Population structure of Nellore cattle in northeastern Brazil

Barbosa, Artur Felipe Santos; Malhado, Carlos Henrıque Mendes; Carneiro, Paulo Luız Souza; Muniz, Lorena Mirelle Santos; Ambrosini, Diego Pagung; Carrillo, José A.; Martins-Filho, Raimundo

doi:10.1590/s1516-35982013000900005

Cited by 10 publications

(6 citation statements)

References 19 publications

(20 reference statements)

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“…F PED was lower than results reported by Barbosa et al [ 42 ] and higher than those described by Santana et al [ 43 ], with values of 8.32% and 1.42% for inbred Nellore populations, respectively.…”

Section: Discussioncontrasting

confidence: 73%

Autozygosity islands and ROH patterns in Nellore lineages: evidence of selection for functionally important traits

et al. 2018

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BackgroundThe aim of this study was to assess genome-wide autozygosity in a Nellore cattle population and to characterize ROH patterns and autozygosity islands that may have occurred due to selection within its lineages. It attempts also to compare estimates of inbreeding calculated from ROH (FROH), genomic relationship matrix (FGRM), and pedigree-based coefficient (FPED).ResultsThe average number of ROH per animal was 55.15 ± 13.01 with an average size of 3.24 Mb. The Nellore genome is composed mostly by a high number of shorter segments accounting for 78% of all ROH, although the proportion of the genome covered by them was relatively small. The genome autozygosity proportion indicates moderate to high inbreeding levels for classical standards, with an average value of 7.15% (178.70 Mb). The average of FPED and FROH, and their correlations (− 0.05 to 0.26) were low. Estimates of correlation between FGRM-FPED was zero, while the correlation (− 0.01 to − 0.07) between FGRM-FROH decreased as a function of ROH length, except for FROH > 8Mb (− 0.03). Overall, inbreeding coefficients were not high for the genotyped animals. Autozygosity islands were evident across the genome (n = 62) and their genomic location did not largely differ within lineages. Enriched terms (p < 0.01) associated with defense response to bacteria (GO:0042742), immune complex reaction (GO:0045647), pregnancy-associated glycoproteins genes (GO:0030163), and organism growth (GO:0040014) were described within the autozygotic islands.ConclusionsLow FPED-FROH correlation estimates indicate that FPED is not the most suitable method for capturing ancient inbreeding when the pedigree does not extend back many generations and FROH should be used instead. Enriched terms (p < 0.01) suggest a strong selection for immune response. Non-overlapping islands within the lineages greatly explain the mechanism underlying selection for functionally important traits in Nellore cattle.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5060-8) contains supplementary material, which is available to authorized users.

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Section: Discussioncontrasting

confidence: 73%

Autozygosity islands and ROH patterns in Nellore lineages: evidence of selection for functionally important traits

et al. 2018

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“…However, the accuracy of these comparisons depends on the degree of connectedness among MU: the higher the connectedness, the more reliable the comparison. Genetic connectedness has traditionally been calculated through pedigree-based methods ( Lewis et al, 1999b ; Kuehn et al, 2007a ); however, these methods may underestimate connectedness in production systems such as the beef cattle industry, where commercial herds are poorly registered and multi-sire mating is practiced ( Caires et al, 2012 ; Barbosa et al, 2013 ; Tonussi et al., 2017 ; Cavani et al, 2018 ). A lack of connectedness occurs: when the MU are genetically isolated (or semi-isolated) or there is limited sharing of genetic material; with the use of an incomplete numerator relationship matrix based on poor pedigree data ( Carneiro et al, 2001 ); and with poor use of artificial insemination (AI).…”

