An Exome-seq Based Tool for Mapping and Selection of Candidate Genes in Maize Deletion Mutants / 基因组蛋白质组与生物信息学报·英文版

Despite the large number of genomic and transcriptomic resources in maize, there is still much to learn about the function of genes in developmental and biochemical processes. Some maize mutants that were generated by gamma-irradiation showed clear segregation for the kernel phenotypes in B73 × Mo17 F2 ears. To better understand the functional genomics of kernel development, we developed a mapping and gene identification pipeline, bulked segregant exome sequencing (BSEx-seq), to map mutants with kernel phenotypes including opaque endosperm and reduced kernel size. BSEx-seq generates and compares the sequence of the exon fraction from mutant and normal plant F2 DNA pools. The comparison can derive mapping peaks, identify deletions within the mapping peak, and suggest candidate genes within the deleted regions. We then used the public kernel-specific expression data to narrow down the list of candidate genes/mutations and identified deletions ranging from several kb to more than 1 Mb. A full deletion allele of the Opaque-2 gene was identified in mutant 531, which occurs within a ∼200-kb deletion. Opaque mutant 1486 has a 6248-bp deletion in the mapping interval containing two candidate genes encoding RNA-directed DNA methylation 4 (RdDM4) and AMP-binding protein, respectively. This study demonstrates the efficiency and cost-effectiveness of BSEx-seq for causal mutation mapping and candidate gene selection, providing a new option in mapping-by-sequencing for maize functional genomics studies.

Mapeamento genético do locus 1q 24.2 – 1q31.3 em famílias segregando periodontite agressiva / Genetic mapping of locus 1q 24.2 – 1q 3.3 in families segregating aggressive periodontitis

Um estudo sugere que o fenótipo da periodontite agressiva localizada está ligado a região 1q25. O objetivo do presente estudo foi aperfeiçoar o mapeamento genético da periodontite agressiva na região cromossômica supracitada em famílias clinicamente bem caracterizadas segregando a doença. A hipótese deste estudo é que variações genéticas localizadas no cromossomo 1 entre as regiões 1q 24.2 e 1q 31.3 contribuem para o fenótipo da periodontite agressiva. Como objetivos específicos, determinamos o modo de herança da periodontite agressiva através de análise de segregação, e verificamos a existência de ligação e/ou associação entre a região 1q 24.2-1q 31.3 e a periodontite agressiva. A análise de segregação foi executada no programa SEGREG do pacote SAGE versão 5.4.2 com base nos dados dos pedigrees das primeiras 74 famílias recrutadas neste estudo, totalizando 475 indivíduos (média de 6.4 indivíduos por família) de origem geográfica similar. Assumiu-se a herança Mendeliana como um locus autossômico com 2 alelos A e B, onde o alelo A estava associado ao fenótipo relevante. Cinco modos de transmissão (não homogêneo, Mendeliano homogêneo, homogêneo geral, semigeral, heterogêneo geral) foram testados assumindo que a prevalência da periodontite agressiva é de 1% sob o Equilíbrio de Hardy-Weinberg. Foram coletadas amostras de saliva de 54 das 74 famílias recrutadas, totalizando 371 amostras de saliva para a extração do DNA genômico. 21 polimorfismos de um único nucleotídeo (SNPs) foram selecionados dentro da região proposta e analisados por reação em cadeia da polimerase (PCR). Os genótipos foram obtidos pelo método TaqMan. A análise não paramétrica de ligação familial foi executada com o Programa Merlin. As detecções de transmissão (associação) foram executadas com os programas FBAT e PLINK. O modo de herança mais adequado para cada teste de susceptibilidade dos alelos executado foi o modelo semigeral (p=0,31)...

