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MOTIVATION: We present Link-HD, an approach to integrate multiple datasets. Link-HD is a generalization of 'Structuration des Tableaux A Trois Indices de la Statistique-Analyse Conjointe de Tableaux', a family of methods designed to integrate information from heterogeneous data. Here, we extend the classical approach to deal with broader datasets (e.g. compositional data), methods for variable selection and taxon-set enrichment analysis. RESULTS: The methodology is demonstrated by integrating rumen microbial communities from cows for which methane yield (CH4y) was individually measured. Our approach reproduces the significant link between rumen microbiota structure and CH4 emission. When analyzing the TARA's ocean data, Link-HD replicates published results, highlighting the relevance of temperature with members of phyla Proteobacteria on the structure and functionality of this ecosystem. AVAILABILITY AND IMPLEMENTATION: The source code, examples and a complete manual are freely available in GitHub https://github.com/lauzingaretti/LinkHD and in Bioconductor https://bioconductor.org/packages/release/bioc/html/LinkHD.html.
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Microbiota , Software , Animais , Bovinos , FemininoRESUMO
BACKGROUND: French beef producers suffer from the decrease in profitability of their farms mainly because of the continuous increase in feed costs. Selection for feed efficiency in beef cattle represents a relevant solution to face this problem. However, feed efficiency is a complex trait that can be assessed by three major criteria: residual feed intake (RFI), residual gain (RG) and feed efficiency ratio (FE), which involve different genetic determinisms. An analysis that combines phenotype and whole-genome sequence data provides a unique framework for genomic studies. The aim of our study was to identify the gene networks and the biological processes that are responsible for the genetic determinism that is shared between these three feed efficiency criteria. RESULTS: A population of 1477 French Charolais young bulls was phenotyped for feed intake (FI), average daily gain (ADG) and final weight (FW) to estimate RFI, RG and FE. A subset of 789 young bulls was genotyped on the BovineSNP50 single nucleotide polymorphism (SNP) array and imputed at the sequence level using RUN6 of the 1000 Bull Genomes Project. We conducted a genome-wide association study (GWAS) to estimate the individual effect of 8.5 million SNPs and applied an association weight matrix (AWM) approach to analyse the results, one for each feed efficiency criterion. The results highlighted co-association networks including 626 genes for RFI, 426 for RG and 564 for FE. Enrichment assessment revealed the biological processes that show the strongest association with RFI, RG and FE, i.e. digestive tract (salivary, gastric and mucin secretion) and metabolic processes (cellular and cardiovascular). Energetic functions were more associated with RFI and FE and cardio-vascular and cellular processes with RG. Several hormones such as apelin, glucagon, insulin, aldosterone, the gonadotrophin releasing hormone and the thyroid hormone were also identified, and these should be tested in future studies as candidate biomarkers for feed efficiency. CONCLUSIONS: The combination of network and pathway analyses at the sequence level led to the identification of both common and specific mechanisms that are involved in RFI, RG and FE, and to a better understanding of the genetic determinism underlying these three criteria. The effects of the genes involved in each of the identified processes need to be tested in genomic evaluations to confirm the potential gain in reliability of using functional variants to select animals for feed efficiency.
