Performance of the tetra-primer PCR technique compared to PCR-RFLP in the search for rs12979860 (C/T) and rs8099917 (T/G) single nucleotide polymorphisms (SNPs) in the IFNL4 gene / Desempenho da técnica tetra-primer PCR em relação a PCR-RFLP na pesquisa de polimorfismos de nucleotídeos únicos (SNPs) rs12979860 (C/T) e rs8099917 (T/G) no gene IFNL4

Single nucleotide polymorphisms (SNPs, rs12979860 e rs8099917) in the Interferon Lambda 4 gene (IFNL4, formerly IFNL3and/or IL28B) has been associated with failure in the innate immune response, sustained virological response in hepatitis C, and HTLV-1-associated myelopathy (HAM) development. To search for these polymorphisms several methodologies can be employed, such as sequencing, real-time or quantitative polymerase chain reaction (qPCR), restriction fragment length polymorphism analysis in PCR products (PCR-RFLP), and tetra-primer PCR. The present study compared the performance of the tetra-primer PCR in relation to the PCR-RFLP, both optimized in the Research HTLV Laboratory of the Center of Immunology of Instituto Adolfo Lutz in São Paulo. One hundred DNA samples obtained from patients of STD/Aids Reference Centre in São Paulo, previously analyzed for IL28B SNPs by PCR-RFLP were selected for analysis, after confirming that they represent all IL28B SNPs patterns described in the literature. The results obtained showed concordance between the PCR-RFLP and the tetra-primer PCR SNPs results, and because of the low cost, easy to perform, and minor employment of biological specimen and reagents, the tetra-primer PCR is of choice to be used in routine. (AU)

Polimorfismos de nucleotídeos únicos (single nucleotide polymorphisms, SNPs rs12979860 e rs8099917) no gene que codifica o Interferon Lambda 4 (IFNL4, antigamente IFNL3 e/ou IL28B) têm sido associados às falhas na resposta imune inata e resposta virológica sustentada na hepatite C, e a mielopatia associada ao HTLV-1 (HTLV-1-associated myelopathy, HAM). A pesquisa destes polimorfismos pode empregar diversas metodologias: sequenciamento, reação em cadeia da polimerase em tempo real ou quantitativa (quantitative polymerase chain reaction, qPCR), análise de fragmentos de restrição enzimática em produtos de PCR (restriction fragment length polymorphism in PCR products, PCR-RFLP) e a tetra-primer PCR. Este estudo comparou o desempenho da tetra-primer PCR em relação a PCR-RFLP, ambas otimizadas no Laboratório de Pesquisa em HTLV do Centro de Imunologia do Instituto Adolfo Lutz de São Paulo. Foram selecionadas 100 amostras de DNA obtidas de pacientes do Centro de Referência e Treinamento em DST/Aids de São Paulo cujos SNPs na IL28B foram anteriormente determinados por PCR-RFLP e representaram todos os perfis descritos em literatura. Os resultados obtidos mostraram concordância entre elas, e pelo fato da tetra-primer PCR ter menor custo, ser de fácil execução, empregar menos tempo, insumos e material biológico, é a técnica de escolha para uso em rotina. (AU)

Genetic diversity analysis in dairy cows of Nariño, southwestern Colombia / Análise da diversidade genética em vacas leiteiras de Nariño, sudoeste da Colômbia

In Colombia, different dairy breeds were introduced from Europe and the United States, which underwent different crossing and selection processes that generated specific qualities or differences and which likely have their own genomic structure. To characterize genetic diversity, population structure, and admixture, we used genotypes from 23,182 autosomal single nucleotide polymorphisms (SNPs) of 130 animals representing four dairy cattle breed groups from Nariño. In addition, we merged genotypes from 43,043 autosomal SNPs, from 137 animals from the Decker database (Decker et al., 2014) (DRYAD doi:10.5061/dryad.th092). After the quality control process of pruning the merged dataset, we were left with 7,475 autosomal SNPs shared by both databases of Nariño (127 samples) and Decker (135 samples). Genetic diversity levels were moderate in all breeds (average observed heterozygosity = 0.40). Based on the fixation index values, we conclude that Brahman individuals were more differentiated than the taurine breeds (-0.374 to 0.076 for Brown Swiss). Pairs between taurine breeds showed low genetic differentiation (0.011-0.479). Principal component analysis revealed that in both the Nariño and Decker databases, the taurine formed the most compact cluster compared with other breeds known not to share the same ancestry, and Jersey, Brown Swiss, and Normand individuals exhibited high similarity with Holstein individuals. Hierarchical cluster analysis with Admixture revealed that Brahman, Jersey, Normand, and Holstein from the Decker databases most of which were clustered together with the dairy breeds of the Nariño highland tropics are not able to create different groups, thus having greater similarity with each other. This can be explained by the crosses made by farmers to increase milk production volume, always based on the Holstein breed with semen of bulls from America and Canada. Detrimental impacts due to intensive selection might cause some specific traits from the region to be fixed in the offspring, which can influence their adaptive capacity to the highland tropics.

