Influence of variance component estimates on genomic predictions for growth and reproductive-related traits in Nellore cattle.

This study aimed to estimate variance components (VCs) for growth and reproductive traits in Nellore cattle using two relationship matrices (pedigree relationship A matrix and pedigree plus genomic relationship H matrix), and records collected before and after genomic selection (GS) implementation. The study also evaluated how genomic breeding values (GEBV) are affected by variance components and discarding old records. The analysed traits were weight at 120 days (W120), weight and scrotal circumference at 450 days (W450 and SC450, respectively). Three datasets were used to estimate VCs, including all phenotypic information (All) or records for animals born before or after GS implementation (Before or After datasets, respectively). Both relationship matrices were considered for VC estimation, the A matrix was used in all three datasets and VC from each combination were named as A_Before, A_After, and A_All). The H was used in two datasets: H_All and H_After. Different VCs were used for GEBV prediction through ssGBLUP. This step used two possible Datasets, using all available phenotypic data (Dataset 1) or just records collected since GS implementation (Dataset 2). Validation was conducted using accuracy, bias and dispersion according to the LR method and prediction accuracy from corrected phenotypes. The heritability of all traits increased from A_Before to A_After, while estimates for A_All were intermediary. In the previous order, the estimates were 0.16, 0.17, and 0.15 for W120; 0.31, 0.39, and 0.35 for W450; 0.35, 0.47, and 0.41 for SC. For W450 and SC, using the H matrix reduced the heritability (0.33 and 0.32 for W450; 0.41 and 0.38 for SC for H_After and H_All, respectively). For W120, Dataset1 and VCs from A_After showed the highest accuracy for direct and maternal GEBV (0.953 and 0.868). For W450, Dataset 1 and VC from H_After allowed the highest accuracy (0.854) but use Dataset 2 and same VC source yield similar value (0.846). For SC, Dataset 2 with VC from H_After showed the highest accuracy (0.925). To use Dataset 2 does not cause important changes in bias or dispersion with respect to Dataset 1. The VC and genetic parameters changed for W120, W450, and SC450, using records before or after the GS implementation. For W450 and SC450, genetic variance and heritability estimates increased with the use of GS. For W120, genomic predictions were more accurate using A for VC estimation. Accuracy gains were observed for W450 and SC450 using H in VC estimation and/or discarding records before GS. It is possible to discard phenotypic records before GS implementation without generating bias or dispersion in the GEBV of young candidates.

Heritability estimates and genome-wide association study of methane emission traits in Nellore cattle.

The objectives of the present study were to estimate the heritability for daily methane emission (CH4) and residual daily methane emission (CH4res) in Nellore cattle, as well as to perform genome-wide association studies (GWAS) to identify genomic regions and candidate genes influencing the genetic variation of CH4 and CH4res. Methane emission phenotypes of 743 Nellore animals belonging to 3 breeding programs were evaluated. CH4 was measured using the sulfur hexafluoride (SF6) tracer technique (which involves an SF6 permeation tube introduced into the rumen, and an appropriate apparatus on each animal), and CH4res was obtained as the difference between observed CH4 and CH4 adjusted for dry matter intake. A total of 6,252 genotyped individuals were used for genomic analyses. Data were analyzed with a univariate animal model by the single-step GBLUP method using the average information restricted maximum likelihood (AIREML) algorithm. The effects of single nucleotide polymorphisms (SNPs) were obtained using a single-step GWAS approach. Candidate genes were identified based on genomic windows associated with quantitative trait loci (QTLs) related to the 2 traits. Annotation of QTLs and identification of candidate genes were based on the initial and final coordinates of each genomic window considering the bovine genome ARS-UCD1.2 assembly. Heritability estimates were of moderate to high magnitude, being 0.42 ±â€…0.09 for CH4 and 0.21 ±â€…0.09 for CH4res, indicating that these traits will respond rapidly to genetic selection. GWAS revealed 11 and 15 SNPs that were significantly associated (P < 10-6) with genetic variation of CH4 and CH4res, respectively. QTLs associated with feed efficiency, residual feed intake, body weight, and height overlapped with significant markers for the traits evaluated. Ten candidate genes were present in the regions of significant SNPs; 3 were associated with CH4 and 7 with CH4res. The identified genes are related to different functions such as modulation of the rumen microbiota, fatty acid production, and lipid metabolism. CH4 and CH4res presented sufficient genetic variation and may respond rapidly to selection. Therefore, these traits can be included in animal breeding programs aimed at reducing enteric methane emissions across generations.

Genetic selection designed to reduce the amount of enteric methane emission from livestock is a mitigation strategy to ensure more sustainable production over generations since genetic gains are cumulative. Brazil is a large producer of beef, and the Nellore breed (Bos taurus indicus) plays a very important role in this production. There are a few studies evaluating genetic and genomic aspects of enteric methane emission in Nellore cattle. The objectives of the present study were to estimate the heritability of daily methane emission (CH4) and residual daily methane emission (CH4res) in Nellore cattle, as well as to identify genomic regions and candidate genes associated with genetic variation of these traits. The heritability estimates for CH4 and CH4res were of moderate to high magnitude (0.42 ±â€…0.09 and 0.21 ±â€…0.09, respectively). Genome-wide association analyses revealed new loci associated with methane emission in Nellore cattle on chromosomes 5, 11, 17, and 20, where 10 candidate genes were identified, 3 for CH4 and 7 for CH4res. The 2 traits possess sufficient genetic variability to be included as selection criteria in breeding programs.