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Ração Animal , Fenômenos Fisiológicos da Nutrição Animal/genética , Bovinos/genética , Redes Reguladoras de Genes , Animais , Peso Corporal/genética , Bovinos/crescimento & desenvolvimento , Digestão/genética , Ingestão de Alimentos/genética , Metabolismo Energético/genética , Polimorfismo de Nucleotídeo Único , Característica Quantitativa HerdávelRESUMO
Mitigation of greenhouse gas emissions is relevant for reducing the environmental impact of ruminant production. In this study, the rumen microbiome from Holstein cows was characterized through a combination of 16S rRNA gene and shotgun metagenomic sequencing. Methane production (CH4 ) and dry matter intake (DMI) were individually measured over 4-6 weeks to calculate the CH4 yield (CH4 y = CH4 /DMI) per cow. We implemented a combination of clustering, multivariate and mixed model analyses to identify a set of operational taxonomic unit (OTU) jointly associated with CH4 y and the structure of ruminal microbial communities. Three ruminotype clusters (R1, R2 and R3) were identified, and R2 was associated with higher CH4 y. The taxonomic composition on R2 had lower abundance of Succinivibrionaceae and Methanosphaera, and higher abundance of Ruminococcaceae, Christensenellaceae and Lachnospiraceae. Metagenomic data confirmed the lower abundance of Succinivibrionaceae and Methanosphaera in R2 and identified genera (Fibrobacter and unclassified Bacteroidales) not highlighted by metataxonomic analysis. In addition, the functional metagenomic analysis revealed that samples classified in cluster R2 were overrepresented by genes coding for KEGG modules associated with methanogenesis, including a significant relative abundance of the methyl-coenzyme M reductase enzyme. Based on the cluster assignment, we applied a sparse partial least-squares discriminant analysis at the taxonomic and functional levels. In addition, we implemented a sPLS regression model using the phenotypic variation of CH4 y. By combining these two approaches, we identified 86 discriminant bacterial OTUs, notably including families linked to CH4 emission such as Succinivibrionaceae, Ruminococcaceae, Christensenellaceae, Lachnospiraceae and Rikenellaceae. These selected OTUs explained 24% of the CH4 y phenotypic variance, whereas the host genome contribution was ~14%. In summary, we identified rumen microbial biomarkers associated with the methane production of dairy cows; these biomarkers could be used for targeted methane-reduction selection programmes in the dairy cattle industry provided they are heritable.
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Bovinos/metabolismo , Bovinos/microbiologia , Indústria de Laticínios , Trato Gastrointestinal/metabolismo , Trato Gastrointestinal/microbiologia , Metano/biossíntese , Animais , Biomarcadores/metabolismo , DNA Bacteriano/genética , Metagenômica , FenótipoRESUMO
BACKGROUND: Studies to identify markers associated with beef tenderness have focused on Warner-Bratzler shear force (WBSF) but the interplay between the genes associated with WBSF has not been explored. We used the association weight matrix (AWM), a systems biology approach, to identify a set of interacting genes that are co-associated with tenderness and other meat quality traits, and shared across the Charolaise, Limousine and Blonde d'Aquitaine beef cattle breeds. RESULTS: Genome-wide association studies were performed using ~500K single nucleotide polymorphisms (SNPs) and 17 phenotypes measured on more than 1000 animals for each breed. First, this multi-trait approach was applied separately for each breed across 17 phenotypes and second, between- and across-breed comparisons at the AWM and functional levels were performed. Genetic heterogeneity was observed, and most of the variants that were associated with WBSF segregated within rather than across breeds. We identified 206 common candidate genes associated with WBSF across the three breeds. SNPs in these common genes explained between 28 and 30 % of the phenotypic variance for WBSF. A reduced number of common SNPs mapping to the 206 common genes were identified, suggesting that different mutations may target the same genes in a breed-specific manner. Therefore, it is likely that, depending on allele frequencies and linkage disequilibrium patterns, a SNP that is identified for one breed may not be informative for another unrelated breed. Well-known candidate genes affecting beef tenderness were identified. In addition, some of the 206 common genes are located within previously reported quantitative trait loci for WBSF in several cattle breeds. Moreover, the multi-breed co-association analysis detected new candidate genes, regulators and metabolic pathways that are likely involved in the determination of meat tenderness and other meat quality traits in beef cattle. CONCLUSIONS: Our results suggest that systems biology approaches that explore associations of correlated traits increase statistical power to identify candidate genes beyond the one-dimensional approach. Further studies on the 206 common genes, their pathways, regulators and interactions will expand our knowledge on the molecular basis of meat tenderness and could lead to the discovery of functional mutations useful for genomic selection in a multi-breed beef cattle context.
