frequencies of 24 Y-STR Loci / 法医学杂志

OBJECTIVES@#To investigate the population genetic polymorphisms of 24 Y-STR loci in unrelated individuals in Eastern Chinese Han population, and to compare the difference of Han group between Eastern China and Guangdong.@*METHODS@#The population genetics of 24 Y-STR loci in 268 unrelated Han individuals from Eastern China were analyzed by GFS 24 Y-STR amplification kit. The allele frequencies in Eastern Chinese Han population were compared with the data in Guangdong Han population, and the difference analysis between two groups was performed.@*RESULTS@#Among the 24 Y-STR loci of 268 unrelated Han individuals from Eastern China, 235 alleles and 267 haplotypes were observed. GD value ranged from 0.564 9 to 0.966 8. The difference between 12 loci （DYS622, DYS552, DYS443, et al.） of Han population in Eastern China and in Guangdong was statistically significance.@*CONCLUSIONS@#GFS 24Y STR amplification system shows favorable polymorphisms, which can be used in patrilineal genetic relationship identification.

Population Difference Analysis of Allele Frequencies of 24 Y-STR Loci / 法医学杂志

Objective To investigate the population genetic polymorphisms of 24 Y-STR loci in unrelat-ed individuals in Eastern Chinese Han population, and to compare the difference of Han group between Eastern China and Guangdong.Methods The population genetics of 24 Y-STR loci in 268 unrelated Han individuals from Eastern China were analyzed by GFS 24 Y-STR amplification kit. The allele fre-quencies in Eastern Chinese Han population were compared with the data in Guangdong Han population, and the difference analysis between two groups was performed.Results Among the 24 Y-STR loci of 268 unrelated Han individuals from Eastern China, 235 alleles and 267 haplotypes were observed. GD value ranged from 0.5649 to 0.9668. The difference between 12 loci(DYS622,DYS552,DYS443etal.) of Han population in Eastern China and in Guangdong was statistically significance.Conclusion GFS 24Y STR amplification system shows favorable polymorphisms, which can be used in patrilineal genetic relationship identification.

TNF, IL12B, and IFNG Gene Polymorphisms in Serbian Patients with Psoriasis

BACKGROUND: Psoriasis is a common chronic inflammatory skin disease with a strong genetic basis. Cytokines such as tumor necrosis factor alpha (TNF-alpha), interleukins (ILs) such are IL-12 and IL-23, and interferon gamma (IFN-gamma) are released from various inflammatory and resident cells, and have been implicated in the initiation/maintenance of inflammation. Certain alleles of the aforementioned cytokines may be associated with disease susceptibility/severity. OBJECTIVE: To investigate the association of three common functional gene polymorphisms, namely TNF -308 G/A (rs1800629), IL12B (encoding the p40 subunit of IL-12/23) +1188 A/C (rs3212227), and IFNG +874 T/A (rs2430561) with psoriasis development and severity in Serbian patients. METHODS: We genotyped 130 patients with psoriasis (26 of whom also had psoriatic arthritis) and 259 controls; rs1800629 and rs3212227, and rs2430561, by real-time PCR assay. RESULTS: The TNF GG genotype was detected at a higher frequency in patients with psoriasis compared to control subjects (OR, 1.420; 95% CI, 0.870~2.403) without statistical significance (p=0.191). Lack of the TNF G allele was associated with lower psoriasis severity (p=0.007). The IL12B AC genotype was underrepresented in the patients with psoriatic arthritis compared to healthy subjects (OR, 0.308; 95% CI, 0.090~1.057; p=0.049). The distribution of the rs2430561 allele and genotype frequencies was similar between patients with psoriasis and controls. CONCLUSION: Our study demonstrates an effect of the rs1800629 on psoriasis severity, and a marginal impact of the rs3212227 on susceptibility to psoriatic arthritis. Collectively, our results obtained in a Serbian cohort expand current knowledge regarding individual predisposition to psoriatic disease.

Duffy Blood Group Genotyping in Thai Blood Donors

BACKGROUND: Duffy (FY) blood group genotyping is important in transfusion medicine because Duffy alloantibodies are associated with delayed hemolytic transfusion reactions and hemolytic disease of the fetus and newborn. In this study, FY allele frequencies in Thai blood donors were determined by in-house PCR with sequence-specific primers (PCR-SSP), and the probability of obtaining compatible blood for alloimmunized patients was assessed. METHODS: Five hundred blood samples from Thai blood donors of the National Blood Centre, Thai Red Cross Society, were included. Only 200 samples were tested with anti-Fy(a) and anti-Fy(b) using the gel technique. All 500 samples and four samples from a Guinea family with the Fy(a-b-) phenotype were genotyped by using PCR-SSP. Additionally, the probability of obtaining antigen-negative red blood cells (RBCs) for alloimmunized patients was calculated according to the estimated FY allele frequencies. RESULTS: The FY phenotyping and genotyping results were in 100% concordance. The allele frequencies of FY*A and FY*B in 500 central Thais were 0.962 (962/1,000) and 0.038 (38/1,000), respectively. Although the Fy(a-b-) phenotype was not observed in this study, FY*B(ES)/FY*B(ES) was identified by PCR-SSP in the Guinea family and was confirmed by DNA sequencing. CONCLUSIONS: Our results confirm the high frequency of the FY*A allele in the Thai population, similar to that of Asian populations. At least 500 Thai blood donors are needed to obtain two units of antigen-negative RBCs for the Fy(a-b+) phenotype.

