Fine mapping and replication of QTL in outbred chicken advanced intercross lines

Background: Linkage mapping is used to identify genomic regions affecting the expression of complex traits. However, when experimental crosses such as F2 populations or backcrosses are used to map regions containing a Quantitative Trait Locus (QTL), the size of the regions identified remains quite large, i.e. 10 or more Mb. Thus, other experimental strategies are needed to refine the QTL locations. Advanced Intercross Lines (AIL) are produced by repeated intercrossing of F2 animals and successive generations, which decrease linkage disequilibrium in a controlled manner. Although this approach is seen as promising, both to replicate QTL analyses and fine-map QTL, only a few AIL datasets, all originating from inbred founders, have been reported in the literature. Methods: We have produced a nine-generation AIL pedigree (n = 1529) from two outbred chicken lines divergently selected for body weight at eight weeks of age. All animals were weighed at eight weeks of age and genotyped for SNP located in nine genomic regions where significant or suggestive QTL had previously been detected in the F2 population. In parallel, we have developed a novel strategy to analyse the data that uses both genotype and pedigree information of all AIL individuals to replicate the detection of and fine-map QTL affecting juvenile body weight. Results: Five of the nine QTL detected with the original F2 population were confirmed and fine-mapped with the AIL, while for the remaining four, only suggestive evidence of their existence was obtained. All original QTL were confirmed as a single locus, except for one, which split into two linked QTL. Conclusions: Our results indicate that many of the QTL, which are genome-wide significant or suggestive in the analyses of large intercross populations, are true effects that can be replicated and fine-mapped using AIL. Key factors for success are the use of large populations and powerful statistical tools. Moreover, we believe that the statistical methods we have developed to efficiently study outbred AIL populations will increase the number of organisms for which in-depth complex traits can be analyzed.

Genome-wide association mapping in a wild avian population identifies a link between genetic and phenotypic variation in a life-history trait

Understanding the genetic basis of traits involved in adaptation is a major challenge in evolutionary biology but remains poorly understood. Here, we use genome-wide association mapping using a custom 50 k single nucleotide polymorphism (SNP) array in a natural population of collared flycatchers to examine the genetic basis of clutch size, an important life-history trait in many animal species. We found evidence for an association on chromosome 18 where one SNP significant at the genome-wide level explained 3.9% of the phenotypic variance. We also detected two suggestive quantitative trait loci (QTLs) on chromosomes 9 and 26. Fitness differences among genotypes were generally weak and not significant, although there was some indication of a sex-by-genotype interaction for lifetime reproductive success at the suggestive QTL on chromosome 26. This implies that sexual antagonism may play a role in maintaining genetic variation at this QTL. Our findings provide candidate regions for a classic avian life-history trait that will be useful for future studies examining the molecular and cellular function of, as well as evolutionary mechanisms operating at, these loci.

Variantes genéticas da calpaína-10 (CAPN-10) numa amostra de pacientes hiperandrogênicas

A síndrome dos ovários policísticos atinge 5 - 10% das mulheres em idade fértil e mais de 40% destas pacientes apresenta obesidade e resistência insulínica, o que aumenta o risco para o desenvolvimento do diabetes mellitus tipo 2 (DM2). Numerosos genes poderiam contribuir para o desenvolvimento do DM2 e outras alterações metabólicas. Dentre estes o gene da calpaína-10 (CAPN-10), tem sido associado com DM2 em populações mexicanosamericanos, e em duas populações do Norte da Europa (Finlândia e Alemanha). No presente estudo analisamos o genótipo de 96 pacientes hiperandrogênicas reunidas em dois grupos: Síndrome dos ovários policísticos (PCOS) e Hirsutismo idiopático (HI), com relação à freqüência de quatro polimorfismos do gene da CAPN-10 (SNP-44, 43, 19 e 63). Foram ainda realizadas análises de associação entre a freqüência alélica dos polimorfismos e características clínicas das pacientes, com ênfase na obesidade e resistência insulínica A variação genética da CAPN-10 foi avaliada a partir do DNA genômico por amplificação pela Polimerase Chain Reaction (PCR) e PCR-aleloespecífico (Teste de AMRS) dos fragmentos que contém os polimorfismos do gene da CAPN-10. Nossos resultados mostraram que não houve diferença entre as freqüências genotípicas e alélicas dos SNPs 44, 43, 19 e 63 entre os grupos PCOS e HI. Por outro lado, a comparação das características clínicas dos dois grupos mostrou que o alelo Ins do SNP-19 da CAPN-10 tendeu a ser mais freqüente entre as pacientes PCOS estratificadas para sobrepeso e obesas (p≤0,05). Não houve diferença na comparação das características clínicas avaliadas e a freqüência alélica para os SNPs 43 e 63. A análise da amostra total de pacientes hirsutas, ou seja, pacientes com PCOS e HI agrupadas não evidenciou diferença entre a freqüência alélica das variantes genéticas estudadas para a CAPN-10 e a presença de resistência insulínica. Tendo em vista o efeito modesto dos SNPs 44, 43, 19 e 63 avaliados isoladamente nestas pacientes, estudos adicionais serão necessários avaliando a freqüência desses polimorfismos na população do Sul do Brasil.