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Bovinos/genética , Estudo de Associação Genômica Ampla/veterinária , Carne Vermelha/análise , Biologia de Sistemas , Animais , Cruzamento , França , Frequência do Gene , Genômica , Genótipo , Desequilíbrio de Ligação/genética , Masculino , Mutação , Fenótipo , Polimorfismo de Nucleotídeo Único , Locos de Características QuantitativasRESUMO
Involuntary temporary feed restriction on commercial cattle is likely to become more frequent with forage shortages in the context of climate change. If general consequences of feed restriction have been the subject of an abundant scientific literature, focus on the inter-individual variability of response is scarce. Here, we explore the response profile in terms of BW, body condition score, milk production, calf weight and cyclicity resumption of 293 lactations from 169 Charolais cows during a winter feed restriction in early lactation and its subsequent recovery at grazing using a principal component analysis followed by a hierarchical clustering on principal component. Results show a very continuous range of response profiles that was divided into three clusters: one with light animals having an intermediate response in terms of milk production and body maintenance, one with animals prioritising body maintenance and cyclicity resumption over milk production and calf weight, and the last one with animals prioritising milk production and calf weight over the rest. Among the animals performing more than one lactation, 57% remain in the same cluster on two successive lactations. This work highlights that an average group response to feed restriction may hide various resilience individual profiles. Further studies are required to determine the existence of a genetic component as well as the consequences of not taking this phenomenon into consideration with the regular use of feed restriction in commercial farms.
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Ração Animal , Lactação , Feminino , Bovinos/genética , Animais , Lactação/fisiologia , Ração Animal/análise , Estações do Ano , Leite , Peso Corporal , Dieta/veterináriaRESUMO
BACKGROUND: Previous research programmes have described muscle biochemical traits and gene expression levels associated with beef tenderness. One of our results concerning the DNAJA1 gene (an Hsp40) was patented. This study aims to confirm the relationships previously identified between two gene families (heat shock proteins and energy metabolism) and beef quality. RESULTS: We developed an Agilent chip with specific probes for bovine muscular genes. More than 3000 genes involved in muscle biology or meat quality were selected from genetic, proteomic or transcriptomic studies, or from scientific publications. As far as possible, several probes were used for each gene (e.g. 17 probes for DNAJA1). RNA from Longissimus thoracis muscle samples was hybridised on the chips. Muscles samples were from four groups of Charolais cattle: two groups of young bulls and two groups of steers slaughtered in two different years. Principal component analysis, simple correlation of gene expression levels with tenderness scores, and then multiple regression analysis provided the means to detect the genes within two families (heat shock proteins and energy metabolism) which were the most associated with beef tenderness. For the 25 Charolais young bulls slaughtered in year 1, expression levels of DNAJA1 and other genes of the HSP family were related to the initial or overall beef tenderness. Similarly, expression levels of genes involved in fat or energy metabolism were related with the initial or overall beef tenderness but in the year 1 and year 2 groups of young bulls only. Generally, the genes individually correlated with tenderness are not consistent across genders and years indicating the strong influence of rearing conditions on muscle characteristics related to beef quality. However, a group of HSP genes, which explained about 40% of the variability in tenderness in the group of 25 young bulls slaughtered in year 1 (considered as the reference group), was validated in the groups of 30 Charolais young bulls slaughtered in year 2, and in the 21 Charolais steers slaughtered in year 1, but not in the group of 19 steers slaughtered in year 2 which differ from the reference group by two factors (gender and year). When the first three groups of animals were analysed together, this subset of genes explained a 4-fold higher proportion of the variability in tenderness than muscle biochemical traits. CONCLUSION: This study underlined the relevance of the GENOTEND chip to identify markers of beef quality, mainly by confirming previous results and by detecting other genes of the heat shock family as potential markers of beef quality. However, it was not always possible to extrapolate the relevance of these markers to all animal groups which differ by several factors (such as gender or environmental conditions of production) from the initial population of reference in which these markers were identified.
