Genotype x location x feeding interactions in Nellore cattle calculated through three-mode principal component analysis

The main objective of this study was to apply three-mode principal component analysis to assess the triple interaction (genotype x location x feeding) on direct genetic value for weight at 205 days of age. We used 60 sires with offspring in three regions of northeastern Brazil (Maranhao, Mata and Agreste, and Reconcavo Baiano) and raised on a pasture regime or with supplementation. There was no interaction between genotype and location, but there was a correlation between genotype and direct effect of feeding. The use of sires should be dictated according to the system of rearing of their offspring.

GGE biplot analysis of multi-environment yield trials of rice produced in a temperate climate

Low temperature is one of the main environmental constraints for rice ( Oryza sativa L.) grain production yield. It is known that multi-environment studies play a critical role in the sustainability of rice production across diverse environments. However, there are few studies based on multi-environment studies of rice in temperate climates. The aim was to study the performance of rice plants in cold environments. Four experimental lines and six cultivars were evaluated at three locations during three seasons. The grain yield data were analyzed with ANOVA, mixed models based on the best linear unbiased predictors (BLUPs), and genotype plus Genotype × Environment interaction (GGE) biplot. High genotype contribution (> 25%) was observed in grain yield and the interaction between genotype and locations was not very important. Results also showed that ‘Quila 241319’ was the best experimental line with the highest grain yield (11.3 t ha-1) and grain yield stability across the environments; commercial cultivars were classified as medium grain yield genotypes.

A "Candidate-Interactome" Aggregate Analysis of Genome-Wide Association Data in Multiple Sclerosis

Though difficult, the study of gene-environment interactions in multifactorial diseases is crucial for interpreting the relevance of non-heritable factors and prevents from overlooking genetic associations with small but measurable effects. We propose a "candidate interactome" (i.e. a group of genes whose products are known to physically interact with environmental factors that may be relevant for disease pathogenesis) analysis of genome-wide association data in multiple sclerosis. We looked for statistical enrichment of associations among interactomes that, at the current state of knowledge, may be representative of gene-environment interactions of potential, uncertain or unlikely relevance for multiple sclerosis pathogenesis: Epstein-Barr virus, human immunodeficiency virus, hepatitis B virus, hepatitis C virus, cytomegalovirus, HHV8-Kaposi sarcoma, H1N1-influenza, JC virus, human innate immunity interactome for type I interferon, autoimmune regulator, vitamin D receptor, aryl hydrocarbon receptor and a panel of proteins targeted by 70 innate immune-modulating viral open reading frames from 30 viral species. Interactomes were either obtained from the literature or were manually curated. The P values of all single nucleotide polymorphism mapping to a given interactome were obtained from the last genome-wide association study of the International Multiple Sclerosis Genetics Consortium & the Wellcome Trust Case Control Consortium, 2. The interaction between genotype and Epstein Barr virus emerges as relevant for multiple sclerosis etiology. However, in line with recent data on the coexistence of common and unique strategies used by viruses to perturb the human molecular system, also other viruses have a similar potential, though probably less relevant in epidemiological terms. © 2013 Mechelli et al.

Genome-Wide Association Studies of Asthma in Population-Based Cohorts Confirm Known and Suggested Loci and Identify an Additional Association near HLA

Rationale: Asthma has substantial morbidity and mortality and a strong genetic component, but identification of genetic risk factors is limited by availability of suitable studies. Objectives: To test if population-based cohorts with self-reported physician-diagnosed asthma and genome-wide association (GWA) data could be used to validate known associations with asthma and identify novel associations. Methods: The APCAT (Analysis in Population-based Cohorts of Asthma Traits) consortium consists of 1,716 individuals with asthma and 16,888 healthy controls from six European-descent population-based cohorts. We examined associations in APCAT of thirteen variants previously reported as genome-wide significant (P<5x10-8) and three variants reported as suggestive (P<5×10-7). We also searched for novel associations in APCAT (Stage 1) and followed-up the most promising variants in 4,035 asthmatics and 11,251 healthy controls (Stage 2). Finally, we conducted the first genome-wide screen for interactions with smoking or hay fever. Main Results: We observed association in the same direction for all thirteen previously reported variants and nominally replicated ten of them. One variant that was previously suggestive, rs11071559 in RORA, now reaches genome-wide significance when combined with our data (P = 2.4×10-9). We also identified two genome-wide significant associations: rs13408661 near IL1RL1/IL18R1 (PStage1+Stage2 = 1.1x10-9), which is correlated with a variant recently shown to be associated with asthma (rs3771180), and rs9268516 in the HLA region (PStage1+Stage2 = 1.1x10-8), which appears to be independent of previously reported associations in this locus. Finally, we found no strong evidence for gene-environment interactions with smoking or hay fever status. Conclusions: Population-based cohorts with simple asthma phenotypes represent a valuable and largely untapped resource for genetic studies of asthma. © 2012 Ramasamy et al.