Efeito de polimorfismos no gene LEP na expressão da leptina em adipócitos de bovinos de corte

Os caracteres produtivos são normalmente influenciados por muitos fatores, sendo difícil determinar todos os locos envolvidos em um fenótipo específico. Por isso, a seleção animal tem se baseado principalmente em uma estimativa direta ou indireta do fenótipo. A leptina é um importante regulador do metabolismo energético, da adiposidade e da reprodução. E por desempenhar diferentes funções, pode ser considerado um bom gene candidato para o estudo de associações entre marcadores moleculares e a eficiência reprodutiva ou ganho de peso. Em várias espécies, têm sido descritos diversos polimorfismos no gene da leptina, influenciando o ganho de peso, a reprodução, e outras características produtivas. Em bovinos, o STR IDVGA51 e o SNP LEPSau3A1, foram descritos por afetarem a performance reprodutiva, os alelos IDVGA51*181 e LEPSau3A1*2 estando associados a um aumento no intervalo entre partos de 79 e 81 dias, respectivamente, e os STRs BMS1074 e BM1500 afetam o ganho de peso, em vacas, no pós-parto: os alelos BMS1074*151 e BM1500*135 reduzindo e aumentando, respectivamente, o ganho de peso diário. Para confirmar o efeito ou não destes alelos na expressão do gene da leptina, este trabalho comparou os níveis de mRNA de leptina em animais portadores e não portadores dos alelos IDVGA51*181, LEPSau3A1*2, BMS1074*151 e BM1500*135, com os objetivos de: 1. Verificar as distribuições genotípicas e alélicas dos marcadores IDVGA51, BMS1074, BM1500 e LEPSau3A1, em uma amostra de 137 bovinos da raça Brangus-Ibagé, provenientes da Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA-Pecuária Sul, Bagé-RS). 2. Identificar, no rebanho, animais portadores e não portadores dos alelos IDVGA51*181, LEPSau3A1*2, BMS1074*151 ou BM1500*135, previamente descritos como associados à eficiência reprodutiva e ganho de peso. 3. Avaliar os animais, criados em campo nativo, com pastagem natural, quanto à sua condição corporal. 4. Realizar procedimento cirúrgico, para obtenção de amostras de tecido adiposo subcutâneo e omental. 5. Dosar os níveis de mRNA de leptina nos adipócitos destes dois tecidos, através do método quantitativo em tempo real (Real-Time RT-PCR), comparando a expressão do gene LEP entre indivíduos portadores e não portadores dos alelos de predisposição a ganho de peso e desempenho reprodutivo.