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Regulação da Expressão Gênica/fisiologia , Dispositivos Lab-On-A-Chip/veterinária , Carne/normas , Músculo Esquelético/metabolismo , Animais , Biomarcadores , Bovinos , Proteínas de Choque Térmico HSP40/genética , Proteínas de Choque Térmico HSP40/metabolismo , MasculinoRESUMO
Residual feed intake (RFI) is one of the preferred traits for feed efficiency animal breeding. However, RFI measurement is expensive and time-consuming and animal ranking may depend on the nature of the diets. We aimed to explore RFI plasma biomarkers and to unravel the underlying metabolic pathways in yearling bulls fed either a corn-silage diet rich in starch (corn diet) or a grass-silage diet rich in fiber (grass diet). Forty-eight extreme RFI animals (Low-RFI, n = 24, versus High-RFI, n = 24, balanced per diet) were selected from a population of 364 Charolais bulls and their plasma was subjected to a targeted LC-MS metabolomic approach together with classical metabolite and hormonal plasma analyses. Greater lean body mass and nitrogen use efficiency, and lower protein turnover were identified as common mechanisms underlying RFI irrespective of the diet. On the other hand, greater adiposity and plasma concentrations of branched-chain amino acids (BCAA) together with lower insulin sensitivity in High-RFI animals were only observed with corn diet. Conversely, greater plasma concentrations of BCAA and total triglycerides, but similar insulin concentrations were noted in efficient RFI cattle with grass diet. Our data suggest that there are diet-specific mechanisms explaining RFI differences in fattening Charolais yearling bulls.
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Ração Animal/análise , Fenômenos Fisiológicos da Nutrição Animal , Dieta/veterinária , Ingestão de Alimentos , Metaboloma , Poaceae/química , Zea mays/química , Animais , Composição Corporal , Bovinos , Dieta/classificação , Comportamento Alimentar , MasculinoRESUMO
The mutation T3811 â G3811 (TG3811) discovered in the myostatin gene of the Blonde d'Aquitaine breed is suspected of contributing to the outstanding muscularity of this breed. An experiment was designed to estimate the effect of this mutation in an F2 and back-cross Blonde d'Aquitaine × Holstein population. By genotyping all known mutations in the myostatin gene, it was ensured that the TG3811 mutation was indeed the only known mutation segregating in this population. Fifty-six calves (43 F2, 13 back-cross) were intensively fattened and slaughtered at 24.0 ± 1.4 wk of age. The effects of the mutation were estimated by comparing the calves with the [T/T] (n = 18), [T/G] (n = 30), and [G/G] (n = 8) genotypes. Highly significant substitution effects (P < 0.001), above + 1.2 phenotypic SD, were shown on carcass yield and muscularity scores. Birth weight (P < 0.001) was positively affected by the mutation (+0.8 SD) but not growth rate (P = 0.97), while carcass length (P = 0.03), and fatness (P ≤ 0.03) were negatively affected (-0.5 to -0.7 SD). The characteristics of the Triceps brachii muscle were affected by the mutation (P < 0.001), with lower ICDH activity (oxidative) and a higher proportion of myosin type 2X muscle fibers (fast twitch). The effects of the TG3811 mutation were similar to those of other known myostatin mutations, although the Blonde d'Aquitaine animals, which are predominantly [G/G] homozygous, do not exhibit extreme double muscling.
