Genome-wide detection of CNVs and their association with performance traits in broilers.

BACKGROUND: Copy number variations (CNVs) are a major type of structural genomic variants that underlie genetic architecture and phenotypic variation of complex traits, not only in humans, but also in livestock animals. We identified CNVs along the chicken genome and analyzed their association with performance traits. Genome-wide CNVs were inferred from Affymetrix® high density SNP-chip data for a broiler population. CNVs were concatenated into segments and association analyses were performed with linear mixed models considering a genomic relationship matrix, for birth weight, body weight at 21, 35, 41 and 42 days, feed intake from 35 to 41 days, feed conversion ratio from 35 to 41 days and, body weight gain from 35 to 41 days of age. RESULTS: We identified 23,214 autosomal CNVs, merged into 5042 distinct CNV regions (CNVRs), covering 12.84% of the chicken autosomal genome. One significant CNV segment was associated with BWG on GGA3 (q-value = 0.00443); one significant CNV segment was associated with BW35 (q-value = 0.00571), BW41 (q-value = 0.00180) and BW42 (q-value = 0.00130) on GGA3, and one significant CNV segment was associated with BW on GGA5 (q-value = 0.00432). All significant CNV segments were verified by qPCR, and a validation rate of 92.59% was observed. These CNV segments are located nearby genes, such as KCNJ11, MyoD1 and SOX6, known to underlie growth and development. Moreover, gene-set analyses revealed terms linked with muscle physiology, cellular processes regulation and potassium channels. CONCLUSIONS: Overall, this CNV-based GWAS study unravels potential candidate genes that may regulate performance traits in chickens. Our findings provide a foundation for future functional studies on the role of specific genes in regulating performance in chickens.

Identification of selection signatures involved in performance traits in a paternal broiler line.

BACKGROUND: Natural and artificial selection leads to changes in certain regions of the genome resulting in selection signatures that can reveal genes associated with the selected traits. Selection signatures may be identified using different methodologies, of which some are based on detecting contiguous sequences of homozygous identical-by-descent haplotypes, called runs of homozygosity (ROH), or estimating fixation index (FST) of genomic windows that indicates genetic differentiation. This study aimed to identify selection signatures in a paternal broiler TT line at generations 7th and 16th of selection and to investigate the genes annotated in these regions as well as the biological pathways involved. For such purpose, ROH and FST-based analysis were performed using whole genome sequence of twenty-eight chickens from two different generations. RESULTS: ROH analysis identified homozygous regions of short and moderate size. Analysis of ROH patterns revealed regions commonly shared among animals and changes in ROH abundance and size between the two generations. Results also suggest that whole genome sequencing (WGS) outperforms SNPchip data avoiding overestimation of ROH size and underestimation of ROH number; however, sequencing costs can limited the number of animals analyzed. FST-based analysis revealed genetic differentiation in several genomic windows. Annotation of the consensus regions of ROH and FST windows revealed new and previously identified genes associated with traits of economic interest, such as APOB, IGF1, IGFBP2, POMC, PPARG, and ZNF423. Over-representation analysis of the genes resulted in biological terms of skeletal muscle, matrilin proteins, adipose tissue, hyperglycemia, diabetes, Salmonella infections and tyrosine. CONCLUSIONS: Identification of ROH and FST-based analyses revealed selection signatures in TT line and genes that have important role in traits of economic interest. Changes in the genome of the chickens were observed between the 7th and 16th generations showing that ancient and recent selection in TT line may have acted over genomic regions affecting diseases and performance traits.

Genetic parameters associated with meat quality of Nellore cattle at different anatomical points of longissimus: Brazilian standards.

The present study estimated genetic parameters and evaluated the genetic and phenotypic correlations between meat quality characteristics of Nellore cattle evaluated at different anatomical points of the longissimus. Data from 1329 Nellore young bulls were used to evaluate, in the 5th and 12th ribs, marbling score (MAR), shear force (SF), cooking weight losses (CWL) and intramuscular fat (IMF). In addition, the subcutaneous fat thickness was measured at the 12th rib (SFT12) and between the last lumbar and the first sacral vertebrae (SFTLR), in the separation of loin and round. Results yielded moderate heritability coefficients for evaluated characteristics, except CWL. High genetic correlations (0.61) were found between measurements of SFT12 and SFTLR. MAR, IMF and SF were evaluated at the 5th and 12th rib. Meat quality and subcutaneous fat thickness measured at different anatomical points of the longissimus are genetically correlated and can be used in genetic selection programs to improve meat quality characteristics in Nellore cattle.