Determinantes genéticos da hanseníase em uma população do Rio Grande do Norte

Background: Leprosy can cause severe disability and disfigurement and is still a major health in different parts of the world. Only a subset of those individuals exposed to the pathogen will go on to develop clinical disease and there is a broad clinical spectrum amongst leprosy patients. The outcome of infection is in part due to host genes that influence control of the initial infection and the host´s immune response to that infection. Aim: Evaluate if polymorphisms type SNP in the 17q118q21 chromosomic region contribute to development of leprosy in Rio Grande do Norte population. Material and methods: A sample composed of 215 leprosy patients and 229 controls drawn from the same population were genotyped by using a Snapshot assay for eight genes (NOS2A, CCL18, CRLF3, CCL23, TNFAIP1, STAT5B, CCR7 and CSF3) located in chromosomic region 17q118q21. The genotype and allele frequency were measured and statistical analysis was performed by chi-square in SPSS version 15 and graph prism pad version 4 software. Results: Ours results indicated that the markers NOS2A8277, NOS2A8rs16949, CCR78rs11574663 and CSF38rs2227322 presented strong association with leprosy and their risk genotype were GG, TT, AA and GG respectively. The risk genotypes for all markers associated to leprosy presented recessive inheritance standard. When we compared the interaction among the markers in different combination we find that the marker NOS2A8277 associated with CCR78rs11574663 presented highest risk probability to development of leprosy. When we evaluated the haplotype of the risk markers it was found a haplotype associated with increase of the protection (CSF38rs22273228CC, CCR78 rs115746638GA, NOS2A8rs169498CT and NOS2A82778GA). The association of the clinical forms paucibacilary and multibacilary with markers showed that to the markers NOS2A8 2778GG, CCR78rs115746638AA and CSF38rs22273228GG there were a strong influence to migration to multibacilary pole and to marker NOS2A8rs169498TT the high proportion was found to the paucibacilary form. Conclusions: Changes in the genes NOS2A, CCR7 and CSF3 can influence the immune response against Mycobacterium leprae. The combination among these polymorphisms alters the risk probability to develop leprosy. The markers type SNP associated to development of the leprosy also are linked to clinical forms and its severity being the polymorphism NOS2A8rs169498TT associated with paucibacilar form and the polymorphisms NOS2A82778GG, CCR78rs115746638AA and CSF38rs22273228GG associated to multibacilar form

Genes candidatos de suscetibilidade a pré-eclampsia: estudo de associação

Preeclampsia is a multifactorial disease of unknown etiology that features with wide clinical symptoms, ranging from mild preeclampsia to severe forms, as eclampsia and HELLP syndrome. As a complex disease, preeclampsia is also influenced by genetic and environmental factors. Aiming to identify preeclampsia susceptibility genes, we genotyped a total of 22 genetic markers (single nucleotides polymorphisms SNPs) distributed in six candidates genes (ACVR2A, FLT1, ERAP1, ERAP2, LNPEP e CRHBP). By a case-control approach, the genotypic frequencies were compared between normotensive (control group) and preeclamptic women. The case s group was classified according to the disease clinical form in: preeclampsia, eclampsia and HELLP syndrome. As results we found the following genetic association: 1) ACVR2A and preeclampsia; 2) FLT1 and severe preeclampsia; 3) ERAP1 and eclampsia; 4) FLT1 and HELLP syndrome. When stratifying preeclampsia group according to symptoms severity (mild and severe preeclampsia) or according to the time of onset (early and late preeclampsia), it was detected that early preeclampsia is strongly associated to risk preeclampsia, eclampsia and HELLP syndrome have different genetic bases, although FLT1 gene seems to be involved in preeclampsia and HELLP syndrome pathophisiology

Análise da contribuição de fatores genéticos e ambientais na manutenção da hanseniase nos estados do Rio Grande do Norte e Pará

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior

Análise do efeito de polimorfismos não-sinônimos em genes de reparo de DNA da via BER na resposta inflamatória da meningite

In vitro and in animal models, APE1, OGG1, and PARP-1 have been proposed as being involved with inflammatory response. In this work, we have investigated if the SNPs APE1 Asn148Glu, OGG1 Ser326Cys, and PARP-1 Val762Ala are associated to meningitis and also developed a system to enable the functional analysis of polymorphic proteins. Patients with bacterial meningitis (BM), aseptic meningitis (AM) and controls (non-infected) genotypes were investigated by PIRA-PCR or PCR-RFLP. DNA damages were detected in genomic DNA by Fpg treatment. IgG and IgA were measured from plasma and the cytokines and chemokines were measured from cerebrospinal fluid samples using Bio-Plex assays. The levels of NF-κB and c-Jun were measured in CSF by dot blot assays. A significant (P<0.05) increase in the frequency of APE1 148Glu allele in BM and AM patients was observed. A significant increase in the genotypes Asn/Asn in control group and Asn/Glu in BM group was also found. For the SNP OGG1 Ser326Cys, the genotype Cys/Cys was more frequent (P<0.05) in BM group. The frequency of PARP-1 Val/Val genotype was higher in control group (P<0.05). The occurrence of combined SNPs increased significantly in BM patients, indicating that these SNPs may be associated to the disease. Increasing in sensitive sites to Fpg was observed in carriers of APE1 148Glu allele or OGG1 326Cys allele, suggesting that SNPs affect DNA repair activity. Alterations in IgG production were observed in the presence of SNPs APE1Asn148Glu, OGG1Ser326Cys or PARP-1Val762Ala. Reductions in the levels ofIL-6, IL-1Ra, MCP-1/CCL2and IL-8/CXCL8 were observed in the presence of APE1148Glu allele in BM patients, however no differences were observed in the levels of NF-κB and c-Jun considering genotypes and analyzed groups. Using APE1 as model, a system to enable the analysis of cellular effects and functional characterization of polymorphic proteins was developed using strategies of cloning APE1 cDNA in pIRES2-EGFP vector, cellular transfection of the construction obtained, siRNA for endogenous APE1 and cellular cultures genotyping. In conclusion, we obtained evidences of an effect of SNPs in DNA repair genes on the regulation of immune response. This is a pioneering work in the field that shows association of BER variant enzymes with an infectious disease in human patients, suggesting that the SNPs analyzed may affect immune response and damage by oxidative stress level during brain infection. Considering these data, new approaches of functional characterization must be developed to better analysis and interactions of polymorphic proteins in response to this context