Na Colômbia foram introduzidas diferentes raças leiteiras trazidas da Europa e dos Estados Unidos, que passaram por diferentes processos de cruzamento e seleção, gerando o desenvolvimento de características ou diferenças específicas nas raças bovinas e provavelmente, exibem sua própria estrutura genômica. Para caracterizar a diversidade genética e estrutura populacional foram utilizados genótipos de 23.182 polimorfismos de nucleotídeo único (SNPs) autossômicos de 130 animais, representando quatro grupos de raças de gado leiteiro de Nariño. Além disso, juntamos genótipos de 43.043 SNPs autossômicos, de 137 animais do banco de dados Decker (Decker et al., 2014) (DRYAD doi:10.5061/dryad.th092). Após o processo de controle de qualidade, o conjunto de dados misto ficou com 7.475 SNPs autossômicos compartilhados em ambos os bancos de dados de Nariño (127 amostras) e Decker (135 amostras). Os níveis de diversidade genética foram moderados em todas as raças (heterozigose média observada = 0,40). Com base nos valores do índice de fixação, concluímos que os indivíduos Brahman (zebuínos) foram mais diferenciados em comparação às raças taurinas (-0,374 a 0,076 para Pardo Suíço). Pares entre as raças taurinas apresentaram baixa diferenciação genética (0,011 ­ 0,479). O resultado dos componentes principais mostra que nos dois bancos de dados, Nariño e Decker, os taurinos formaram o cluster mais compacto em comparação com outras raças conhecidas por não compartilharem a mesma ancestralidade; indivíduos Jersey, Pardo Suíço e Normando denotaram alta similaridade com indivíduos Holandeses. A análise de agrupamento hierárquico com Admixture mostrou que Brahman, Jersey, Normando e Holandês da base de dados Decker, a maioria deles também agrupados com as raças leiteiras do alto trópico de Nariño, não são capazes de criar grupos diferentes, portanto, mostram maior semelhança entre eles. Isso pode ser explicado devido aos cruzamentos feitos pelos pecuaristas para aumentar o volume de produção de leite, sempre tendo como base a raça Holandesa com sêmen de touros da América e Canadá. Impactos prejudiciais, devido à seleção intensiva, podem fazer com que algumas características específicas da região sejam fixadas na prole e isso pode influenciar a sua capacidade adaptativa aos trópicos altos.

Polymorphism in the BIEC2-808543 locus and its association with growth curve in Brasileiro de Hipismo horse breed

Our objective was to evaluate whether the single nucleotide polymorphism (SNP) BIEC2-808543, identified in some horse breeds, also occurs in the Brasileiro de Hipismo (BH) breed. In addition, we verified if this SNP is related to the growth curve profile of these animals for the variables body mass, height at withers, and height at croup, using nonlinear mixed models. For the DNA isolation, we collected blood samples from 167 young BH horses. We obtained the genotypes of these animals using the polymerase chain reaction-restriction fragment length polymorphism technique. For the association studies of this polymorphism with the growth curve in foals, we selected three traits: body mass, height at withers, and height at croup. Polymorphism C/T exists in BH horses and is significantly associated with the evaluated traits. Animals that presented the TT genotype were smaller and lighter when compared with animals of the CT and CC genotypes. By the Akaike information criterion, the model that best described the growth curve for the body mass variable is the Brody model associated with the power of the mean variance function. For the height at withers variable, the best-fit model was von Bertalanffy, adjusted without polymorphism effect in parameter b, associated with the asymptotic variance. For the height at croup trait, the model that best described the growth curve was Brody model, associated with asymptotic variance. This polymorphism represents a good molecular marker. Nonlinear models are promising for describing growth curves in horses, particularly by the possibility of associating SNP effects to model parameters.

Association Analysis Between Polymorphism of Gonadotrophin Releasing Hormone Genes and Growth Traits of Quail (Coturnix Coturnix)

This study investigated SNP mutation sites of Gonadotrophin releasing hormone (GnRH) gene in China yellow quail, Beijing white quail and Korean quail through PCR amplification and DNA sequencing technologies. Moreover, polymorphism of GnRH gene and its association with growth traits of quail were analyzed, aiming to get molecular markers associated to growth traits of quail, which could provide references for breeding of new quail species. According to research results, a total of 14 SNP mutation sites of GnRH were detected in China yellow quail, Beijing white quail and Korean quail, which were C71T, C108T, C168T, C178T, A184G, C206T, A209C, C215T, A252G, A279T, C281T, C293G, C339T and C458T. Except that only 2 genotypes were detected for A209C and C281T in China yellow quail and Beijing white quail, 3 genotypes were detected for all of the remaining 12 SNP mutation sites in three quail species. Of the 14 SNP sites, C71T, A209C, C215T, C281T, C293G, C339T and C458T were significantly associated with body weight (p 0.05), C71T, C108T, C168T, C178T, A184G, C206T, C215T, A252G, C293G, C339T and C458T were significantly associated with shank length (p 0.05), C71T, C215T, C293G and C458T were significantly associated with breastbone length (p 0.05), A209C and C281T were significantly associated with shank circumference (p 0.05).(AU)

Association Analysis Between Polymorphism of Gonadotrophin Releasing Hormone Genes and Growth Traits of Quail (Coturnix Coturnix)