Increased yield performance of mutation induced Soybean genotypes at varied agro-ecological conditions / Aumento no desempenho de rendimento de genótipos de soja induzidos por mutação em condições agroecológicas variadas

Abstract In soybean breeding program, continuous selection pressure on traits response to yield created a genetic bottleneck for improvements of soybean through hybridization breeding technique. Therefore an initiative was taken to developed high yielding soybean variety applying mutation breeding techniques at Plant Breeding Division, Bangladesh Institute of Nuclear Agriculture (BINA), Bangladesh. Locally available popular cultivar BARI Soybean-5 was used as a parent material and subjected to five different doses of Gamma ray using Co60. In respect to seed yield and yield attributing characters, twelve true breed mutants were selected from M4 generation. High values of heritability and genetic advance with high genotypic coefficient of variance (GCV) for plant height, branch number and pod number were considered as favorable attributes for soybean improvement that ensure expected yield. The mutant SBM-18 obtained from 250Gy provided stable yield performance at diversified environments. It provided maximum seed yield of 3056 kg ha-1 with highest number of pods plant-1 (56). The National Seed Board of Bangladesh (NSB) eventually approved SBM-18 and registered it as a new soybean variety named 'Binasoybean-5' for large-scale planting because of its superior stability in various agro-ecological zones and consistent yield performance.

Resumo No programa de melhoramento da soja, a pressão pela seleção contínua para a resposta das características de rendimento criou um gargalo genético para melhorias da soja por meio da técnica de melhoramento por hibridação. Portanto, foi desenvolvida uma variedade de soja de alto rendimento, aplicando técnicas de reprodução por mutação, na Divisão de Melhoramento de Plantas, no Instituto de Agricultura Nuclear de Bangladesh (BINA), em Bangladesh. A cultivar popular BARI Soybean-5, disponível localmente, foi usada como material original e submetida a cinco doses diferentes de raios gama usando Co60. Em relação ao rendimento de sementes e às características de atribuição de rendimento, 12 mutantes genuínos foram selecionados a partir da geração M4. Altos valores de herdabilidade e avanço genético com alto coeficiente de variância genotípico (GCV) para altura da planta, número de ramos e número de vagens foram considerados atributos favoráveis ​​ao melhoramento da soja, garantindo, assim, a produtividade esperada. O mutante SBM-18, obtido a partir de 250Gy, proporcionou desempenho de rendimento estável em ambientes diversificados e produtividade máxima de sementes de 3.056 kg ha-1 com o maior número de vagens planta-1 (56). O Conselho Nacional de Sementes de Bangladesh (NSB) finalmente aprovou o SBM-18 e o registrou como uma nova variedade de soja, chamada 'Binasoybean-5', para plantio em larga escala por causa de sua estabilidade superior em várias zonas agroecológicas e desempenho de rendimento consistente.

Increased yield performance of mutation induced Soybean genotypes at varied agro-ecological conditions

Abstract In soybean breeding program, continuous selection pressure on traits response to yield created a genetic bottleneck for improvements of soybean through hybridization breeding technique. Therefore an initiative was taken to developed high yielding soybean variety applying mutation breeding techniques at Plant Breeding Division, Bangladesh Institute of Nuclear Agriculture (BINA), Bangladesh. Locally available popular cultivar BARI Soybean-5 was used as a parent material and subjected to five different doses of Gamma ray using Co60. In respect to seed yield and yield attributing characters, twelve true breed mutants were selected from M4 generation. High values of heritability and genetic advance with high genotypic coefficient of variance (GCV) for plant height, branch number and pod number were considered as favorable attributes for soybean improvement that ensure expected yield. The mutant SBM-18 obtained from 250Gy provided stable yield performance at diversified environments. It provided maximum seed yield of 3056 kg ha-1 with highest number of pods plant-1 (56). The National Seed Board of Bangladesh (NSB) eventually approved SBM-18 and registered it as a new soybean variety named Binasoybean-5 for large-scale planting because of its superior stability in various agro-ecological zones and consistent yield performance.

Resumo No programa de melhoramento da soja, a pressão pela seleção contínua para a resposta das características de rendimento criou um gargalo genético para melhorias da soja por meio da técnica de melhoramento por hibridação. Portanto, foi desenvolvida uma variedade de soja de alto rendimento, aplicando técnicas de reprodução por mutação, na Divisão de Melhoramento de Plantas, no Instituto de Agricultura Nuclear de Bangladesh (BINA), em Bangladesh. A cultivar popular BARI Soybean-5, disponível localmente, foi usada como material original e submetida a cinco doses diferentes de raios gama usando Co60. Em relação ao rendimento de sementes e às características de atribuição de rendimento, 12 mutantes genuínos foram selecionados a partir da geração M4. Altos valores de herdabilidade e avanço genético com alto coeficiente de variância genotípico (GCV) para altura da planta, número de ramos e número de vagens foram considerados atributos favoráveis ao melhoramento da soja, garantindo, assim, a produtividade esperada. O mutante SBM-18, obtido a partir de 250Gy, proporcionou desempenho de rendimento estável em ambientes diversificados e produtividade máxima de sementes de 3.056 kg ha-1 com o maior número de vagens planta-1 (56). O Conselho Nacional de Sementes de Bangladesh (NSB) finalmente aprovou o SBM-18 e o registrou como uma nova variedade de soja, chamada Binasoybean-5, para plantio em larga escala por causa de sua estabilidade superior em várias zonas agroecológicas e desempenho de rendimento consistente.