Promise and pitfalls of the Immunochip

Genomewide association studies (GWAS) have proven a powerful hypothesis-free method to identify common disease-associated variants. Even quite large GWAS, however, have only at best identified moderate proportions of the genetic variants contributing to disease heritability. To provide cost-effective genotyping of common and rare variants to map the remaining heritability and to fine-map established loci, the Immunochip Consortium has developed a 200,000 SNP chip that has been produced in very large numbers for a fraction of the cost of GWAS chips. This chip provides a powerful tool for immunogenetics gene mapping.

Genetic studies of osteoporosis: A rethink required

It has been 10 years since the seminal paper by Morrison and colleagues reporting the association of alleles of the vitamin D receptor and bone density [1], a paper which arguably kick-started the study of osteoporosis genetics. Since that report there have been literally thousands of osteoporosis genetic studies published, and large numbers of genes have been reported to be associated with the condition [2]. Although some of these reported associations are undoubtedly true, this snow-storm of papers and abstracts has clouded the field to such a great extent that it is very difficult to be certain of the veracity of most genetic associations reported hereto. The field needs to take stock and reconsider the best way forward, taking into account the biology of skeletal development and technological and statistical advances in human genetics, before more effort and money is wasted on continuing a process in which the primary achievement could be said to be a massive paper mountain. I propose in this review that the primary reasons for the paucity of success in osteoporosis genetics has been: •the absence of a major gene effect on bone mineral density (BMD), the most commonly studied bone phenotype; •failure to consider issues such as genetic heterogeneity, gene–environment interaction, and gene–gene interaction; •small sample sizes and over-optimistic data interpretation; and •incomplete assessment of the genetic variation in candidate genes studied.

Genetic determinants of bone density and fracture risk: State of the art and future directions

Context: Osteoporosis is a common, highly heritable condition that causes substantial morbidity and mortality, the etiopathogenesis of which is poorly understood. Genetic studies are making increasingly rapid progress in identifying the genes involved. Evidence Acquisition and Synthesis: In this review, we will summarize the current understanding of the genetics of osteoporosis based on publications from PubMed from the year 1987 onward. Conclusions: Most genes involved in osteoporosis identified to date encode components of known pathways involved in bone synthesis or resorption, but as the field progresses, new pathways are being identified. Only a small proportion of the total genetic variation involved in osteoporosis has been identified, and new approaches will be required to identify most of the remaining genes.

CIMMYT-selected derived synthetic bread wheats for rainfed environments: Yield evaluation in Mexico and Australia.

Synthetic backcrossed-derived bread wheats (SBWs) from CIMMYT were grown in the Northwest of Mexico at Centro de Investigaciones Agrícolas del Noroeste (CIANO) and sites across Australia during three seasons. During three consecutive years Australia received “shipments” of different SBWs from CIMMYT for evaluation. A different set of lines was evaluated each season, as new materials became available from the CIMMYT crop enhancement program. These consisted of approximately 100 advanced lines (F7) per year. SBWs had been top and backcrossed to CIMMYT cultivars in the first two shipments and to Australian wheat cultivars in the third one. At CIANO, the SBWs were trialled under receding soil moisture conditions. We evaluated both the performance of each line across all environments and the genotype-by-environment interaction using an analysis that fits a multiplicative mixed model, adjusted for spatial field trends. Data were organised in three groups of multienvironment trials (MET) containing germplasm from shipment 1 (METShip1), 2 (METShip2), and 3 (METShip3), respectively. Large components of variance for the genotype × environment interaction were found for each MET analysis, due to the diversity of environments included and the limited replication over years (only in METShip2, lines were tested over 2 years). The average percentage of genetic variance explained by the factor analytic models with two factors was 50.3% for METShip1, 46.7% for METShip2, and 48.7% for METShip3. Yield comparison focused only on lines that were present in all locations within a METShip, or “core” SBWs. A number of core SBWs, crossed to both Australian and CIMMYT backgrounds, outperformed the local benchmark checks at sites from the northern end of the Australian wheat belt, with reduced success at more southern locations. In general, lines that succeeded in the north were different from those in the south. The moderate positive genetic correlation between CIANO and locations in the northern wheat growing region likely reflects similarities in average temperature during flowering, high evaporative demand, and a short flowering interval. We are currently studying attributes of this germplasm that may contribute to adaptation, with the aim of improving the selection process in both Mexico and Australia.