This study investigated SNP mutation sites of Gonadotrophin releasing hormone (GnRH) gene in China yellow quail, Beijing white quail and Korean quail through PCR amplification and DNA sequencing technologies. Moreover, polymorphism of GnRH gene and its association with growth traits of quail were analyzed, aiming to get molecular markers associated to growth traits of quail, which could provide references for breeding of new quail species. According to research results, a total of 14 SNP mutation sites of GnRH were detected in China yellow quail, Beijing white quail and Korean quail, which were C71T, C108T, C168T, C178T, A184G, C206T, A209C, C215T, A252G, A279T, C281T, C293G, C339T and C458T. Except that only 2 genotypes were detected for A209C and C281T in China yellow quail and Beijing white quail, 3 genotypes were detected for all of the remaining 12 SNP mutation sites in three quail species. Of the 14 SNP sites, C71T, A209C, C215T, C281T, C293G, C339T and C458T were significantly associated with body weight (p 0.05), C71T, C108T, C168T, C178T, A184G, C206T, C215T, A252G, C293G, C339T and C458T were significantly associated with shank length (p 0.05), C71T, C215T, C293G and C458T were significantly associated with breastbone length (p 0.05), A209C and C281T were significantly associated with shank circumference (p 0.05).

Identification of patterns related to linkage groups or disequilibrium by factor analysis / Identificação de padrões relacionados a grupos de ligação ou de desequilíbrio por análise de fatores

Empirical patterns of linkage disequilibrium (LD) can be used to increase the statistical power of genetic mapping. This study was carried out with the objective of verifying the efficacy of factor analysis (AF) applied to data sets of molecular markers of the SNP type, in order to identify linkage groups and haplotypes blocks. The SNPs data set used was derived from a simulation process of an F2 population, containing 2000 marks with information of 500 individuals. The estimation of the factorial loadings of FA was made in two ways, considering the matrix of distances between the markers (A) and considering the correlation matrix (R). The number of factors (k) to be used was established based on the graph scree-plot and based on the proportion of the total variance explained. Results indicated that matrices A and R lead to similar results. Based on the scree-plot we considered k equal to 10 and the factors interpreted as being representative of the bonding groups. The second criterion led to a number of factors equal to 50, and the factors interpreted as being representative of the haplotypes blocks. This showed the potential of the technique, making it possible to obtain results applicable to any type of population, helping or corroborating the interpretation of genomic studies. The study demonstrated that AF was able to identify patterns of association between markers, identifying subgroups of markers that reflect factor binding groups and also linkage disequilibrium groups.(AU)

Padrões empíricos de desequilíbrio de ligação (LD) podem ser utilizados para aumentar o poder estatístico do mapeamento genético. Este trabalho foi realizado com o objetivo de verificar a eficácia da análise de fatores (AF) aplicada a conjuntos de dados de marcadores moleculares do tipo SNP, visando identificar grupos de ligação e blocos de haplótipos. O conjunto de dados SNPs utilizado foi oriundo de um processo de simulação de uma população F2, contendo 2000 marcas com informações de 500 indivíduos. A estimação das cargas fatoriais (loadings) da AF foi feita de duas formas, considerando a matriz de distâncias entre os marcadores (A) e considerando a matriz de correlação (R). O número de fatores (k) a ser utilizado foi estabelecido com base no gráfico scree-plot e com base na proporção da variância total explicada. Os resultados indicam que as matrizes A e R conduzem a resultados similares. Com base no scree-plot considerou-se k igual a 10 e os fatores interpretados como sendo representativos dos grupos de ligação. O segundo critério conduziu a um número de fatores igual a 50, e os fatores interpretados como sendo representativos dos blocos de haplótipos. Isto mostra o potencial da técnica que permite obter resultados aplicáveis a qualquer tipo de população, corroborando a interpretação de estudos genômicos. O trabalho demonstrou que a AF foi capaz de identificar padrões de associação entre marcadores, identificando subgrupos de marcadores que refletem grupos de ligação fatorial e também grupos de desequilíbrio de ligação.(AU)

Effect of LCORL gene polymorphism on body size traits in horse populations

The aim of this study was to determine polymorphism of LCORL gene in horse breeds and its association with body size. PCR-RFLP technique was performed using AluI for genotyping of 306 horses. Results showed that C is the rare allele in Iranian Breeds, because these horses have been used since ancient times as a courier and for war and archery, hence selection has done to benefit of spiky horses with medium body that need less food and are tireless. While, for foreign breeds; frequency of C allele was high that can be concluded these breeds used in fields, forests, and mines. A UPGMA dendrogram based on the Nei's standard genetic distance among studied breeds showed separate clusters for Iranian native and exotic breeds. Statistical association analysis of three observed genotypes with body size showed that there is an association between this polymorphism and body size criteria (p < 0.01). Overall, it can be concluded that studied mutation in LCORL gene can be used as candidate marker for improving body weight in horse.(AU)

Influence of temperament-related genes on live weight traits of Charolais cows

We investigated whether a panel of molecular markers previously associated with temperament has an effect on live growth traits. Phenotypic data from 412 Charolais cows categorized according to their age in adult and young cows were used to determine Pearson's correlations between birth (BW), weaning (WW), and yearling live (YW) weight and temperament traits (measured as exit velocity [EV] and temperament score [TS]). For association analysis, selective genotyping of a group of 80 cows identified as the most docile and temperamental were genotyped with a 151-SNP (single-nucleotide polymorphisms) panel of molecular markers previously associated with temperament. Significant Pearson's correlations between birth weight and weaning weight and the two temperament measurements (EV and TS) were observed only in the young cow group. Significant effects of ten SNP on BW and WW were observed. Four markers located on candidate genes for temperament traits also had an effect on birth weight and weaning weight in Charolais cows, which indicates that both traits could be influenced by the same genes.(AU)