Evaluation of Bayesian methods of genomic association via chromosomic regions using simulated data

The development of efficient methods for genome-wide association studies (GWAS) between quantitative trait loci (QTL) and genetic values is extremely important to animal and plant breeding programs. Bayesian approaches that aim to select regions of single nucleotide polymorphisms (SNPs) proved to be efficient, indicating genes with important effects. Among the selection criteria for SNPs or regions, selection criterion by percentage of variance can be explained by genomic regions (%var), selection of tag SNPs, and selection based on the window posterior probability of association (WPPA). To also detect potentially associated regions, we proposed measuring posterior probability of the interval PPint), which aims to select regions based on the markers of greatest effects. Therefore, the objective of this work was to evaluate these approaches, in terms of efficiency in selecting and identifying markers or regions located within or close to genes associated with traits. This study also aimed to compare these methodologies with single-marker analyses. To accomplish this, simulated data were used in six scenarios, with SNPs allocated in non-overlapping genomic regions. Considering traits with oligogenic inheritance, WPPA criterion followed by %var and PPint criteria were shown to be superior, presenting higher values of detection power, capturing higher percentages of genetic variance and larger areas. For traits with polygenic inheritance, PPint and WPPA criteria were considered superior. Single-marker analyses identified SNPs associated only in oligogenic inheritance scenarios and was lower than the other criteria.(AU)

Compared Heritability of Chronotype Instruments in a Single Population Sample.

It is well established that the oldest chronotype questionnaire, the morningness-eveningness questionnaire (MEQ), has significant heritability, and several associations have been reported between MEQ score and polymorphisms in candidate clock genes, a number of them reproducibly across populations. By contrast, there are no reports of heritability and genetic associations for the Munich chronotype questionnaire (MCTQ). Recent genome-wide association studies (GWAS) from large cohorts have reported multiple associations with chronotype as assessed by a single self-evaluation question. We have taken advantage of the availability of data from all these instruments from a single sample of 597 participants from the Brazilian Baependi Heart Study. The family-based design of the cohort allowed us to calculate the heritability (h2) for these measures. Heritability values for the best-fitted models were 0.37 for MEQ, 0.32 for MCTQ, and 0.28 for single-question chronotype (MEQ Question 19). We also calculated the heritability for the two major factors recently derived from MEQ, "Dissipation of sleep pressure" (0.32) and "Build-up of sleep pressure" (0.28). This first heritability comparison of the major chronotype instruments in current use provides the first quantification of the genetic component of MCTQ score, supporting its future use in genetic analysis. Our findings also suggest that the single chronotype question that has been used for large GWAS analyses captures a larger proportion of the dimensions of chronotype than previously thought.

Additive genetic variance and covariance between relatives in synthetic wheat crosses with variable parental ploidy levels.

Cultivated bread wheat (Triticum aestivum L.) is an allohexaploid species resulting from the natural hybridization and chromosome doubling of allotetraploid durum wheat (T. turgidum) and a diploid goatgrass Aegilops tauschii Coss (Ae. tauschii). Synthetic hexaploid wheat (SHW) was developed through the interspecific hybridization of Ae. tauschii and T. turgidum, and then crossed to T. aestivum to produce synthetic hexaploid wheat derivatives (SHWDs). Owing to this founding variability, one may infer that the genetic variances of native wild populations vs improved wheat may vary due to their differential origin and evolutionary history. In this study, we partitioned the additive variance of SHW and SHWD with respect to their breed origin by fitting a hierarchical Bayesian model with heterogeneous covariance structure for breeding values to estimate variance components for each breed category, and segregation variance. Two data sets were used to test the proposed hierarchical Bayesian model, one from a multi-year multi-location field trial of SHWD and the other comprising the two species of SHW. For the SHWD, the Bayesian estimates of additive variances of grain yield from each breed category were similar for T. turgidum and Ae. tauschii, but smaller for T. aestivum. Segregation variances between Ae. tauschii-T. aestivum and T. turgidum-T. aestivum populations explained a sizable proportion of the phenotypic variance. Bayesian additive variance components and the Best Linear Unbiased Predictors (BLUPs) estimated by two well-known software programs were similar for multi-breed origin and for the sum of the breeding values by origin for both data sets. Our results support the suitability of models with heterogeneous additive genetic variances to predict breeding values in wheat crosses with variable ploidy levels.

Estimating dominance genetic variances for growth traits in American Angus males using genomic models.

Estimates of dominance variance for growth traits in beef cattle based on pedigree data vary considerably across studies, and the proportion of genetic variance explained by dominance deviations remains largely unknown. The potential benefits of including nonadditive genetic effects in the genomic model combined with the increasing availability of large genomic data sets have recently renewed the interest in including nonadditive genetic effects in genomic evaluation models. The availability of genomic information enables the computation of covariance matrices of dominant genomic relationships among animals, similar to matrices of additive genomic relationships, and in a more straightforward manner than the pedigree-based dominance relationship matrix. Data from 19,357 genotyped American Angus males were used to estimate additive and dominant variance components for 3 growth traits: birth weight, weaning weight, and postweaning gain, and to evaluate the benefit of including dominance effects in beef cattle genomic evaluations. Variance components were estimated using 2 models: the first one included only additive effects (MG) and the second one included both additive and dominance effects (MGD). The dominance deviation variance ranged from 3% to 8% of the additive variance for all 3 traits. Gibbs sampling and REML estimates showed good concordance. Goodness of fit of the models was assessed by a likelihood ratio test. For all traits, MG fitted the data as well as MGD as assessed either by the likelihood ratio test or by the Akaike information criterion. Predictive ability of both models was assessed by cross-validation and did not improve when including dominance effects in the model. There was little evidence of nonadditive genetic variation for growth traits in the American Angus male population as only a small proportion of genetic variation was explained by nonadditive effects. A genomic model including the dominance effect did not improve the model fit. Consequently, including nonadditive effects in the genomic evaluation model is not beneficial for growth traits in the American Angus male population.