Genetic trends of abdominal fat content in a male broiler chicken line.

Data of chickens from a broiler-breeding program were collected and used to determine the genetic trends of absolute and relative abdominal fat content. The genetic trends were estimated by the regression of trait genetic value averages on hatch-years. Genetic values from 32,485 individuals were used for regression analysis. The genetic trend estimate for absolute abdominal fat content was +0.39 g per year, indicating that abdominal fat deposition in the analyzed line, in absolute terms, tended to increase, making the existing excess fat deposition in the broilers even worse. However, the genetic trend of relative abdominal fat content was not significant, indicating that there is no increase on abdominal fat content when it is corrected for body weight.

Características de carcaça e qualidade de carne em linhagens da raça Nelore / Carcass and meat quality traits in lineages of Nellore breed

O objetivo deste estudo foi avaliar diferenças entre linhagens da raça Nelore para características de carcaça e qualidade de carne. Foram avaliadas treze linhagens da raça Nelore para as características de peso de carcaça quente, área de olho de lombo, espessura de gordura subcutânea, marmoreio e força de cisalhamento aos 7,14 e 21 dias de maturação. Para isso, foram utilizadas informações fenotípicas de 516 animais da raça Nelore e estimadas as diferenças esperadas na progênie para comparação entre as linhagens. Dentre os genearcas estudados, Golias obteve os melhores valores das diferenças esperadas na progênie para peso de carcaça quente (+1,20kg), área de olho de lombo (+0,88cm), marmoreio (+3,47un) e força de cisalhamento média (-0,09kg) e Akasamu para espessura de gordura subcutânea (+0,05mm). As diferenças entre linhagens da raça Nelore encontradas neste estudo podem ser utilizadas na escolha de touros para melhoria genética de características de carcaça e carne em rebanhos de gado de corte brasileiros.

The aim of this study was to evaluate the differences between lineages of Nellore breed for carcass and meat quality traits. Thirteen lineages of Nellore breed were evaluated from data of carcass and meat quality of 516 animals for estimating the expected progeny difference for hot carcass weight, rib eye area, fat thickness, marbling and shear force values at 7, 14 and 21 days of ageing. The founder Golias reached the better values of expected progeny difference for hot carcass weight (+1.20kg), rib eye area (+0.88cm), marbling (+3.47un) and average shear force (-0,09kg), and Akasamu the better value for fat thickness (+0.05mm). The differences between lineages of Nellore breed found in this study couldbe used to select sires for genetic improvement of carcass and meat quality traits in Brazilian beef cattle herds.

Estimativas de herdabilidade para os escores visuais do coração e do fígado em linhagem macho de frangos / Heritability estimates for heart and liver visual scores in a male broiler line

O objetivo deste estudo foi estimar os coeficientes de herdabilidade para os escores visuais de coração e de fígado em uma linhagem macho de frangos de corte. As análises dos dados foram realizadas através do método da máxima verossimilhança restrita e do método R, utilizando-se informações de 6167 animais. Os escores visuais de coração e de fígado não pareceram ser capazes de apresentar resposta à seleção, tendo em vista as estimativas de herdabilidade obtidas através do método da máxima verossimilhança restrita, que foram de 0,05±0,02 para ambas as características. Possivelmente devido à pouca variabilidade dos dados dos escores visuais de coração e de fígado, as análises realizadas pelo método R não atingiram convergência.

The objective of this study was to estimate the heritability coefficients for heart and liver visual scores in a male broiler line. Dataset analysis was realized by restricted maximum likelihood and by R method. Data from 6167 individuals were used. Heart and liver visual scores did not seem to be able to respond to selection, since the heritability estimates obtained by restricted maximum likelihood were 0,05±0,02 for both traits. Possibly due to the low variability of visual scores data, the analyses by R method did not converge.