Marcadores genéticos associados com a resposta inflamatória na meningite bacteriana

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior

Whole-genome analysis for backfat thickness in a tropically adapted, composite cattle breed from Brazil

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Prospecting candidate SNPs for backfat in Canchim beef cattle

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Venous tone and cardiac function in the South American rattlesnake Crotalus durissus: mean circulatory filling pressure during adrenergic stimulation in anaesthetised and fully recovered animals

The effects of adrenergic stimulation on mean circulatory filling pressure (MCFP), central venous pressure (P-CV) and stroke volume (Vs), as well as the effects of altered MCFP through changes of blood volume were investigated in rattlesnakes (Crotalus durissus). MCFP is an estimate of the upstream pressure driving blood towards the heart and is determined by blood volume and the activity of the smooth muscle cells in the veins (venous tone). MCFP can be determined as the plateau in P-CV during a total occlusion of blood flow from the heart.Vs decreased significantly when MCFP was lowered by reducing blood volume in anaesthetised snakes, whereas increased MCFP through infusion of blood (up to 3 ml kg(-1)) only led to a small rise in Vs. Thus, it seems that end-diastolic volume is not affected by an elevated MCFP in rattlesnakes. To investigate adrenergic regulation on venous tone, adrenaline as well as phenylephrine and isoproterenol (alpha- and beta-adrenergic agonists, respectively) were infused as bolus injections (2 and 10 mu g kg(-1)). Adrenaline and phenylephrine caused large increases in MCFP and P-CV, whereas isoproterenol decreased both parameters. This was also the case in fully recovered snakes. Therefore, adrenaline affects venous tone through both alpha- and beta-adrenergic receptors, but the alpha-adrenergic receptor dominates at the dosages used in the present study. Injection of the nitric oxide donor SNP caused a significant decrease in P-CV and MCFP. Thus, nitric oxide seems to affect venous tone.

The role of nitric oxide in the regulation of the systemic and pulmonary vasculature of the rattlesnake, Crotalus durissus terrificus

The functional role of nitric oxide (NO) was investigated in the systemic and pulmonary circulations of the South American rattlesnake, Crotalus durissus terrificus. Bolus, intra-arterial injections of the NO donor, sodium nitroprusside (SNP) caused a significant systemic vasodilatation resulting in a reduction in systemic resistance (Rsys). This response was accompanied by a significant decrease in systemic pressure and a rise in systemic blood flow. Pulmonary resistance (Rpul) remained constant while pulmonary pressure (Ppul) and pulmonary blood flow (Qpul) decreased. Injection of L-Arginine (L-Arg) produced a similar response to SNP in the systemic circulation, inducing an immediate systemic vasodilatation, while Rpul was unaffected. Blockade of NO synthesis via the nitric oxide synthase inhibitor, L-NAME, did not affect haemodynamic variables in the systemic circulation, indicating a small contribution of NO to the basal regulation of systemic vascular resistance. Similarly, Rpul and Qpul remained unchanged, although there was a significant rise in Ppul. Via injection of SNP, this study clearly demonstrates that NO causes a systemic vasodilatation in the rattlesnake, indicating that NO may contribute in the regulation of systemic vascular resistance. In contrast, the pulmonary vasculature seems far less responsive to NO.

Assessment of DGAT1 and LEP gene polymorphisms in three Nelore (Bos indicus) lines selected for growth and their relationship with growth and carcass traits

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

First polymorphisms in JY-1 gene in cattle (Bos taurus indicus) and their association with sexual precocity and growth traits

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)