Sliding window haplotype approaches overcome single SNP analysis limitations in identifying genes for meat tenderness in Nelore cattle.

BACKGROUND: Traditional single nucleotide polymorphism (SNP) genome-wide association analysis (GWAA) can be inefficient because single SNPs provide limited genetic information about genomic regions. On the other hand, using haplotypes in the statistical analysis may increase the extent of linkage disequilibrium (LD) between haplotypes and causal variants and may also potentially capture epistastic interactions between variants within a haplotyped locus, providing an increase in the power and robustness of the association studies. We performed GWAA (413,355 SNP markers) using haplotypes based on variable-sized sliding windows and compared the results to a single-SNP GWAA using Warner-Bratzler shear force measured in the longissimus thorasis muscle of 3161 Nelore bulls to ascertain the optimal window size for identifying the genomic regions that influence meat tenderness. RESULTS: The GWAA using single SNPs identified eight variants influencing meat tenderness on BTA 3, 4, 9, 10 and 11. However, thirty-three putative meat tenderness QTL were detected on BTA 1, 3, 4, 5, 8, 9, 10, 11, 15, 17, 18, 24, 25, 26 and 29 using variable-sized sliding haplotype windows. Analyses using sliding window haplotypes of 3, 5, 7, 9 and 11 SNPs identified 57, 61, 42, 39, and 21% of all thirty-three putative QTL regions, respectively; however, the analyses using the 3 and 5 SNP haplotypes, cumulatively detected 88% of the putative QTL. The genes associated with variation in meat tenderness participate in myogenesis, neurogenesis, lipid and fatty acid metabolism and skeletal muscle structure or composition processes. CONCLUSIONS: GWAA using haplotypes based on variable-sized sliding windows allowed the detection of more QTL than traditional single-SNP GWAA. Analyses using smaller haplotypes (3 and 5 SNPs) detected a higher proportion of the putative QTL.

Genome-wide association studies for tick resistance in Bos taurus × Bos indicus crossbred cattle: A deeper look into this intricate mechanism.

Rhipicephalus (Boophilus) microplus is the main cattle ectoparasite in tropical areas. Gir × Holstein crossbred cows are well adapted to different production systems in Brazil. In this context, we performed genome-wide association study (GWAS) and post-GWAS analyses for R. microplus resistance in an experimental Gir × Holstein F2 population. Single nucleotide polymorphisms (SNP) identified in GWAS were used to build gene networks and to investigate the breed of origin for its alleles. Tick artificial infestations were performed during the dry and rainy seasons. Illumina BovineSNP50 BeadChip (Illumina Inc., San Diego, CA) and single-step BLUP procedure was used for GWAS. Post-GWAS analyses were performed by gene ontology terms enrichment and gene transcription factors networks, generated from enriched transcription factors, identified from the promoter sequences of selected gene sets. The genetic origin of marker alleles in the F2 population was assigned using the breed of origin of alleles approach. Heritability estimates for tick counts were 0.40 ± 0.11 in the rainy season and 0.54 ± 0.11 in the dry season. The top ten 0.5-Mbp windows with the highest percentage of genetic variance explained by SNP markers were found in chromosomes 10 and 23 for both the dry and rainy seasons. Gene network analyses allowed the identification of genes involved with biological processes relevant to immune system functions (TREM1, TREM2, and CD83). Gene-transcription factors network allowed the identification of genes involved with immune functions (MYO5A, TREML1, and PRSS16). In resistant animals, the average proportion of animals showing significant SNPs with paternal and maternal alleles originated from Gir breed was 44.8% whereas the proportion of animals with both paternal and maternal alleles originated from Holstein breed was 11.3%. Susceptible animals showing both paternal and maternal alleles originated from Holstein breed represented 44.6% on average, whereas both paternal and maternal alleles originated from Gir breed animals represented 9.3%. This study allowed us to identify candidate genes for tick resistance in Gir × Holstein crossbreds in both rainy and dry seasons. According to the origin of alleles analysis, we found that most animals classified as resistant showed 2 alleles from Gir breed, while the susceptible ones showed alleles from Holstein. Based on these results, the identified genes may be thoroughly investigated in additional experiments aiming to validate their effects on tick resistance phenotype in cattle.