Identification of candidate genes associated with milk yield trait in buffaloes ( Bubalus bubalis ) by restriction-site-associated DNA sequencing

The objectives of our present study included the screening of single nucleotide polymorphisms (SNP) that show significant differences in allelic frequencies between two buffalo populations (Egyptian and Chinese buffaloes), categorization of functional genes associated with these SNP by gene ontology, and pathway analyses to further understand their potential values as candidate genes closely associated with milk yield trait in buffaloes. In this study, double digest restrictionsite associated DNA sequencing was performed on Illumina HiSeq 2500 platform for 20 and 25 female buffaloes from Egypt and China, respectively. Approximately 118 Gb of sequencing data were obtained, and a total of 110,129 and 150,535 putative SNP were detected in Egyptian and Chinese buffaloes, respectively. Focused only on those SNP that differed significantly in allelic frequencies between the two populations, we found that genes associated with these SNP were significantly over-represented in the ionotropic glutamate receptor pathway, the endothelin signaling pathway, and the gonadotropin-releasing hormone receptor pathway, which contained a total of 29 genes. Of these, nine genes (ADCY5, CACNA1A, CREB1, INHBA, INHBB, PIK3R1, PLCB1, PRKCE, and SMAD2) participating in the hormonal regulation of lactation, were considered to be promising candidate genes worthy of further investigations for favorable alleles associated with milk yield. Our results provide useful information about genetic variations in Egyptian and Chinese buffaloes. The potential influences of nine candidate genes and their associated SNP on milk yield need to be validated in more buffalo populations.(AU)

Effect of LCORL gene polymorphism on body size traits in horse populations

The aim of this study was to determine polymorphism of LCORL gene in horse breeds and its association with body size. PCR-RFLP technique was performed using AluI for genotyping of 306 horses. Results showed that C is the rare allele in Iranian Breeds, because these horses have been used since ancient times as a courier and for war and archery, hence selection has done to benefit of spiky horses with medium body that need less food and are tireless. While, for foreign breeds; frequency of C allele was high that can be concluded these breeds used in fields, forests, and mines. A UPGMA dendrogram based on the Nei's standard genetic distance among studied breeds showed separate clusters for Iranian native and exotic breeds. Statistical association analysis of three observed genotypes with body size showed that there is an association between this polymorphism and body size criteria (p < 0.01). Overall, it can be concluded that studied mutation in LCORL gene can be used as candidate marker for improving body weight in horse.

Association mapping of drought tolerance indices in wheat: QTL-rich regions on chromosome 4A

Drought is likely the main abiotic stress that affects wheat yield. The identification of drought-tolerant genotypes represents an effective way of dealing with the continuous decrease in water resources as well as the increase in world population. The aim of this study was to identify single nucleotide polymorphisms (SNP) associated with drought tolerance indices in wheat by using a genome-wide association study (GWAS) under fully irrigated and rain-fed conditions. The drought tolerance indices (i.e., Stress Susceptibility Index, Stress Tolerance Index, Tolerance Index and Yield Stability Index) were calculated based on grain yield, 1,000-kernel weight and kernels per spike. The association panel was genotyped using genotyping-by-sequencing (GBS). A total of 175 SNPs exhibited statistical evidence of association with at least one drought tolerance index, explaining up to 6 % of the phenotypic variation. Forty-five SNPs were associated with more than one tolerance index (up to 4 agronomic traits). Most associations were located on chromosome 4A, supporting the hypothesis that this chromosome has a key role in drought tolerance which should be exploited for wheat improvement. In addition, statistical analysis detected SNPs associated with tolerance indices in both growing seasons, providing information about genetic regions with stable effects under different environmental conditions. This GWAS experiment serves as one of the few studies on association mapping for drought tolerance indices in wheat, which could increase the efficiency of rain-fed and irrigated crop production.

Association mapping of drought tolerance indices in wheat: QTL-rich regions on chromosome 4A

Drought is likely the main abiotic stress that affects wheat yield. The identification of drought-tolerant genotypes represents an effective way of dealing with the continuous decrease in water resources as well as the increase in world population. The aim of this study was to identify single nucleotide polymorphisms (SNP) associated with drought tolerance indices in wheat by using a genome-wide association study (GWAS) under fully irrigated and rain-fed conditions. The drought tolerance indices (i.e., Stress Susceptibility Index, Stress Tolerance Index, Tolerance Index and Yield Stability Index) were calculated based on grain yield, 1,000-kernel weight and kernels per spike. The association panel was genotyped using genotyping-by-sequencing (GBS). A total of 175 SNPs exhibited statistical evidence of association with at least one drought tolerance index, explaining up to 6 % of the phenotypic variation. Forty-five SNPs were associated with more than one tolerance index (up to 4 agronomic traits). Most associations were located on chromosome 4A, supporting the hypothesis that this chromosome has a key role in drought tolerance which should be exploited for wheat improvement. In addition, statistical analysis detected SNPs associated with tolerance indices in both growing seasons, providing information about genetic regions with stable effects under different environmental conditions. This GWAS experiment serves as one of the few studies on association mapping for drought tolerance indices in wheat, which could increase the efficiency of rain-fed and irrigated crop production.(AU)