Significant effects of Pgi genotype and body reserves on lifespan in the Glanville fritillary butterfly

Individuals with a particular variant of the gene phosphoglucose isomerase (Pgi ) have been shown to have superior dispersal capacity and fecundity in the Glanville fritillary butterfly (Melitaea cinxia), raising questions about the mechanisms that maintain polymorphism in this gene in the field. Here, we investigate how variation in the Pgi genotype affects female and male life history under controlled conditions. The most striking effect is the longer lifespan of genotypes with high dispersal capacity, especially in nonreproducing females. Butterflies use body reserves for somatic maintenance and reproduction, but
different resources (in thorax versus abdomen) are used under dissimilar conditions, with some interactions with the Pgi genotype. These results indicate life-history trade-offs that involve resource allocation and genotype!environment interactions, and these trade-offs are likely to contribute to the maintenance of Pgi polymorphism in the natural populations.

A repeated measures experiment of school playing environment to increase physical activity and enhance self esteem in UK school children

School playtime provides daily opportunities for children to be active outdoors, but only makes small contributions to physical activity (PA) requirements. Natural environments facilitate unstructured PA and children report a preference for play in nature. Thus, play on the school field might encourage children to be more active during playtime. The primary aim of this study was to examine the impact of the school playing environment on children's PA. Descriptive data and fitness were assessed in 25 children aged 8–9 years from a single primary school. Over two consecutive weeks participants were allocated to either play on the school field or playground during playtime. The order of play in the two areas was randomised and counterbalanced. Moderate to vigorous PA (MVPA) was assessed during playtime on the last two days of each week using accelerometers. There was a significant interaction of environment and sex on MVPA during morning play (F(1,22) = 6.27; P<0.05; np2 = 0.222), but not during lunch (P>0.05; np2 = 0.060) or all of playtime combined (P>0.05; np2 = 0.140). During morning play boys were significantly more active than girls on the playground (t(23) = 1.32; P<0.01; n2 = 0.291), but not on the field (P>0.05; n2 = 0.071). For lunch (F(1,22) = 24,11; P<0.001; np2 = 0.523) and all of playtime combined (F(1,22) = 33.67; P<0.001; np2 = 0.616) there was a significant effect of environment. There was also a significant main effect of sex during lunch (F(1,22) = 11.56; P<0.01; np2 = 0.344) and all of playtime combined (F(1,22) = 12.37; P<0.01; np2 = 0.371). MVPA was higher on the field and boys were more active than girls. Play on the field leads to increases in MVPA, particularly in girls. The promising trend for the effect of the natural environment on MVPA indicates that interventions aimed at increasing MVPA should use the natural environment and that schools should encourage greater use of their natural areas to increase PA.

Produtividade, adaptabilidade e estabilidade fenotípica de cultivares de tomateiro sob diferentes condições de ambiente

O objetivo deste trabalho foi estudar o desempenho produtivo, adaptabilidade e estabilidade fenotípica de seis genótipos de tomateiro na região de Marília, SP. Os experimentos foram conduzidos em nove ambientes (seis sob condições de cultivo protegido e três sob condições de céu aberto), com seis genótipos (Carmen, Diva, Donador, Graziela, Vita e HE-295), em blocos casualizados, com quatro repetições. Ocorreram diferenças significativas entre ambientes, e a média geral dos cultivos protegidos superou a dos cultivos a céu aberto quanto à produtividade, apesar de a média geral dos cultivos a céu aberto ser superior quanto ao peso médio de frutos. As cultivares, à exceção de HE-295, demonstraram alta estabilidade, merecendo destaque as cultivares Carmen, Donador e Vita, que tiveram rendimento médio superior ao da média geral, adaptabilidade geral e comportamento previsível em todos os ambientes estudados. Quanto ao peso médio dos frutos, as cultivares Diva e Vita foram as únicas que mostraram ampla adaptabilidade a todos os ambientes, comportamento previsível, além de apresentarem peso médio do fruto superior ao da média geral.

Efeito da interação genótipo × ambiente sobre o peso ao nascimento, aos 205 e aos 550 dias de idade de bovinos da raça Nelore na Região Sul do Brasil

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Interação genótipo x ambiente em cultivares de alface na região de Jaboticabal