PARÁMETROS GENÉTICOS DE LAS CARACTERÍSTICAS BIOMÉTRICAS DEL FRUTO Y SEMILLAS EN Pachira aquatica Aubl / GENETIC PARAMETERS OF FRUIT AND SEED BIOMETRIC CHARACTERISTICS IN Pachira aquatica Aubl

RESUMEN Pachira aquatica es un árbol, cuyos frutos y semillas se aprovechan en la alimentación humana y animal, en regiones tropicales; sin embargo, aún no se han reportado investigaciones de su variabilidad genética para elegir el mejor método de mejoramiento de la especie. El objetivo del estudio fue evaluar los parámetros genéticos de las características biométricas del fruto y sus semillas. El estudio, se realizó en la Universidad de Córdoba, Colombia. Se seleccionaron 10 árboles y de cada uno, 10 frutos al azar. Se llevaron a cabo análisis de varianza y de estimación de parámetros genéticos, para 15 características, de los órganos mencionados. Se detectaron diferencias significativas entre árboles para peso/fruto (PEF), peso de cáscara/fruto (PCF), porcentaje de semillas/fruto (POSF), ancho de semilla (ANS), grosor de semilla (GROS), volumen de una semilla (V1S) y densidad de una semilla (D1S). Los mayores estimadores de variabilidad genética se presentaron en GROS, POSF, PCF y PEF, en donde el componente genético representó más del 50% de la varianza fenotípica. La heredabilidad más alta, tanto en sentido amplio (h2A>76%) como estrecho (h2E>30%), fue para GROS y POSF. La ganancia genética esperada (GGE), como porcentaje de la media general, fue menor del 10%, en 14 de las 15 características estudiadas, excepto para PCF (10,86%), por lo que se espera un progreso genético modesto, para tales características. Se recomienda ampliar la base genética de la población local y hacer ensayos genéticos en varias zonas productoras potenciales.

SUMMARY Pachira aquatica is a tree whose fruits and seeds are used for human and animal nutrition in tropical regions. However, no research of its genetic variability have yet been reported to choose the best breeding method for the species. The objective of the study was to evaluate the genetic parameters of the biometric characteristics of the fruit and its seeds. The study was conducted at the Universidad de Córdoba, Colombia. Ten trees were selected and, of each, 10 fruits were randomly selected. Analysis of variance and estimation of genetic parameters were carried out for 15 characteristics of both organs. Significant differences were detected between trees for weight/fruit (FW), weight of husk/fruit (FHW), percentage of seeds/fruit (FSP), seed width (SW), seed thickness (ST), volume of a seed (S1V) and density of a seed (S1D). The greatest estimators of genetic variability were presented in ST, FSP, FHW and FW, where the genetic component represented more than 50% of the phenotypic variance. The highest heritability, both broad (h2A>76%) and narrow (h2E>30%), was for ST and FSP. The expected genetic gain, as a percentage of the general average, was less than 10% in 14 of the 15 characteristics studied, except for FHW (10.86%), therefore a modest genetic progress is expected for such characteristics. It is recommended to increase the local population genetic base and make genetic assays in several potential producing areas.

Genetic and environmental (physical fitness and sedentary activity) interaction effects on cardiometabolic risk factors in Mexican American children and adolescents.

Knowledge on genetic and environmental (G × E) interaction effects on cardiometabolic risk factors (CMRFs) in children is limited.  The purpose of this study was to examine the impact of G × E interaction effects on CMRFs in Mexican American (MA) children (n = 617, ages 6-17 years). The environments examined were sedentary activity (SA), assessed by recalls from "yesterday" (SAy) and "usually" (SAu) and physical fitness (PF) assessed by Harvard PF scores (HPFS). CMRF data included body mass index (BMI), waist circumference (WC), fat mass (FM), fasting insulin (FI), homeostasis model of assessment-insulin resistance (HOMA-IR), high-density lipoprotein cholesterol (HDL-C), triglycerides (TG), systolic (SBP) and diastolic (DBP) blood pressure, and number of metabolic syndrome components (MSC). We examined potential G × E interaction in the phenotypic expression of CMRFs using variance component models and likelihood-based statistical inference. Significant G × SA interactions were identified for six CMRFs: BMI, WC, FI, HOMA-IR, MSC, and HDL, and significant G × HPFS interactions were observed for four CMRFs: BMI, WC, FM, and HOMA-IR. However, after correcting for multiple hypothesis testing, only WC × SAy, FM × SAy, and FI × SAu interactions became marginally significant. After correcting for multiple testing, most of CMRFs exhibited significant G × E interactions (Reduced G × E model vs. Constrained model). These findings provide evidence that genetic factors interact with SA and PF to influence variation in CMRFs, and underscore the need for better understanding of these relationships to develop strategies and interventions to effectively reduce or prevent cardiometabolic risk in children.

Accounting for genetic architecture in single- and multipopulation genomic prediction using weights from genomewide association studies in pigs.

We studied the effect of including GWAS results on the accuracy of single- and multipopulation genomic predictions. Phenotypes (backfat thickness) and genotypes of animals from two sire lines (SL1, n = 1146 and SL3, n = 1264) were used in the analyses. First, GWAS were conducted for each line and for a combined data set (both lines together) to estimate the genetic variance explained by each SNP. These estimates were used to build matrices of weights (D), which was incorporated into a GBLUP method. Single population evaluated with traditional GBLUP had accuracies of 0.30 for SL1 and 0.31 for SL3. When weights were employed in GBLUP, the accuracies for both lines increased (0.32 for SL1 and 0.34 for SL3). When a multipopulation reference set was used in GBLUP, the accuracies were higher (0.36 for SL1 and 0.32 for SL3) than in single-population prediction. In addition, putting together the multipopulation reference set and the weights from the combined GWAS provided even higher accuracies (0.37 for SL1, and 0.34 for SL3). The use of multipopulation predictions and weights estimated from a combined GWAS increased the accuracy of genomic predictions.