It has been suggested that the localized aggressive periodontitis phenotype is linked to the region 1q25. The aim of this study was to fine map the chromosome interval suggested as containing a localized aggressive periodontitis locus in clinically well characterized group of families segregating aggressive periodontitis. The hypothesis of this study is that genetic variation located between 1q24.2 to 1q31.3 contributes to the phenotype of aggressive periodontitis. As specific aims, we evaluated the inheritance mode of aggressive periodontitis performing segregation analysis and, we tested the presence of linkage and or association between the target region of chromosome 1 and aggressive periodontitis. Segregation analysis was performed in pedigree data from the first 74 families, comprised of 475 individuals (average of 6.4 individuals per family) with similar geographic origin by the use of the SEGREG program of SAGE v.5.4.2. Mendelian inheritance was assumed to be through an autosomal locus with two alleles A and B, where the A allele was associated with the relevant phenotype. Five inheritance modes (homogeneous no transmission, homogeneous Mendelian transmission, homogeneous general transmission, semi-general transmission, heterogeneous general transmission) were tested assuming the prevalence of aggressive periodontitis as 1% and no deviations from Hardy-Weinberg equilibrium. Saliva samples were collected from 54 families, 371 individuals and DNA was extracted from this biological material. Twenty-one single nucleotide polymorphisms (SNPs) were selected and analyzed by standard polymerase chain reaction. The genotypes were obtained by the TaqMan method. The non-parametric analysis of familial linkage was performed with Merlin software. Analyses of transmission detection (association) were performed by FBAT and PLINK programs. The most parsimonious mode of inheritance in each susceptibility type tested was the semi-general transmission mode (p=0,31)...

Análise genética de problemas craniofaciais: revisão da literatura e diretrizes para investigações clínico-laboratoriais (parte 2) / Genetic analysis of craniofacial problems: a review of the literature and some guidelines for clinical and laboratorial investigation (part 2)

OBJETIVO: esse artigo tem como objetivo ser uma fonte de informação acerca das técnicas e análises genéticas mais utilizadas em investigações clínicas e laboratoriais visando a identificação e a caracterização de genes relacionados a doenças ou distúrbios complexos, especialmente os que atingem as estruturas do crânio e da face. METODOLOGIA: são traçadas algumas diretrizes para guiar os futuros pesquisadores nos processos de seleção de amostras e obtenção de heredogramas para estudos genéticos e fornecidos conceitos e princípios gerais que norteiam métodos de análises genéticas. Tais métodos exigem conhecimento a respeito de transmissão gênica, genética molecular e utilização de marcadores moleculares, assim como envolvem o domínio de técnicas laboratoriais como, por exemplo, reações de polimerização em cadeia (PCR), eletroforese e seqüenciamento de DNA. RESULTADOS E CONCLUSÕES: as análises genéticas, em especial as análises de segregação e de ligação, representam importantes ferramentas à disposição dos pesquisadores na tentativa de relacionar fenótipos a genes específicos e na busca da exata localização cromossômica dos mesmos. Espera-se com esse artigo que os cirurgiões-dentistas clínicos possam começar a perceber a importância do assunto e buscar se aprofundar nessa área.

AIM: The aim of this paper is to inform the reader about genetic techniques and analysis used in clinical and laboratorial investigations for the identification and characterization of the genetic determinants for complex disorders, especially those that attain craniofacial structures. METHODS: General concepts and principles of important methods of genetic analysis are given as well as some guidelines for future researchers, concerning sample gathering and pedigrees construction. These methods described here require knowledge about genetic transmission, molecular genetics and DNA markers, and involve the ability to deal with the current laboratorial techniques, including polymerase chain reactions, agarose or polyacrilamide gel and the use of DNA sequencers. RESULTS AND CONCLUSIONS: Those genetic analysis, mainly the segregation and the linkage analysis, are considered important tools in the attempt to make the relationship between some phenotypes and specific genotypes, and to search for the exact chromosomal localization of each one of these genes. The knowledge of these information can help clinical dentists to understand the important role played by genetics, leading them to get deeper into the subject.