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Miostatina , Carne Vermelha , Animais , Bovinos/genética , Genótipo , Mutação , Miostatina/genética , FenótipoRESUMO
Improving the ability of animals to convert feed resources into food for humans is needed for more sustainable livestock systems. Genetic selection for animals eating less while maintaining their performance (i.e., low residual feed intake [RFI]) appears a smart strategy but its effectiveness relies on high-throughput animal phenotyping. Here, we explored plasma nitrogen (N) isotope ratios in an attempt to identify easily superior young bulls in terms of RFI. For this, 48 Charolais young bulls fed two contrasting diets (corn vs. grass silage diets) were selected from a larger population as extreme RFI animals (24 low-RFI vs. 24 high-RFI) and their plasma analyzed for natural 15N abundance (δ15N) in the whole protein (bulk protein) and in the individual protein-bound amino acids (PbAA). For the first time, we showed that the δâ15N in plasma bulk protein differed (P = 0.007) between efficient (low-RFI) and inefficient (high-RFI) cattle regardless of diet. Furthermore, most analyzed PbAA followed the same trend as the bulk protein, with lower (P < 0.05) δâ15N values in more efficient (low-RFI) compared with less efficient (high-RFI) cattle, again regardless of diet. The only three exceptions were Phe, Met, and Lys (P > 0.05) for which the first metabolic reaction before being catabolized does not involve transamination, a pathway known naturally to enrich AAs in 15N. The contrasted isotopic signatures across RFI groups only in those PbAA undergoing transamination are interpreted as differences in transamination rates and N-use efficiency between low- and high-RFI phenotypes. Natural isotopic N signatures in bulk proteins and specific PbAA can be proposed as biomarkers of RFI in growing beef cattle fed different diets. However, the current study cannot delineate whether this effect only occurs post-absorption or to some extent also in the rumen. Our data support the conclusion that most efficient cattle in terms of RFI upregulate N conservation mechanisms compared with less efficient cattle and justify future research on this topic.
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Aminoácidos/química , Aminoácidos/metabolismo , Ração Animal/análise , Bovinos/fisiologia , Dieta/veterinária , Comportamento Alimentar , Isótopos de Nitrogênio/química , Animais , Masculino , Rúmen/metabolismo , Silagem/análiseRESUMO
Inbreeding and effective population size (Ne) are fundamental indicators for the management and conservation of genetic diversity in populations. Genomic inbreeding gives accurate estimates of inbreeding, and the Ne determines the rate of the loss of genetic variation. The objective of this work was to study the distribution of runs of homozygosity (ROHs) in order to estimate genomic inbreeding (FROH) and an effective population size using 38,789 Single Nucleotide Polymorphisms (SNPs) from the Illumina Bovine 50K BeadChip in 86 samples from populations of Charolais de Cuba (n = 40) cattle and to compare this information with French (n = 20) and British Charolais (n = 26) populations. In the Cuban, French, and British Charolais populations, the average estimated genomic inbreeding values using the FROH statistics were 5.7%, 3.4%, and 4%, respectively. The dispersion measured by variation coefficient was high at 43.9%, 37.0%, and 54.2%, respectively. The effective population size experienced a very similar decline during the last century in Charolais de Cuba (from 139 to 23 individuals), in French Charolais (from 142 to 12), and in British Charolais (from 145 to 14) for the ~20 last generations. However, the high variability found in the ROH indicators and FROH reveals an opportunity for maintaining the genetic diversity of this breed with an adequate mating strategy, which can be favored with the use of molecular markers. Moreover, the detected ROH were compared to previous results obtained on the detection of signatures of selection in the same breed. Some of the observed signatures were confirmed by the ROHs, emphasizing the process of adaptation to tropical climate experienced by the Charolais de Cuba population.
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To analyse the effects of genetic selection in favour of high muscle development on muscle gene expression, oligonucleotide microarrays were used to compare the transcriptome of Longissimusthoracis muscle from 15- and 19-month-old Charolais bull calves divergently selected for high (H) or low (L) muscle growth. Transcriptome data revealed that about two thirds of the genes involved in glycolysis were up-regulated at 15 and at 19months of age in H animals. Lastly, some differentially expressed genes were associated with muscle mass in the carcass (FGF6, PLD2) independently of fat deposition and meat quality. Selection for muscle growth potential is associated with modified expression of some genes involved in growth, and also with increased expression of genes involved in glycolysis. Furthermore, this change in muscle metabolism is likely to be dissociated from fat deposition and beef quality, providing new criteria for genetic selection in favour of muscle growth.