Modelos de norma de reação para estudo das características de qualidade da carne de codornas de corte em função das razões (metionina + cistina): lisina da dieta / Reaction norm models for the study of meat quality of european quail in function of (methionine + cysteine): lysine diet ratio

Objetivou-se avaliar a sensibilidade dos valores genéticos para características de qualidade da carne em codornas de corte alimentadas com dietas contendo diferentes relações de (metionina + cistina): lisina, do nascimento aos 21 dias de idade, por meio de modelos de normas de reação. Utilizaram-se 9011 informações de qualidade de carne referentes a 1400 progênies de 80 reprodutores e 160 matrizes de duas linhas (LF1 e LF2). Para o ajuste dos modelos de regressão aleatória, foi usado o programa WOMBAT, considerando-se nas análises homogeneidade de variância residual. As codornas foram alimentadas do nascimento aos 21 dias de idade com dietas contendo as relações 0,61; 0,66; 0,71; 0,76 e 0,81 de (metionina + cistina): lisina, mantendo os níveis de proteína bruta de 26,12% e de energia em 2900 kcal EM/kg da dieta. Dos 22 aos 35 dias de idade, todas as codornas foram alimentadas com dieta contendo 22% de proteína bruta e 3050 kcal EM/kg da dieta. As estimativas da variância genética e da herdabilidade foram influenciadas pelo gradiente ambiental e pela linha, com mudanças nessas estimativas com o aumento do gradiente ambiental. Os valores genéticos das características de qualidade de carne referentes a cada uma das linhas se alteraram com o aumento das relações de aminoácidos das dietas em razão das mudanças no ordenamento dos valores genéticos, evidenciando a existência da interação genótipo x nível de relação dos aminoácidos da dieta para características de qualidade de carne. Predições de valores genéticos de características de qualidade de carne com base em determinada relação de (metionina + cistina): lisina da dieta não são válidas para outras relações desses aminoácidos.

This study aimed to evaluate the sensitivity of breeding values for meat quality traits of European quails fed different (methionine + cystine): lysine ratio diets from hatch to 21 days of age, using reaction norm models. A total of 9011 meat quality records from 1400 progenies of 80 sires and 160 dams from two lines (LF1 and LF2) were used in the analyses considering homogeneity of residual variance. The quails from hatch to 21 days of age were fed diets containing 0.61, 0.66, 0.71, 0.76 and 0.81 (methionine + cystine): lysine ratios, 26.12% of crude protein and 2900 ME/kcal of diet. From 22 to 35 days of age all quail were fed a diet containing 22% of crude protein and 3050 kcal ME/kg of diet. The random regression model analyses was performed using the WOMBAT program considering homogeneity of residual variance. Genetic variance and heritability estimates were affected by the environment gradient of diet and line, increasing these estimates with the increase of the (methionine + cystine): lysine ratio of the diet. The breeding values changed with the increase of the environment gradient of the diet with changes in the rank of genetic breeding values characterizing the existence of genotype by environment interaction for meat quality traits. Predictions of meat quality trait breeding values based on a given (methionine + cystine): lysine ratio are not valid for other levels of the amino acid ratio.

Modelos de norma de reação para estudo das características de qualidade da carne de codornas de corte em função das razões (metionina + cistina): lisina da dieta / Reaction norm models for the study of meat quality of European quail in function of (methionine + cysteine): lysine diet ratio

Objetivou-se avaliar a sensibilidade dos valores genéticos para características de qualidade da carne em codornas de corte alimentadas com dietas contendo diferentes relações de (metionina + cistina): lisina, do nascimento aos 21 dias de idade, por meio de modelos de normas de reação. Utilizaram-se 9011 informações de qualidade de carne referentes a 1400 progênies de 80 reprodutores e 160 matrizes de duas linhas (LF1 e LF2). Para o ajuste dos modelos de regressão aleatória, foi usado o programa WOMBAT, considerando-se nas análises homogeneidade de variância residual. As codornas foram alimentadas do nascimento aos 21 dias de idade com dietas contendo as relações 0,61; 0,66; 0,71; 0,76 e 0,81 de (metionina + cistina): lisina, mantendo os níveis de proteína bruta de 26,12% e de energia em 2900 kcal EM/kg da dieta. Dos 22 aos 35 dias de idade, todas as codornas foram alimentadas com dieta contendo 22% de proteína bruta e 3050 kcal EM/kg da dieta. As estimativas da variância genética e da herdabilidade foram influenciadas pelo gradiente ambiental e pela linha, com mudanças nessas estimativas com o aumento do gradiente ambiental. Os valores genéticos das características de qualidade de carne referentes a cada uma das linhas se alteraram com o aumento das relações de aminoácidos das dietas em razão das mudanças no ordenamento dos valores genéticos, evidenciando a existência da interação genótipo x nível de relação dos aminoácidos da dieta para características de qualidade de carne. Predições de valores genéticos de características de qualidade de carne com base em determinada relação de (metionina + cistina): lisina da dieta não são válidas para outras relações desses aminoácidos.(AU)