Frequency of FCGR3B Alleles in Thai Blood Donors

BACKGROUND: Human neutrophil antigens (HNAs) are involved in autoimmune and alloimmune neutropenia and transfusion-related acute lung injury. The HNA-1 system is important in immunogenetics, and allele frequencies have been described in different populations. This study investigated the frequency of FCGR3B alleles encoding HNA-1a, HNA-1b, and HNA-1c among Thai blood donors and compared these frequencies with those previously reported for other populations. METHODS: Eight hundred DNA samples obtained from unrelated healthy blood donors at the National Blood Centre, Thai Red Cross Society, Bangkok, and the Blood Bank, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand, were included. Samples were simultaneously typed for each FCGR3B allele using an in-house polymerase chain reaction with sequence-specific primer (PCR-SSP) technique. RESULTS: The frequencies of FCGR3B*1, FCGR3B*2, and FCGR3B*3 alleles in central Thai blood donors were 0.548, 0.452, and 0.004, respectively; only FCGR3B*1 and FCGR3B*2 alleles were found in northern Thai blood donors (0.68 and 0.32, respectively). Compared with other Asian populations, central Thais had higher frequencies of the FCGR3B*2 allele (P<0.001), while the frequencies of the FCGR3B*1 and FCGR3B*2 alleles in northern Thais were similar to those previously reported in Taiwanese and Japanese populations. In contrast, the frequencies of the FCGR3B*1 and FCGR3B*2 alleles in the northern Thai population were statistically different from those observed in central Thai, Korean, German, and Turkish populations. CONCLUSIONS: FCGR3B allele frequencies were significantly different between central and northern Thai blood donors. Our in-house PCR-SSP method is a simple, cost-effective, and convenient method for FCGR3B allele detection.

Study of polymorphisms in autosomal microsatellite loci among mongolian population / Монголын Анагаах Ухаан

IndroductionThe short tandem repeats (STR) are rich source of highly polymorphic markers in the human genome. In this study, we used a commercially available multiplex STR typing kit to study 15 STR systems (D3S1358, THO1, D21S11, D18S51, Penta E, D5S818, D13S317, D7S820, D16S539, CSF1PO, Penta D, vWA, D8S1179, TPOX and FGA,) in the Mongolians population, and estimated the allele and genotype frequencies. These 15 STR loci include 2 new pentanucleotide repeat STR loci, Penta E and Penta D, so are not studied in Mongolians.GoalTo determine allele frequency of STR loci D3S1358, THO1,D21S11, D18S51, D5S818, D13S317, D7S820, D16S539, CSF1PO, vWA, D8S1179, TPOX, FGA Penta E, Penta D in Mongolian population.Materials and MethodsThe liquid blood, blood stain and saliva samples were taken from 165 unrelated individuals from Mongolian. Extraction DNA: Genomic DNA was extracted from whole blood samples by the standard method of phenol-chloroform-isoamyl alcohol and Wizard Genomic DNA Purification kit, Promega Corporation [21], from blood stain and saliva samples QIAamp DNA micro kit, Qiagen [25], AccuPrep Genomic DNA Extration kit, Bioneer, Koreans extraction method respectively.PCR: PCR amplification was performed using 10-15 ng genomic DNA template according to manufacturer’s protocol (PowerPlex® 16 and PowerPlex® 16HS kit, Promega Corporation, USA). Typing: DNA typing was performed on the ABI Prism 310 Genetic Analyzer (Applied Biosystems) using the recommended protocol. The results were analyzed by Data Collection (Version 1.1), GeneScan (Version 3.1), and Genotyper (Version 3.1) softwares (AppliedBiosystems).ResultsWe assessed forensic and population genetic studies using 15 STR loci included in s sample of 165 unrelated individuals from Mongolian. Allele frequency were listed in Table 2. Totally 20 alleles /5, 7-25/ were found from microsatellite Penta E locus and allele 11 has most frequent (0.1128). 6-16 alleles were found from Penta D locus and allele 9 has most frequent (0.3262). This result is interesting because allele 6 of Penta D locus was found rarely among other populations. But relatively higher frequency of allele 6 (0.0183) was found in Mongolian population. A population comparison based in genetic distance and genetic diversity calculated from allele frequencies of the 15 STR loci from obtained five different populations is shown the Table 3. Conclusions:1. Penta E locus was highly polymorphic, and 20 alleles were found in this Mongolians population and allele 11 was most frequent.2. Penta D locus was 20 alleles were found in this Mongolians population and allele 9 was most frequent.