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Reducing enteric methane production and improving the feed efficiency of heifers on roughage diets are important selection objectives for sustainable beef production. The objective of the current study was to assess the relationship between different methane production and feed efficiency criteria of beef heifers fed ad libitum roughage diets. A total of 326 Charolais heifers aged 22 months were controlled in two farms and fed either a grass silage (n = 252) or a natural meadow hay (n = 74) diet. Methane (CH4) and carbon dioxide (CO2) emission rates (g/day) were measured with GreenFeed systems. The dry matter intake (DMI), average daily gain (ADG), CH4 and CO2 were measured over 8 to 12 weeks. Positive correlations were observed among body weight, DMI, ADG, CH4 and CO2. The residual feed intake (rwgDMI) was not related to CH4 or residual methane (rwiCH4). It was negatively correlated with methane yield (CH4/DMI): Rp = -0.87 and -0.83. Residual gain (rwiADG) and ADG/DMI were weakly and positively related to residual methane (rwiCH4): Rp = 0.21 on average. The ratio ADG/CO2 appeared to be a useful proxy of ADG/DMI (Rp = 0.64 and 0.97) and CH4/CO2 a proxy of methane yield (Rp = 0.24 and 0.33) for selecting low-emitting and efficient heifers.
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Improving feed efficiency is of interest to French beef producers so as to increase their profitability. To enable this improvement through selection, genetic correlations with production traits need to be quantified. The objective of this study was to estimate the genetic parameters for growth, feed efficiency (FE), and slaughter performance of young beef bulls of the French Charolais breed. Three feed efficiency criteria were calculated: residual feed intake (RFI), residual gain (RG), and ratio of FE. Data on feed intake, growth, and FE were available for 4,675 Charolais bulls tested in performance test stations and fed with pelleted diet. Between 1985 and 1989, 60 among 510 of these bulls were selected to procreate one generation of 1,477 progeny bulls which received the same pelleted diet at the experimental farm in Bourges. In addition to feed intake, growth, and FE traits, these terminal bulls also had slaughter traits of carcass yield, carcass composition, and weight of visceral organs collected. Genetic parameters were estimated using linear mixed animal models. Between performance test bulls and terminal bulls, the genetic correlation of RFI was 0.80 ± 0.18; it was 0.70 ± 0.21 for RG and 0.46 ± 0.20 for FE. For carcass traits, RFI was negatively correlated with carcass yield (-0.18 ± 0.14) and muscle content (-0.47 ± 0.14) and positively with fat content (0.48 ± 0.13). Conversely, RG and FE were positively correlated with carcass yield and muscle content and negatively with fat content. For the three FE criteria, efficient animals had leaner carcass. For visceral organs (as a proportion of empty body weight), RFI was genetically correlated with the proportions of the 5th quarter (0.51 ± 0.17), internal fat (0.36 ± 0.14), abomasum (0.46 ± 0.20), intestines (0.38 ± 0.17), liver (0.36 ± 0.16), and kidneys (0.73 ± 0.11). Conversely, RG and FE were negatively associated with these traits. The high-energy expenditure associated with the high-protein turnover in visceral organs may explain this opposite relationship between FE and the proportion of visceral organs. Selection for final weight and RFI increased growth and FE in progeny, and also improved carcass yield and muscle content in the carcass. To conclude, determinations of growth and feed intake in performance test stations are effective to select bulls to improve their growth, FE, and muscle content in carcass.