Section: Introductionmentioning

confidence: 99%

An assessment of genomic connectedness measures in Nellore cattle

Amorim

Hyeong-keun

Momen

et al. 2020

Journal of Animal Science

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An important criterion to consider in genetic evaluations is the extent of genetic connectedness across management units (MU), especially if they differ in their genetic mean. Reliable comparisons of genetic values across MU depend on the degree of connectedness; the higher the connectedness, the more reliable the comparison. Traditionally, genetic connectedness was calculated through pedigree-based methods; however, in the era of genomic selection, this can be better estimated utilizing new approaches based on genomics. Most procedures consider only additive genetic effects, which may not accurately reflect the underlying gene action of the evaluated trait, and little is known about the impact of non-additive gene action on connectedness measures. The objective of this study was to investigate the extent of genomic connectedness measures, for the first time, in Brazilian field data by applying additive and non-additive relationship matrices using a fatty acid profile dataset from seven farms located in the three regions of Brazil, which are part of the three breeding programs. Myristic acid (C14:0) was used due to its importance for human health, and reported presence of non-additive gene action. The pedigree included 427,740 animals and 925 of them were genotyped using the Bovine high-density genotyping chip. Six relationship matrices were constructed, parametrically and non-parametrically capturing additive and non-additive genetic effects from both pedigree and genomic data. We assessed genome-based connectedness across MU using the prediction error variance of difference (PEVD) and the coefficient of determination (CD). PEVD values ranged from 0.540 - 1.707, and CD from 0.146 - 0.456. Genomic information consistently enhanced the measures of connectedness compared to the numerator relationship matrix by at least 63%. Combining additive and non-additive genomic kernel relationship matrices or a non-parametric relationship matrix increased the capture of connectedness. Overall, the Gaussian kernel yielded the largest measure of connectedness. Our findings showed that connectedness metrics can be extended to incorporate genomic information and non-additive genetic variation using field data. We propose that different genomic relationship matrices can be designed to capture additive and non-additive genetic effects, increase the measures of connectedness, and to more accurately estimate the true state of connectedness in herds

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“…Nos últimos anos, têm sido registrados ganhos genéticos pequenos em zebuínos da região Nordeste do Brasil (Barbosa et al, 2013;Amaral et al, 2014).…”

Section: Introductionunclassified

Interação genótipo x ambiente via modelos de normas de reação para características de crescimento em bovinos Nelore

Ambrosini

Malhado²,

Filho

et al. 2016

Pesq. agropec. bras.

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Resumo -O objetivo deste trabalho foi avaliar a sensibilidade ao ambiente em bovinos da raça Nelore por meio de diferentes modelos de normas de reação e estimar o progresso genético no gradiente ambiental. Determinaram-se os parâmetros ganho de peso da desmama ao sobreano (GP345) e o peso ajustado aos 205 dias de idade (P205). Um modelo animal padrão (MA), dois modelos hierárquicos de normas de reação com homocedasticidade de variância residual e dois com heterogeneidade foram utilizados. O modelo hierárquico de normas de reação homocedástico com um passo apresentou o melhor ajuste. Os coeficientes de herdabilidade diretos do ambiente baixo para o ambiente alto, no gradiente ambiental, foram de 0,03 a 0,63 e de 0,13 a 0,62, respectivamente, para GP345 e P205. As correlações entre o intercepto e a inclinação da norma de reação foram de: 0,93, para GP345 (direto); 0,95, para GP345 (materno); 0,92, para P205 (direto); e 0,82, para P205 (materno). As correlações indicam que animais com alto valor genético tendem a responder positivamente aos melhores ambientes. As tendências genéticas mostraram ganhos para os efeitos diretos, principalmente nos melhores ambientes. Há variação genética quanto à sensibilidade dos animais, nos diferentes ambientes, fato que permite a seleção de animais com genótipos mais adequados para a produção em determinado ambiente.Termos para indexação: avaliação genética, correlação genética, parâmetros genéticos, plasticidade fenotípica, reprodutores, sensibilidade ambiental. Genotype x environment interaction via models of reaction norms for growth traits in Nelore cattleAbstract -The objective of this work was to evaluate the sensitivity of Nelore cattle to the environment by different models of reaction norms and to estimate the genetic progress in environmental gradient. The parameters weight gain from weaning to yearling (WG345) and adjusted weight at 205 days of age (W205) were determined. A standard animal model (AM), two reaction norm hierarchical models with residual variance homoscedasticity, and two with heterogeneity were used. The homoscedastic reaction norm hierarchical model with one step showed the best fit. The direct heritability coefficients from the low environment to the high one, in environmental gradient, were 0.03 to 0.63 and 0.13 to 0.62, respectively, for WG345 and W205. The correlations between the intercept and the slope of the reaction norm were: 0.93, for WG345 (direct); 0.95, for WG345 (maternal); 0.92, for W205 (direct); and 0.82, for W205 (maternal). The correlations indicate that animals with high genetic value tend to positively respond to better environments. The genetic trends showed gains for the direct effects, mainly in the best environments. There is genetic variation for sensitivity of animals, in different environments, a fact that allows of the selection of animals of more appropriate genotypes for the production in a particular environment.

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Population structure of Nellore cattle in northeastern Brazil

Cited by 10 publications

References 19 publications

Autozygosity islands and ROH patterns in Nellore lineages: evidence of selection for functionally important traits

Autozygosity islands and ROH patterns in Nellore lineages: evidence of selection for functionally important traits

An assessment of genomic connectedness measures in Nellore cattle

Interação genótipo x ambiente via modelos de normas de reação para características de crescimento em bovinos Nelore

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