This study aimed to evaluate the sensitivity of breeding values for meat quality traits of European quails fed different (methionine + cystine): lysine ratio diets from hatch to 21 days of age, using reaction norm models. A total of 9011 meat quality records from 1400 progenies of 80 sires and 160 dams from two lines (LF1 and LF2) were used in the analyses considering homogeneity of residual variance. The quails from hatch to 21 days of age were fed diets containing 0.61, 0.66, 0.71, 0.76 and 0.81 (methionine + cystine): lysine ratios, 26.12% of crude protein and 2900 ME/kcal of diet. From 22 to 35 days of age all quail were fed a diet containing 22% of crude protein and 3050 kcal ME/kg of diet. The random regression model analyses was performed using the WOMBAT program considering homogeneity of residual variance. Genetic variance and heritability estimates were affected by the environment gradient of diet and line, increasing these estimates with the increase of the (methionine + cystine): lysine ratio of the diet. The breeding values changed with the increase of the environment gradient of the diet with changes in the rank of genetic breeding values characterizing the existence of genotype by environment interaction for meat quality traits. Predictions of meat quality trait breeding values based on a given (methionine + cystine): lysine ratio are not valid for other levels of the amino acid ratio.(AU)

Phenotypic integration in flowers of neotropical lianas: diversification of form with stasis of underlying patterns.

Phenotypic integration is essential to the understanding of organismal evolution as a whole. In this study, a phylogenetic framework is used to assess phenotypic integration among the floral parts of a group of Neotropical lianas. Flowers consist of plant reproductive organs (carpels and stamens), usually surrounded by attractive whorls (petals and sepals). Thus, flower parts might be involved in different functions and developmental constraints, leading to conflicting selective forces. We found that Bignonieae flowers have very similar patterns of variance/covariance among traits and that such patterns are uncorrelated with the phylogenetic relationships between species. However, in spite of pattern stasis, our results also indicate that diversification of floral morphology in this group has occurred throughout the evolution of magnitudes of correlation among traits. Thus, we suggest that stabilizing selection has played an important role in phenotypic integration, resulting in the long-term stasis of covariance patterns underlying flower diversification during the ca. 50 Myr of evolution of Bignonieae. This is the first report of long-term stasis in the phenotypic integration of angiosperms, suggesting that patterns of floral morphology can be recognizable as specific attributes of distinct botanical families.

Repetibilidade de caracteres de fruto em araçazeiro e pitangueira / Repeatability traits of strawberry guava and surinam cherry fruits

O objetivo deste trabalho foi estimar a repetibilidade de carateres de fruto em araçazeiro e pitangueira. Foram avaliados, em quatro ciclos produtivos, os caracteres peso, diâmetro, sólidos solúveis totais e produção de frutos em 10 seleções de araçazeiro e peso, diâmetro e sólidos solúveis totais em nove seleções de pitangueira, do Banco de Germoplasma da Embrapa Clima Temperado, em Pelotas-RS. O coeficiente de repetibilidade, o número de medições necessárias e o coeficiente de determinação foram estimados pelos métodos de análise de variância, componentes principais e análise estrutural. O coeficiente de repetibilidade foi mais eficientemente estimado pelo método dos componentes principais, com base na matriz de covariâncias. O caractere peso de fruto é mais adequado para ser utilizado na seleção fenotípica em araçazeiro e pitangueira. É necessária apenas uma medição para predizer o valor de peso de fruto de genótipos de araçazeiro, com 90 por cento de acurácia. Com quatro anos de avaliação, é possível inferir o valor real com confiabilidade acima de 80 por cento para todos os caracteres. Isso facilita a seleção fenotípica para esses caracteres em programas de melhoramento de araçazeiro e pitangueira.

The aim of this research was to estimate the repeatability traits of strawberry guava and surinam cherry fruits. It was evaluated in four productive cycles, the traits weight, diameter, total soluble solids and fruit production in ten selection of strawberry guava and weight, diameter and total soluble solids in nine selection of surinam cherry from the Germplasm Bank of the Embrapa Clima Temperado, in Pelotas-RS, Brazil. The repeatability coefficient, minimum observations number and determination coefficient were estimated by analysis of variance, principal components analysis and structural analysis. The repeatability coefficient was better estimated by the method of principal components analysis, based on covariance matrix. The fruit weight is adequate to phenotypic selection in strawberry guava and surinam cherry. It's only required a measurement to obtain the value of fruit weight value of strawberry guava selections, with 90 percent accuracy. With four years of evaluation, it's possible to infer the actual value with reliability above 80 percent for all characters. This facilitates phenotypic selection for these traits in strawberry guava and surinam cherry breeding programs.

Repetibilidade de caracteres de fruto em araçazeiro e pitangueira

The aim of this research was to estimate the repeatability traits of strawberry guava and surinam cherry fruits. It was evaluated in four productive cycles, the traits weight, diameter, total soluble solids and fruit production in ten selection of strawberry guava and weight, diameter and total soluble solids in nine selection of surinam cherry from the Germplasm Bank of the Embrapa Clima Temperado, in Pelotas-RS, Brazil. The repeatability coefficient, minimum observations number and determination coefficient were estimated by analysis of variance, principal components analysis and structural analysis. The repeatability coefficient was better estimated by the method of principal components analysis, based on covariance matrix. The fruit weight is adequate to phenotypic selection in strawberry guava and surinam cherry. It's only required a measurement to obtain the value of fruit weight value of strawberry guava selections, with 90% accuracy. With four years of evaluation, it's possible to infer the actual value with reliability above 80% for all characters. This facilitates phenotypic selection for these traits in strawberry guava and surinam cherry breeding programs.