The Single Nucleotide Polymorphisms of Myostatin Gene and Their Associations with Growth and Carcass Traits in Daheng Broiler

Myostatin (MSTN) is a negative regulator of skeletal muscle growth. In order to investigate whether there is a correlation between MSTN polymorphisms and chicken production performance, in this study, single nucleotide polymorphisms (SNPs) in MSTN gene were examined across 180 Daheng broilers by direct sequencing of PCR product, and the correlations between the genotype and body weight at the age of 1-10 weeks and carcass traits at the age of 73 day were analyzed. Five SNPs (rs313622770, rs313744840, rs316247861, rs314431084, rs317126751) of MSTN gene were identified across Daheng broiler samples, and four haplotypes were reconstructed based on the five SNPs. Results of association analysis showed that four (rs313622770, rs313744840, rs316247861 and rs317126751) of these SNPs had significant association with some growth traits (p 0.05), but there were no significant effect on carcass traits and the four SNPs were strong linkage. For rs314431084, there was no significant correlation between different genotypes and growth or carcass traits. The AA genotype of rs313622770, GG genotype of rs313744840, CC genotype of rs316247861, TT genotype of rs317126751 were good for chicken growth. Diplotypes were significantly associated with chest muscle and leg muscle weight (p 0.05). Overall, these results provide evidence that polymorphisms in MSTN gene are associated with growth traits in chicken. The SNPs in MSTN gene could be utilized as potential markers for marker-assisted selection (MAS) during chicken breeding.(AU)

The Single Nucleotide Polymorphisms of Myostatin Gene and Their Associations with Growth and Carcass Traits in Daheng Broiler

Myostatin (MSTN) is a negative regulator of skeletal muscle growth. In order to investigate whether there is a correlation between MSTN polymorphisms and chicken production performance, in this study, single nucleotide polymorphisms (SNPs) in MSTN gene were examined across 180 Daheng broilers by direct sequencing of PCR product, and the correlations between the genotype and body weight at the age of 1-10 weeks and carcass traits at the age of 73 day were analyzed. Five SNPs (rs313622770, rs313744840, rs316247861, rs314431084, rs317126751) of MSTN gene were identified across Daheng broiler samples, and four haplotypes were reconstructed based on the five SNPs. Results of association analysis showed that four (rs313622770, rs313744840, rs316247861 and rs317126751) of these SNPs had significant association with some growth traits (p 0.05), but there were no significant effect on carcass traits and the four SNPs were strong linkage. For rs314431084, there was no significant correlation between different genotypes and growth or carcass traits. The AA genotype of rs313622770, GG genotype of rs313744840, CC genotype of rs316247861, TT genotype of rs317126751 were good for chicken growth. Diplotypes were significantly associated with chest muscle and leg muscle weight (p 0.05). Overall, these results provide evidence that polymorphisms in MSTN gene are associated with growth traits in chicken. The SNPs in MSTN gene could be utilized as potential markers for marker-assisted selection (MAS) during chicken breeding.

AMH Polymorphisms and their association with traits indicative of sexual precocity in nelore heifers / Polimorfismos do AMH e suas associações com características indicadoras de precocidade sexual em novilhas nelore

Anti-Müllerian Hormone (AMH) is a protein expressed in the gonads and related to ovarian follicular development. The aim of this study was to investigate the presence of polymorphisms in the AMH gene in a Nelore herd to analyze the genetic constitution of this population and to perform association studies with early pregnancy occurrence (EPO) and age at first calving (AFC). Phenotypic data consisted of verification of early pregnancy and age at first calving of 197 unrelated heifers exposed to the mating season and aged between 15 and 17 months (precocious group) and 24 months (non-precocious group). The “precocious” group consisted of 67 heifers with age at first calving of 26.5 ± 0.59 months, and the “non-precocious” group was composed of 130 heifers with age at first calving of 36.4 ± 0.99 months. All five exons of the AMH gene were amplified by Polymerase Chain Reaction (PCR) and sequenced. A total of three SNPs were identified in this study, all of them located in exon 5 (rs527023314, rs722016629, and rs134387246), the latter one positioned in the stop codon. All three SNPs identified in exon 5 characterized synonymous mutations. Only SNP rs134387246 exhibited a significant value (P ≤ 0.10) for EPO and AFC. The association study of SNP rs134387246 revealed an over-dominance effect (P = 0.056), and no additive effect was observed (P = 0.67). A reduction of 2.5 months (75 days) in the age at first calving of heterozygous heifers for the SNP rs134387246 was observed. For the first time, polymorphisms of the AMH gene were described in Nelore heifers and associated with sexual precocity traits.