Heritability and segregation analysis of the level of HDL-cholesterol / 한국역학회지

OBJECTIVES: The purpose of this study was to investigate the familial correlation and heritability in HDL cholesterol through segregation analysis. METHODS: This study, based on data from 11,117 Korean individuals ascertained pedigrees who had participated in 1998 and 2001 Korean National Health & Nutrition Examination Survey. The subjects of segregation analysis were 4,688 Korean who had more than five members in their family. RESULTS: Serum lipid levels revealed strong familial correlation among spouses, parent-offspring and siblings with low correlation of spouse. The heritability of HDL cholesterol was 54.8% after controlling for age, age2, gender, agexgender, waist circumference, smoking, alcohol drinking, exercise and education. Two models of inheritance, the Mendelian dominant model and the Mendelian codominant model were found in HDL cholesterol. In the codominant model, the predicted HDL-cholesterol for genotype AA, AB, and BB were 44.96, 49.13, and 69.67 mg/dl, respectively. However the Mendelian codominant model only was found in high risk families. CONCLUSIONS: In conclusion, randomly ascertained Korean families of this study showed strong familial aggregation in HDL cholesterol. The results suggested that the variations in HDL cholesterol may be influencing by major effect of gene.

Segregation Analysis of Serum LDL-cholesterol in Korean Families of Coronary Heart Disease Patients / 한국역학회지

PURPOSES: The aim of this study was to investigate the familial correlation of lipid profile and the mode of inheritance of LDL-cholesterol through segregation analysis. The study population included 414 family members of 67 Probands who had a coronary heart disease. METHODS: Gene frequency(qH) of the allele for high LDL-cholesterol levels, means of each genotypes, and other putative gene related parameters were estimated. Maximum likelihood methods were used to fit several genetic and nongenetic modes of inheritance to these data to determine if an unobserved Mendelian major gene could explain the familial distribution of LDL-cholesterol. LDL-cholesterol levels were adjusted for age, gender, body mass index, smoking and alcohol consumption. RESULTS: LDL-cholesterol levels revealed familial correlation among spouses, parent-offsprings and siblings with correlations of 0.10, 0.22, and 0.32, respectively. The heritability of LDL-cholesterol was 53%. Two models of inheritance in LDL-cholesterol distribution, the Mendelian codominant model and the polygenic equal transmission model were found. Comparison of these two models in each family among 67 families showed that thiry-six families favored the major gene model with Mendelian codominant and thirty-one families favored the polygenic model of equal transmission. In families favoring Mendelian codominant inheritance, means of each genotypes; LL, HL, HH were 102.1, 143.3, 248.4 mg/dl and gene frequency of H allele was 0.08. In families favoring equal transmission inheritance, means of each genotypes were 101.6, 122.7, 185.5 mg/dl and gene frequency of H allele was 0.14. CONCLUSIONS: In conclusion, families of coronary heart disease patients of this study showed substantial familial correlation and results suggested that variation in LDL-cholesterol may be influenced by major gene effect.

Study on Genetic Model of Attention Deficit Hyperactivity Disorder / 实用儿科临床杂志

Objective To analyze the genetic model of attention deficit hyperactivity disorder(ADHD).Methods The segregation analysis and polygenic multiple threshold model were used to prove the polygenic model and to estimate the heritability and recurrence risk of ADHD in each degree relatives.Results 1. The average heritability of ADHD was (102.47?9.78)%;2.The first-degree relatives of probands were in high risk for ADHD(23.0%)compared with colony prevalence rate(2.6%). The ADHD prevalence of each degree relatives rapidly decreased with the increased magnitude of consanguineous relationship of each degree relatives and ADHD probands. Conclusions The genetic model of ADHD is the most likely polygenic inheritance with major genes, which suggested that the genetic factor might play an important role in the liability variance of ADHD.Apart from the involvement of multiple genes,each gene contributes a small additive effect,and the major genes may be involved as well.