Estudou-se a interação genótipo x ambiente de doze cultivares de alface, sendo quatro do grupo lisa (Babá de Verão, Karla, Nacional e Elisa), quatro do grupo crespa (Simpson, Hortência, Verônica e Grand Rapids) e quatro do grupo americana (Laidy, Tainá, Lucy Brown e Raider). Os tratamentos foram constituídos pelo cultivo da alface em dez ambientes (casa de vegetação, túnel baixo de cultivo, túnel baixo com sombrite, agrotêxtil e campo, na presença e ausência de mulching). Foram utilizados dois períodos de cultivo, agosto a novembro de 2001 e março a junho de 2002 em Jaboticabal. Cada experimento (ambiente de cultivo) foi conduzido utilizando-se o delineamento de blocos casualizados, com doze cultivares e três repetições. A análise de variância conjunta demonstrou valores de F significativos (p<0,01) para a interação genótipo x ambiente. Para o cultivo de agosto a novembro/2001, as melhores respostas foram obtidas para as cultivares do Grupo Lisa, nos ambientes casa de vegetação com mulching, túnel baixo de cultivo sem mulching e campo sem mulching. Todas as cultivares apresentaram piores desempenhos nos ambientes túnel com sombrite sem mulching, agrotêxtil com e sem mulching. No cultivo de março a junho/2002, houve maior variabilidade quanto ao comportamento das cultivares avaliadas nos ambientes estudados. Na análise multivariada de agrupamento, a superioridade das cultivares do grupo lisa parece ter sido influenciada pelo número de folhas, tanto para a época 1, quanto para a época 2. Ressalta-se que, apesar das cultivares do grupo americana apresentarem pior desempenho, as mesmas tiveram os maiores valores de massa seca da parte aérea. Quando se tem como objetivo uma maior produção de alface visando massa seca da parte aérea ou massa fresca da parte aérea, deve-se optar por cultivares do grupo americana, que apresentaram as maiores médias para esta característica. As cultivares do grupo crespa apresentaram as maiores médias para volume de plantas.

Testes multiambientais na seleção de genótipos de arroz utilizando o modelo de regressão nos sítios ou locais

A análise da interação genótipo x ambiente utilizda no melhoramento de plantas tem sofrido mudanças na última década, melhorando a sua eficiência quanto à seleção dos genótipos sob diferentes condições ambientais. O objetivo deste trabalho foi analisar a produtividade e estabilidade de 12 genótipos de arroz em oito ambientes, durante os anos 2005 e 2006, na Colômbia. O delineamento utilizado foi o de blocos ao acaso com quatro repetições. Os parâmetros de estabilidade fenotípica e o agrupamento dos ambientes foram estimados pelo estudo da interação genótipo x ambiente, segundo o método SREG (Regressão nos sítios ou locais) e seu gráfico biplot (GGE). As análises estatísticas indicaram diferenças significativas (com 5% de probabilidade de erro) entre genótipos e entre ambientes e significância (com 5% de probabilidade de erro) da interação genótipo x ambiente, sugerindo uma resposta diferente dos genótipos nos vários ambientes. No método SREG, os dois primeiros componentes principais da interação explicaram 75,29% da interação. Os genótipos 400094, 350361 e a variedade Fedearroz 50 foram considerados os de maior produtividade. Segundo o gráfico biplot GGE, os ambientes La Libertad e Escobal foram os mais favoráveis para o cultivo do arroz.

Efeito da interação reprodutor x rebanho sobre as produções de leite e de gordura na raça Pardo-Suíça

Dados de 4.959 lactações de 2.414 vacas da raça Pardo-Suíça, filhas de 70 reprodutores, distribuídos em 51 rebanhos, foram utilizados para se estimar o componente de variância para a interação reprodutor x rebanho das produções de leite e de gordura e verificar o efeito desta interação sobre a avaliação genética dos reprodutores, por meio de modelos que diferiam na presença e ausência do termo de interação. As produções de leite e de gordura foram ajustadas para duas ordenhas diárias, 305 dias de lactação e idade adulta da vaca. O teste da razão de verossimilhança foi utilizado na verificação da efetividade da inclusão da interação no modelo. As médias das produções de leite e de gordura foram 6085,79 ± 1629,73 kg e 225,61 ± 60,44 kg, respectivamente. A proporção da variância total decorrente da interação reprodutor x rebanho foi 0,4%, para a produção de leite, e 1%, para a produção de gordura. A estimativa de herdabilidade foi 0,38, para a produção de leite, utilizando-se ambos os modelos, e reduziu de 0,40 para 0,39, para a produção de gordura, quando o modelo com interação foi considerado. A função de verossimilhança aumentou significativamente com a inclusão da interação no modelo. A correlação de Spearman foi próxima de um para ambas as características, quando todos os reprodutores foram considerados. Houve redução de 1% na estimativa de acurácia dos valores genéticos preditos para ambas as características, porém, a correlação de Pearson estimada entre as acurácias obtidas para cada modelo estudado foi próxima à unidade. A interaçãoreprodutor x rebanho não afetou as estimativas de componentes de variâncias genética e residual e a ordem de classificação dos reprodutores para ambas as características.