Genome-wide scan reveals population stratification and footprints of recent selection in Nelore cattle

Abstract Background This study aimed at (1) assessing the genomic stratification of experimental lines of Nelore cattle that have experienced different selection regimes for growth traits, and (2) identifying genomic regions that have undergone recent selection. We used a sample of 763 animals genotyped with the Illumina BovineHD BeadChip, among which 674 animals originated from two lines that are maintained under directional selection for increased yearling body weight and 89 animals from a control line that is maintained under stabilizing selection. Results Multidimensional analysis of the genomic dissimilarity matrix and admixture analysis revealed a substantial level of population stratification between the directional selection lines and the stabilizing selection control line. Two of the three tests used to detect selection signatures (F ST, XP-EHH and iHS) revealed six candidate regions with indications of selection, which strongly indicates truly positive signals. The set of identified candidate genes included several genes with roles that are functionally related to growth metabolism, such as COL14A1, CPT1C, CRH, TBC1D1, and XKR4. Conclusions The current study identified genetic stratification that resulted from almost four decades of divergent selection in an experimental Nelore population, and highlighted autosomal genomic regions that present patterns of recent selection. Our findings provide a basis for a better understanding of the metabolic mechanism that underlies the growth traits, which are modified by selection for yearling body weight

Dias ao Parto de Fêmeas Nelore de um Experimento de Seleção para Crescimento: II - Modelo de Regressão Aleatória Days to Calving of Nelore Cows from a Selection Experiment for Growth: II - Random Regression Model

Os parâmetros genéticos para dias ao parto foram estimados usando um modelo de regressão aleatória, com polinômios ortogonais da idade na monta (em anos) como covariável. Os registros de dias ao parto (4.118) foram provenientes de 926 vacas de três rebanhos Nelore experimentais, sendo os rebanhos seleção e tradicional selecionados para maior peso ao sobreano, e o rebanho controle selecionado para a média do peso ao sobreano. As variâncias genética aditiva e permanente de ambiente foram descritas por uma função polinomial de ordem 4, com nove medidas de erro, resultando em variâncias fenotípica e genética aditiva altas nas idades mais avançadas, principalmente após a 6ª monta. As herdabilidades estimadas aumentaram de 0,08 a 0,28 da 1ª à 6ª monta. As correlações genéticas foram médias entre o primeiro desempenho e os demais (0,32 a 0,66), altas entre os desempenhos adjacentes (0,98 a 0,99), e um pouco menores entre os não adjacentes (0,63 a 0,98). A seleção para peso não alterou o valor genético médio das vacas dos rebanhos selecionados, entretanto, os valores genéticos médios das vacas do rebanho controle mostraram tendência de queda no decorrer dos anos.<br>Genetic parameters for days to calving were estimated using a random regression model, with orthogonal polynomials of age at breeding season (in years) as covariable. The records of days to calving (4,118) came from 929 cows from three experimental Nelore herds, been the selection and traditional herds selected for higher yearling weight and the control herd selected for the mean of yearling weight. Genetic and permanent environmental variances were described by a fourth order polynomial function, with 9 measures of error. The phenotypic and additive genetic variances were high in late records, especially after the 6th breeding season. Heritabilities estimates increased from 0.08 to 0.28, from first up to 6th breeding season. Genetic correlations were moderate between the first and the later records (0.32 to 0.66), high between adjacent records (0.98 to 0.99), and a little smaller between non adjacent records (0.63 to 0.98). The selection for weight did not alter the average breeding value of cows of selection herds, however the average genetic breeding values of control cows declined through the years

Free radical scavenging activity of ethanolic extracts from herbs and spices commercialized in Brazil

Ethanolic extracts from 23 different dried herbs and spices commercialized in Brazil were investigated for their free radical scavenging properties using the stable free radicals 2,2'-diphenyl-&#946;-picrylhydrazyl (DPPH&#8226;) and 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS&#8226;+), and Trolox as reference (TEAC) for both radicals. The kinetic curves for both radicals showed to follow the first order kinetics model and the decay rate constant (k obs) was calculated. For all the samples, the two methods showed a good linear TEAC correlation, indicating that the average reactivity of the compounds present in the ethanolic extracts was similar. Sage and rosemary extracts showed the highest free radical scavenging capacities, while onion showed negligible activity and colorifico, one of the most consumed spices in Brazil, showed low ABTS&#8226;+ scavenging activity. Three distinct situations were found for the extracts concerning the DPPH&#8226; scavenging capacities: (1) extracts, like rosemary and laurel, that presented the same efficient concentrations (EC50 ) but differed in the TEAC values and velocities of action (k obs), (2) extracts, such as garlic and basil, that showed similar EC50 and TEAC values, but different k obs values and (3) extracts that reacted at the same velocities but completely differed in the free radical scavenging capacities, like black pepper, savory, nutmeg, rosemary and sage. Similar considerations could be done for the ABTS&#8226;+ results. For the first time the ABTS&#8226;+ scavenging activity for allspice, basil, cardamom, chives, colorifico, cumin, dill, laurel, marjoram, parsley and tarragon was reported.<br>Extratos etanólicos de 23 ervas e condimentos desidratados comercializados no Brasil foram analisados quanto as suas propriedades antioxidantes utilizando os radicais 2,2'-difenil-&#946;-picrilhidrazil (DPPH&#8226;) e ácido 2,2'-azino-bis(3-etilbenzotiazolina-6-sulfônico) (ABTS&#8226;+), Trolox foi usado como referência para ambos radicais. As curvas cinéticas seguiram o modelo cinético de primeira ordem, e a partir destas foram calculadas as constantes de velocidade de (k obs). Os extratos de sálvia e de alecrim apresentaram as maiores capacidades redutoras de radicais livres, enquanto o extrato de cebola praticamente não apresentou atividade e o colorífico, um dos condimentos mais consumidos no Brasil, apresentou baixa atividade de aprisionamento de radicaisABTS&#8226;+. Três situações distintas foram observadas em relação à capacidade de aprisionar radicais DPPH&#8226;: (1) extratos, como os de alecrim e de louro, que apresentaram as mesmas concentrações eficientes (EC50), porém, valores de TEAC e velocidade de ação (k obs) distintos ; (2) extratos, como os de alho e de manjericão, que apresentaram valores similares de EC50 e TEAC, com valores distintos de k obs e (3) extratos com a mesma velocidade de ação que diferiram totalmente na capacidade de aprisionamento de radicais livres, como de pimenta preta, segurelha, noz moscada, alecrim e sálvia. Considerações semelhantes podem ser feitas para os resultados de ABTS&#8226;+. Osdois métodos apresentaram boa correlação de TEAC, indicando que a reatividade dos compostos presentes nos extratos etanólicos foi similar. A atividade redutora de ABTS&#8226;+ para pimenta da Jamaica, manjericão, cardamomo, cebolinha, colorífico, cominho, dill, louro, manjerona, salsinha e estragão foi reportada pela primeira vez