Analysis Of Polymorphic Loci Research Articles

Targeted analysis of polymorphic loci from low-coverage shotgun sequence data allows accurate genotyping of HLA genes in historical human populations

The highly polymorphic human leukocyte antigen (HLA) plays a crucial role in adaptive immunity and is associated with various complex diseases. Accurate analysis of HLA genes using ancient DNA (aDNA) data is crucial for understanding their role in human adaptation to pathogens. Here, we describe the TARGT pipeline for targeted analysis of polymorphic loci from low-coverage shotgun sequence data. The pipeline was successfully applied to medieval aDNA samples and validated using both simulated aDNA and modern empirical sequence data from the 1000 Genomes Project. Thus the TARGT pipeline enables accurate analysis of HLA polymorphisms in historical (and modern) human populations.

Influence of ecological and geographical features of breeding brown Carpathian rocks on its genetic structure

Studying the genetic structure of cattle makes it possible to characterize it by molecular genetic markers, which in the future enable effective breeding work with animals breed to achieve the desired characteristics. Lately is becoming more apparent the need to preserve genetic diversity namely due to the peculiarities of breeding in different ecological and geographical regions. Therefore, we conducted an investigation of the genetic structure of animals of pure-bred Brown Carpathian (BC), Schwyz (S) breeds, their mixtures of the first (F1) generation (1/2BС+1/2S), Brown Carpathian with a share of hereditary breed of Schwyz breed up to 50 and more than 50%, as well as Brown Carpathian, raised in flat and mountain farms. Genetic structure was evaluated by genetically determined polymorphism of groups of genetic-biochemical systems. Of the 14 investigated loci that encode proteins and blood enzymes, polymorphism was identified in five loci, namely: transferrin (Tf), ceruloplasmin (Cr), amylase-1 (Am-1), hemoglobin (Hb), and purine nucleoside phosphorylase (NP). As a result of population-genetic analysis of polymorphic loci of proteins and enzymes of blood in animals of Brown Carpathian breed the following data were obtained:the highest level of heterozygosity (H) was found at the transferrin locus – 95%, the lowest – at the hemoglobin locus – 9.5%.The heterozygosity at the ceruloplasmin locus was 68%. Evaluation of heterozygosity at the purinnucleoside phosphorylase locus was not possible because part of the animals with the NP-H (high activity) phenotype could carry a low activity variant in the heterozygous state. For all polymorphic systems in the Brown Carpathian breed genotype frequency distribution was in a balanced state according to Hardy-Weinberg law, except for the transferrin locus,where a statistically significant deficiency of homozygotes (P > 0.95) in the most common allelic variants is detected. Analysis of the dendrogram showed that groups of animals of Brown Carpathian breed with different proportion of hereditary Schwyz form one cluster that is clearly differentiated from purebred schwyzes. First-generation domestic animals (F1), by genetic structure, are significantly closer to the maternal Brown Carpathian breed than to the Schwyz one. Thus, the data obtained indicate that the specific characteristic of Brown Carpathian breed may be a relatively increased breeding value of a number of allelic interlocal associations, in which the loci of the genetic-biochemical systems are involved in one way or another. Genetic analysis of these systems showed the presence in the breed of its specific features, which are specific to it.

Variabilidade genética e sensibilidade de acessos de Pistia stratiotes ao herbicida glyphosate

A alface-d'água (Pistia stratiotes) é uma das principais entre as macrófitas aquáticas que causam problemas em corpos hídricos no Brasil e são consideradas como plantas daninhas. O presente trabalho foi realizado com os objetivos de conhecer melhor a variabilidade genética dessa macrófita e relacionar essa variabilidade com a resposta à aplicação do herbicida glyphosate. Para isso, foram coletados indivíduos em 12 corpos hídricos em diferentes cidades do território nacional (Americana, Cambaratiba, Curitiba, Itapura, Jaboticabal, Lagoa Santa, Piraí, Rio Grande, Rubinéia, Salto Grande, Santa Gertrudes e Três Lagoas). Os acessos foram caracterizados pelo uso de marcadores RAPD (DNA Polimórfico Amplificado ao Acaso), que permitiram, com o auxílio de iniciadores aleatórios, a caracterização dos locos polimórficos identificados por uma matriz de ausência e presença de bandas. Utilizando essa matriz, a análise de agrupamento permitiu nítida classificação dos acessos em três grupos com diferenças genéticas entre eles. Um ensaio de controle químico, com plantas mantidas em vasos plásticos (5 L) e pulverizadas com o herbicida glyphosate nas concentrações de 0,0, 0,6, 1,2, 1,8 e 2,4 kg ha-1, identificou, utilizando avaliações aos 7, 14 e 21 dias após aplicação, que as duas maiores doses promoveram melhor efeito herbicida. Foi verificado também que os acessos de Curitiba e Cambaratiba apresentaram menor suscetibilidade ao herbicida glyphosate. Não houve correspondência entre a estrutura de grupos dos acessos pela análise multivariada de agrupamento com a técnica RAPD e a suscetibilidade da alface-d'água ao glyphosate.

Analysis of HLA-DRB1*-A* and -B* alleles in prenatal diagnosis for determination of maternal contamination in fetal DNA.

During chorionic villi sampling for prenatal diagnosis with molecular biology techniques, contamination by maternal decidua frequently occurs and can lead to misinterpretation of the test results. To avoid such problems, we present a new method for appraising maternal contamination of fetal DNA, based on genomic typing of the highly variable human leukocyte antigen (HLA) locus-DRB1*, locus A* and locus B* regions by genetic amplification with sequence-specific primers and PCR. Fetal DNA samples obtained for beta-thalassemia diagnosis were analysed after artificial contamination with increasing maternal DNA concentrations ranging from 0.5 to 10% (0.5, 1, 3, 5 and 10%). The approach was found to be rapid, specific, reproducible and highly sensitive and permits recognition of 1-3% contamination by maternal DNA concentrations. The system currently used for detecting maternal DNA contamination in fetal samples is the analysis of polymorphic loci by variable number of tandem repeats and/or short tandem repeats. We propose that the analysis of HLA alleles may provide a valid alternative or complement to this system.