Análisis de marcadores STR sobre el cromosoma X en una población de Bogotá / STR markers analysis on X chromosome in a population from Bogotá

El análisis de marcadores del cromosoma X ha sido ampliamente usado en el área de la genética clínica, particularmente, para el análisis molecular de enfermedades ligadas al X. Recientemente, se han reconocido muchas repeticiones cortas en tándem (Short Tandem Repeats, STR) sobre este cromosoma, por su importancia en análisis forense y de paternidad. Los marcadores gonosómicos son especialmente eficientes para resolver casos difíciles, ya que las probabilidades de exclusión media son mayores que con los marcadores STR autosómicos. Objetivo. Determinar la frecuencia alélica y haplotípica de 10 marcadores STRs sobre el cromosoma X en 200 muestras de hombres no relacionados de la ciudad de Bogotá. Materiales y métodos. Se analizaron 200 muestras de sangre de hombres no emparentados nacidos en Bogotá. El ADN genómico fue extraído mediante la técnica Whatman FTA y amplificados por PCR. Los productos se analizaron en un secuenciador automático ABI Prism 310, con el software GeneMapper, versión 3.2. Resultados. Los sistemas evaluados indicaron la presencia de 6 a 11 alelos, con el mayor polimorfismo para los sistemas DXS6809 y DXS6789, seguido por el sistema DXS9902. Las frecuencias alélicas oscilaron entre 0,005 y 0,565, mientras que la frecuencia haplotípica fue de 0,005. Los parámetros forenses utilizados en este estudio reportaron que el sistema DXS7132 mostró una mayor diversidad y PD (0,832211 y 0,82805) respectivamente indicando que este sistema es altamente informativo; el sistema que presentó menor diversidad y PD fue el sistema DXS7133. Conclusión. Los diez marcadores analizados en este estudio permiten la genotipificación simultánea de los 10 STRs en solo una PCR, adicionalmente se evidenció que los marcadores analizados son ampliamente informativos y que su utilización puede ser de gran aporte en la práctica forense, particularmente en los casos de parentesco u otras deficiencias.

X chromosome markers analysis has been used widely in the clinical genetics area, particularly in molecular diseases X-linked analysis. Recently, many short tandem repeats (Short Tandem Repeats, STRs) on this chromosome has been recognized, by importance in forensic and paternity analysis. The gonosomal markers are particularly efficient resolve difficult cases, since the odds of half exclusion outweigh the STR autosomes markers. Objective. Determine the allelic frequency and haplotype frequency of 10 STRs markers located on the X chromosome, in 200 samples of unrelated men in the Bogotá city. Materials and methods. 200 blood samples were analyzed from unrelated males born in Bogotá. DNA extraction was performed using the Whatman FTA technique and PCR amplified. The products were analyzed in automatic sequencer ABI Prism 310, software GeneMapper, version 3.2. Results. The systems tested, showed of 6-11 alleles, with greater polymorphism DXS6809 and DXS6789 systems and this followed for DXS9902 system. The range of Allele frequencies from 0.005 to 0.565, while the haplotype frequency was 0.005. The forensic parameters used in this study, reported that the DXS7132 system showed greater diversity and PD (0.832211 and 0.82805) respectively, suggesting that this system is highly informative, the system had lower PD and diversity DXS7133 system. Conclusion. The ten analyzed markers in this study allow simultaneous genotyping of 10 STRs in only one PCR additionally revealed that informative markers are widely analyzed and their use can greatly contribute in forensics practice, particularly in cases of family or other deficiencies.

Allele frequencies for 12 autosomal short tandem repeat loci in two bolivian populations

Two hundred and sixty unrelated subjects who asked for paternity testing at two Bolivian Laboratories in La Paz and Santa Cruz were studied. The loci D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820, TH01, TPOX, and CSF1PO were typed from blood samples, amplifying DNA by polymerase chain reactions and electrophoresis. Allele frequencies were estimated by simple counting and the unbiased heterozygosity was calculated. Hardy-Weinberg equilibrium was studied and gene frequencies were compared between the two samples. All loci conformed to the Hardy-Weinberg law and allele frequencies were similar in samples from the two cities. The Bolivian gene frequencies estimated were significantly different from those described for Chile and the United States Hispanic-Americans for most of the loci.

Allele frequencies of HLA class I and HLA class II in the Vietnamese Kinh ethnic

Experimental study for extracting DNA and determining HLA of I and II class by PCR-SSO was carried out. The percentage of allele frequency was estimated in comparison with that was reported in 1991 conference. Result showed no difference in locus A and DR12. Locus A demonstrated the highest percentage with some differences of 2-4%. In Locus DR12 with the highest percentage of differences of 3%. Highest difference was estimated in locus B. In this study, B15 has 25.7% (in comparing with 0%). B62 had 0% (in comparing with 10.1%), B75 6.7% (in comparing with 0%), B7 12.2% (in comparing with 0%)