O objetivo deste trabalho foi estimar a repetibilidade de carateres de fruto em araçazeiro e pitangueira. Foram avaliados, em quatro ciclos produtivos, os caracteres peso, diâmetro, sólidos solúveis totais e produção de frutos em 10 seleções de araçazeiro e peso, diâmetro e sólidos solúveis totais em nove seleções de pitangueira, do Banco de Germoplasma da Embrapa Clima Temperado, em Pelotas-RS. O coeficiente de repetibilidade, o número de medições necessárias e o coeficiente de determinação foram estimados pelos métodos de análise de variância, componentes principais e análise estrutural. O coeficiente de repetibilidade foi mais eficientemente estimado pelo método dos componentes principais, com base na matriz de covariâncias. O caractere peso de fruto é mais adequado para ser utilizado na seleção fenotípica em araçazeiro e pitangueira. É necessária apenas uma medição para predizer o valor de peso de fruto de genótipos de araçazeiro, com 90% de acurácia. Com quatro anos de avaliação, é possível inferir o valor real com confiabilidade acima de 80% para todos os caracteres. Isso facilita a seleção fenotípica para esses caracteres em programas de melhoramento de araçazeiro e pitangueira.

Repetibilidade de caracteres de fruto em araçazeiro e pitangueira

The aim of this research was to estimate the repeatability traits of strawberry guava and surinam cherry fruits. It was evaluated in four productive cycles, the traits weight, diameter, total soluble solids and fruit production in ten selection of strawberry guava and weight, diameter and total soluble solids in nine selection of surinam cherry from the Germplasm Bank of the Embrapa Clima Temperado, in Pelotas-RS, Brazil. The repeatability coefficient, minimum observations number and determination coefficient were estimated by analysis of variance, principal components analysis and structural analysis. The repeatability coefficient was better estimated by the method of principal components analysis, based on covariance matrix. The fruit weight is adequate to phenotypic selection in strawberry guava and surinam cherry. It's only required a measurement to obtain the value of fruit weight value of strawberry guava selections, with 90% accuracy. With four years of evaluation, it's possible to infer the actual value with reliability above 80% for all characters. This facilitates phenotypic selection for these traits in strawberry guava and surinam cherry breeding programs.

O objetivo deste trabalho foi estimar a repetibilidade de carateres de fruto em araçazeiro e pitangueira. Foram avaliados, em quatro ciclos produtivos, os caracteres peso, diâmetro, sólidos solúveis totais e produção de frutos em 10 seleções de araçazeiro e peso, diâmetro e sólidos solúveis totais em nove seleções de pitangueira, do Banco de Germoplasma da Embrapa Clima Temperado, em Pelotas-RS. O coeficiente de repetibilidade, o número de medições necessárias e o coeficiente de determinação foram estimados pelos métodos de análise de variância, componentes principais e análise estrutural. O coeficiente de repetibilidade foi mais eficientemente estimado pelo método dos componentes principais, com base na matriz de covariâncias. O caractere peso de fruto é mais adequado para ser utilizado na seleção fenotípica em araçazeiro e pitangueira. É necessária apenas uma medição para predizer o valor de peso de fruto de genótipos de araçazeiro, com 90% de acurácia. Com quatro anos de avaliação, é possível inferir o valor real com confiabilidade acima de 80% para todos os caracteres. Isso facilita a seleção fenotípica para esses caracteres em programas de melhoramento de araçazeiro e pitangueira.

Repetibilidade de caracteres de fruto em araçazeiro e pitangueira

The aim of this research was to estimate the repeatability traits of strawberry guava and surinam cherry fruits. It was evaluated in four productive cycles, the traits weight, diameter, total soluble solids and fruit production in ten selection of strawberry guava and weight, diameter and total soluble solids in nine selection of surinam cherry from the Germplasm Bank of the Embrapa Clima Temperado, in Pelotas-RS, Brazil. The repeatability coefficient, minimum observations number and determination coefficient were estimated by analysis of variance, principal components analysis and structural analysis. The repeatability coefficient was better estimated by the method of principal components analysis, based on covariance matrix. The fruit weight is adequate to phenotypic selection in strawberry guava and surinam cherry. It's only required a measurement to obtain the value of fruit weight value of strawberry guava selections, with 90% accuracy. With four years of evaluation, it's possible to infer the actual value with reliability above 80% for all characters. This facilitates phenotypic selection for these traits in strawberry guava and surinam cherry breeding programs.

O objetivo deste trabalho foi estimar a repetibilidade de carateres de fruto em araçazeiro e pitangueira. Foram avaliados, em quatro ciclos produtivos, os caracteres peso, diâmetro, sólidos solúveis totais e produção de frutos em 10 seleções de araçazeiro e peso, diâmetro e sólidos solúveis totais em nove seleções de pitangueira, do Banco de Germoplasma da Embrapa Clima Temperado, em Pelotas-RS. O coeficiente de repetibilidade, o número de medições necessárias e o coeficiente de determinação foram estimados pelos métodos de análise de variância, componentes principais e análise estrutural. O coeficiente de repetibilidade foi mais eficientemente estimado pelo método dos componentes principais, com base na matriz de covariâncias. O caractere peso de fruto é mais adequado para ser utilizado na seleção fenotípica em araçazeiro e pitangueira. É necessária apenas uma medição para predizer o valor de peso de fruto de genótipos de araçazeiro, com 90% de acurácia. Com quatro anos de avaliação, é possível inferir o valor real com confiabilidade acima de 80% para todos os caracteres. Isso facilita a seleção fenotípica para esses caracteres em programas de melhoramento de araçazeiro e pitangueira.