O hormônio Anti-Mülleriano (AMH) é uma proteína expressa nas gônadas e está relacionada ao desenvolvimento folicular ovariano. O objetivo desse trabalho foi investigar a presença de polimorfismos do gene AMH em um rebanho Nelore, analisar a constituição genética da população para o gene e estudar a associação entre os polimorfismos e as características ocorrência de prenhez precoce (OPP) e idade ao primeiro parto (IPP). Os dados fenotípicos consistiram da verificação da prenhez precoce e idade ao primeiro parto de 197 novilhas, não aparentadas, expostas à estação de monta com idade entre 15 e 17 meses (grupo precoce) ou 24 meses (grupo não precoce). O grupo denominado “precoce” foi composto por 67 novilhas com idade ao primeiro parto de 26.5±0.59 meses, e o segundo denominado “não precoce” composto por 130 novilhas com idade ao primeiro parto de 36.4±0.99 meses. Os cinco éxons do gene AMH foram amplificados por meio da técnica de Reação em Cadeia da Polimerase (PCR) e sequenciados. Um total de três SNPs foram identificados nesse estudo, todos localizados no éxon 5 (rs527023314, rs722016629 and rs134387246), sendo o último posicionado stop codon. Os três SNPs identificados caracterizaram mutações sinônimas. Somente o SNP rs134387246 exibiu associação significante (P ≤ 0.10) para ambas características (OPP e IPP). O estudo de associação do SNP rs134387246 revelou um efeito de sobre dominância (P=0,056), e ausência de ação gênica aditiva (P=0,67). Foi observada redução de 2,5 meses (75 dias) na idade ao primeiro parto de novilhas heterozigotas para o SNP rs134387246. Pela primeira vez na literatura, polimorfismos do gene AMH foram descritos em novilhas da raça Nelore e associados a características indicadoras de precocidade sexual.

Genetic association of variations in the kappa-casein and beta-lactoglobulin genes with milk traits in girolando cattle / Associação genética de variações nos genes da kappa-caseina and beta-lactoglobulina com características do leite de bovinos da raça Girolando

In dairy farm animals, one the most important goal of the selection is the improvement of milk yield and composition. Several studies have demonstrated that the candidate genes of the kappa-casein (CSN3) and β - lactoglobulin (β-LG) are associated with milk yield, milk quality and health traits in dairy animals. Therefore the aim of this study was to detect polymorphisms in CSN3 and β-LG genes and its association with milk yield in up to 305 days (305MY) and predicted transmission capacity (PTA) for 305MY in Girolando cattle. Totally, 138 bulls and 729 cows (n=867) were sampled. The genotypes of both genes were obtained by the PCR-RFLP method using HinfI and HaeIII enzymes for CSN3 and β-LG genes, respectively. Statistical results revealed two alleles A and B for both genes. The genotypes and alleles more frequents for CSN3 and β-LG genes were respectively: AA (0.7324) and A (0.8558), and AB (0.4827) and A (0.5017). The x2 test revealed that the two loci were at Hardy-Weinberg equilibrium (p<0.001). The allele substitution effects for the variants were not significant on 305MY and PTA for 305MY (p>0.05). The allele variants of β-LG and CSN3 might be more investigated before include them into future breeding schemes designed for Girolando dairy cattle with objective of improving milk traits as milk yield in up to 305 days (305MY) and predicted transmission capacity (PTA) for 305MY.(AU)

Em rebanhos leiteiros, um dos objetivos mais importantes da seleção é a melhoria da produção e composição do leite. Vários estudos demonstraram que os genes candidatos da kappa-caseína (CSN3) e da β-lactoglobulina (β-LG) estão associados a produção de leite, qualidade do leite e características de saúde em animais leiteiros. Portanto, o objetivo deste estudo foi detectar polimorfismos nos genes CSN3 e β-LG e avaliar possíveis associaçoes desses polimorfismos com a produção de leite em até 305 dias (305MY) e a capacidade de transmissão prevista (PTA) de leite em bovinos da raça Girolando. No total, 138 touros e 729 vacas (n = 867) foram amostrados. A genotipagem foi realizada pelo método PCR-RFLP utilizando as enzimas HinfI e HaeIII para os genes CSN3 e β-LG, respectivamente. Os resultados estatísticos revelaram dois alelos A e B para ambos os genes. Os genotipos e alelos mais frequentes para os genes CSN3 e β-LG foram respectivamente: AA (0,7324) e A (0,8558) e AB (0,4827) e A (0,5017). O teste x2 revelou que os dois loci estavam em equilibrio de Hardy-Weinberg (p <0,001). Os efeitos de substituiçao alélica para as variantes nao foram significativos para as características 305 MY e PTA para 305MY (p> 0,05). Portanto, as variantes alélicas identificadas nos genes β-LG e CSN3 devem ser mais investigadas antes de serem incluidas nos programas de melhoramento desenhados para bovinos leiteiros Girolando objetivando melhorar as características do leite analisadas no presente estudo.(AU)

AMH Polymorphisms and their association with traits indicative of sexual precocity in nelore heifers / Polimorfismos do AMH e suas associações com características indicadoras de precocidade sexual em novilhas nelore

Anti-Müllerian Hormone (AMH) is a protein expressed in the gonads and related to ovarian follicular development. The aim of this study was to investigate the presence of polymorphisms in the AMH gene in a Nelore herd to analyze the genetic constitution of this population and to perform association studies with early pregnancy occurrence (EPO) and age at first calving (AFC). Phenotypic data consisted of verification of early pregnancy and age at first calving of 197 unrelated heifers exposed to the mating season and aged between 15 and 17 months (precocious group) and 24 months (non-precocious group). The “precocious” group consisted of 67 heifers with age at first calving of 26.5 ± 0.59 months, and the “non-precocious” group was composed of 130 heifers with age at first calving of 36.4 ± 0.99 months. All five exons of the AMH gene were amplified by Polymerase Chain Reaction (PCR) and sequenced. A total of three SNPs were identified in this study, all of them located in exon 5 (rs527023314, rs722016629, and rs134387246), the latter one positioned in the stop codon. All three SNPs identified in exon 5 characterized synonymous mutations. Only SNP rs134387246 exhibited a significant value (P ≤ 0.10) for EPO and AFC. The association study of SNP rs134387246 revealed an over-dominance effect (P = 0.056), and no additive effect was observed (P = 0.67). A reduction of 2.5 months (75 days) in the age at first calving of heterozygous heifers for the SNP rs134387246 was observed. For the first time, polymorphisms of the AMH gene were described in Nelore heifers and associated with sexual precocity traits.(AU)

O hormônio Anti-Mülleriano (AMH) é uma proteína expressa nas gônadas e está relacionada ao desenvolvimento folicular ovariano. O objetivo desse trabalho foi investigar a presença de polimorfismos do gene AMH em um rebanho Nelore, analisar a constituição genética da população para o gene e estudar a associação entre os polimorfismos e as características ocorrência de prenhez precoce (OPP) e idade ao primeiro parto (IPP). Os dados fenotípicos consistiram da verificação da prenhez precoce e idade ao primeiro parto de 197 novilhas, não aparentadas, expostas à estação de monta com idade entre 15 e 17 meses (grupo precoce) ou 24 meses (grupo não precoce). O grupo denominado “precoce” foi composto por 67 novilhas com idade ao primeiro parto de 26.5±0.59 meses, e o segundo denominado “não precoce” composto por 130 novilhas com idade ao primeiro parto de 36.4±0.99 meses. Os cinco éxons do gene AMH foram amplificados por meio da técnica de Reação em Cadeia da Polimerase (PCR) e sequenciados. Um total de três SNPs foram identificados nesse estudo, todos localizados no éxon 5 (rs527023314, rs722016629 and rs134387246), sendo o último posicionado stop codon. Os três SNPs identificados caracterizaram mutações sinônimas. Somente o SNP rs134387246 exibiu associação significante (P ≤ 0.10) para ambas características (OPP e IPP). O estudo de associação do SNP rs134387246 revelou um efeito de sobre dominância (P=0,056), e ausência de ação gênica aditiva (P=0,67). Foi observada redução de 2,5 meses (75 dias) na idade ao primeiro parto de novilhas heterozigotas para o SNP rs134387246. Pela primeira vez na literatura, polimorfismos do gene AMH foram descritos em novilhas da raça Nelore e associados a características indicadoras de precocidade sexual.(AU)

Genetic association of variations in the kappa-casein and beta-lactoglobulin genes with milk traits in girolando cattle / Associação genética de variações nos genes da kappa-caseina and beta-lactoglobulina com características do leite de bovinos da raça Girolando

In dairy farm animals, one the most important goal of the selection is the improvement of milk yield and composition. Several studies have demonstrated that the candidate genes of the kappa-casein (CSN3) and β - lactoglobulin (β-LG) are associated with milk yield, milk quality and health traits in dairy animals. Therefore the aim of this study was to detect polymorphisms in CSN3 and β-LG genes and its association with milk yield in up to 305 days (305MY) and predicted transmission capacity (PTA) for 305MY in Girolando cattle. Totally, 138 bulls and 729 cows (n=867) were sampled. The genotypes of both genes were obtained by the PCR-RFLP method using HinfI and HaeIII enzymes for CSN3 and β-LG genes, respectively. Statistical results revealed two alleles A and B for both genes. The genotypes and alleles more frequents for CSN3 and β-LG genes were respectively: AA (0.7324) and A (0.8558), and AB (0.4827) and A (0.5017). The x2 test revealed that the two loci were at Hardy-Weinberg equilibrium (p0.05). The allele variants of β-LG and CSN3 might be more investigated before include them into future breeding schemes designed for Girolando dairy cattle with objective of improving milk traits as milk yield in up to 305 days (305MY) and predicted transmission capacity (PTA) for 305MY.

Em rebanhos leiteiros, um dos objetivos mais importantes da seleção é a melhoria da produção e composição do leite. Vários estudos demonstraram que os genes candidatos da kappa-caseína (CSN3) e da β-lactoglobulina (β-LG) estão associados a produção de leite, qualidade do leite e características de saúde em animais leiteiros. Portanto, o objetivo deste estudo foi detectar polimorfismos nos genes CSN3 e β-LG e avaliar possíveis associaçoes desses polimorfismos com a produção de leite em até 305 dias (305MY) e a capacidade de transmissão prevista (PTA) de leite em bovinos da raça Girolando. No total, 138 touros e 729 vacas (n = 867) foram amostrados. A genotipagem foi realizada pelo método PCR-RFLP utilizando as enzimas HinfI e HaeIII para os genes CSN3 e β-LG, respectivamente. Os resultados estatísticos revelaram dois alelos A e B para ambos os genes. Os genotipos e alelos mais frequentes para os genes CSN3 e β-LG foram respectivamente: AA (0,7324) e A (0,8558) e AB (0,4827) e A (0,5017). O teste x2 revelou que os dois loci estavam em equilibrio de Hardy-Weinberg (p 0,05). Portanto, as variantes alélicas identificadas nos genes β-LG e CSN3 devem ser mais investigadas antes de serem incluidas nos programas de melhoramento desenhados para bovinos leiteiros Girolando objetivando melhorar as características do leite analisadas no presente estudo.

Genome prediction accuracy of common bean via Bayesian models

ABSTRACT: We aimed to apply genomic information based on SNP (single nucleotide polymorphism) markers for the genetic evaluation of the traits stay-green (SG), plant architecture (PA), grain aspect (GA) and grain yield (GY) in common bean through Bayesian models. These models were compared in terms of prediction accuracy and ability for heritability estimation for each one of the mentioned traits. A total of 80 cultivars were genotyped for 377 SNP markers, whose effects were estimated by five different Bayesian models: Bayes A (BA), B (BB), C (BC), LASSO (BL) e Ridge regression (BRR). Although, prediction accuracies calculated by means of cross-validation have been similar within each trait, the BB model stood out for the trait SG, whereas the BRR was indicated for the remaining traits. The heritability estimates for the traits SG, PA, GA and GY were 0.61, 0.28, 0.32 and 0.29, respectively. In summary, the Bayesian methods applied here were effective and ease to be implemented. The used SNP markers can help in the early selection of promising genotypes, since incorporating genomic information increase the prediction accuracy of the estimated genetic merit.

RESUMO: Objetivou-se incorporar informações genômicas de marcadores SNP (single nucleotide polymorphism) na avaliação genética das características stay-green (SG), arquitetura de planta (AP), aspecto de grãos (AG) e produtividade de grãos (PG) em feijoeiro-comum via modelos Bayesianos. Estes modelos foram comparados quanto a acurácia de predição e habilidade de estimação da herdabilidade para cada característica. Utilizaram-se informações de 80 cultivares genotipadas para 377 marcadores SNP, cujos efeitos de substituição alélica foram estimados por meio de cinco diferentes modelos Bayesianos: Bayes A (BA), B (BB), C (BC), LASSO (BL) e regressão ridge (BRR). Embora as acurácias de predição calculadas por meio de análise de validação cruzada tenham sido similares dentro de cada característica, o modelo BB se destacou para a característica SG, enquanto o modelo BRR foi indicado para as demais. As herdabilidades estimadas para SG, AP, AG e PG foram, respectivamente, 0,61, 0,28, 0,32 e 0,29. Em resumo, os métodos contemplados mostraram-se efetivos e de fácil implementação. O conjunto de marcadores utilizado pode auxiliar na seleção precoce de genótipos promissores, uma vez que a incorporação de informações genômicas aumenta a acurácia de predição do mérito genético estimado.

Genome prediction accuracy of common bean via Bayesian models / Acurácia de predição genômica em feijoeiro-comum via modelos Bayesianos

We aimed to apply genomic information based on SNP (single nucleotide polymorphism) markers for the genetic evaluation of the traits stay-green (SG), plant architecture (PA), grain aspect (GA) and grain yield (GY) in common bean through Bayesian models. These models were compared in terms of prediction accuracy and ability for heritability estimation for each one of the mentioned traits. A total of 80 cultivars were genotyped for 377 SNP markers, whose effects were estimated by five different Bayesian models: Bayes A (BA), B (BB), C (BC), LASSO (BL) e Ridge regression (BRR). Although, prediction accuracies calculated by means of cross-validation have been similar within each trait, the BB model stood out for the trait SG, whereas the BRR was indicated for the remaining traits. The heritability estimates for the traits SG, PA, GA and GY were 0.61, 0.28, 0.32 and 0.29, respectively. In summary, the Bayesian methods applied here were effective and ease to be implemented. The used SNP markers can help in the early selection of promising genotypes, since incorporating genomic information increase the prediction accuracy of the estimated genetic merit.(AU)

Objetivou-se incorporar informações genômicas de marcadores SNP (single nucleotide polymorphism) na avaliação genética das características stay-green (SG), arquitetura de planta (AP), aspecto de grãos (AG) e produtividade de grãos (PG) em feijoeiro-comum via modelos Bayesianos. Estes modelos foram comparados quanto a acurácia de predição e habilidade de estimação da herdabilidade para cada característica. Utilizaram-se informações de 80 cultivares genotipadas para 377 marcadores SNP, cujos efeitos de substituição alélica foram estimados por meio de cinco diferentes modelos Bayesianos: Bayes A (BA), B (BB), C (BC), LASSO (BL) e regressão ridge (BRR). Embora as acurácias de predição calculadas por meio de análise de validação cruzada tenham sido similares dentro de cada característica, o modelo BB se destacou para a característica SG, enquanto o modelo BRR foi indicado para as demais. As herdabilidades estimadas para SG, AP, AG e PG foram, respectivamente, 0,61, 0,28, 0,32 e 0,29. Em resumo, os métodos contemplados mostraram-se efetivos e de fácil implementação. O conjunto de marcadores utilizado pode auxiliar na seleção precoce de genótipos promissores, uma vez que a incorporação de informações genômicas aumenta a acurácia de predição do mérito genético estimado.(AU)