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Ração Animal/análise , Bovinos/fisiologia , Ingestão de Alimentos , Metabolismo Energético , Animais , Composição Corporal , Peso Corporal , Bovinos/genética , Bovinos/crescimento & desenvolvimento , Dieta/veterinária , Modelos Lineares , Masculino , FenótipoRESUMO
Residual energy intake (REI) on two successive diets (hay and maize based) and slaughter traits, including visceral organs, were phenotyped in 584 adult purebred Charolais cows. To investigate the relationships between these traits and their genetic determinism, we first estimated the genetic parameters, including correlations, using REML modeling under WOMBAT software. The animals were then genotyped on the BovineSNP50 SNPchip before being imputed to the 600K density and genome wide association study was performed with GCTA software. We found low heritability for REI (h2 = 0.12 in each of the diet phases). Although the phenotypic correlation between the two diet phases was moderate (0.36), the genetic correlation was high (0.83), indicating a common genetic determinism for feed efficiency regardless of the diet. Correlations between REI and slaughter traits were negative regarding muscle-related traits and positive for fat-related traits, indicating that efficient animals generally had a more muscular carcass. It was also seen that feed efficiency was genetically and phenotypically correlated with smaller organs when expressed as a proportion of their empty body weight. From the GWAS analysis, seven QTLs were found to be associated with a trait at the genome-wide level of significance and 18 others at the chromosome-wide level. One important QTL was detected in BTA 2, reflecting the essential effect of the myostatin gene on both carcass composition and relative organ weight. Three QTLs were detected for REI during the maize diet phase on BTA 13, 19, and 28, the latter being significant at the genome-wide level. The QTLs on BTA 19 mapped into the TANC2 gene and the QTLs on BTA 28 into the KIF1BP gene, which are both known to interact with the same protein (KIF1A). However, no obvious functional link between these genes and feed efficiency could be made. Among the other QTLs detected, one association on BTA 4 with liver proportion mapped to the candidate gene WASL, which has previously been shown to be differentially expressed in liver cells and linked to feed restriction or cancer development. No QTLs were found to be common between feed efficiency and any slaughter traits.
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Ração Animal/análise , Bovinos/genética , Ingestão de Energia , Estudo de Associação Genômica Ampla/veterinária , Locos de Características Quantitativas/genética , Animais , Bovinos/fisiologia , Dieta/veterinária , Ingestão de Alimentos , Feminino , Genótipo , FenótipoRESUMO
In this study, we used BovineSNP50 Genotyping BeadChip data to estimate the structure, putative ancestral origin as well as to identify regions with selective sweeps that may have had an important role in the adaptation to tropical conditions of the 'Charolais de Cuba' (CHCU) breed. According to a principal component analysis, CHCU samples cluster together with taurine breeds with an estimated 93% of taurus ancestral alleles. Despite the short period since importation, we detected differentiation (Fst = 0.049) between the French Charolaise (CHA) and CHCU. However, CHA breed was the closest breed to CHCU followed by other hybrids breed with a clear CHA origin. Linkage disequilibrium (r2) decay tends to be lower in CHCU compared to CHA probably due to a less intense artificial selection programs of CHCU. Signals of recent adaptation to tropical conditions between CHCU and CHA were identified. Genes mapping within those regions reflect different functions related to immunity, metabolic changes and heat tolerance (CHCU) and muscle development and meat quality (CHA) that may have had an important role in the phenotypic differentiation of these breeds. Further studies will expand our knowledge on the molecular basis of adaptation of cattle to tropical conditions and molecular process associated with meat quality traits.
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Cruzamento/normas , Filogeografia , Carne Vermelha/normas , Seleção Genética/genética , Animais , Biodiversidade , Bovinos , Cuba , França , Desequilíbrio de Ligação/genética , FenótipoRESUMO
In the current study the collagen, texture, and sensory characteristics of meat from 712 yearling males of 10 local Spanish and French beef breeds raised in their typical production systems were described. The breed-production system affected collagen and texture variables but affected sensory variables only slightly. There was a large amount of intra breed-production system variation for all the variables. French breeds had lower values for collagen solubility (~12%) than Spanish breeds (~40%). Stress (WB) varied from 36 N/cm2 in Casina to 44 N/cm2 in Salers, whereas compression stress at 80% ranged from 35 N/cm2 in Asturiana de los Valles to 40 N/cm2 in Salers. Oven cooking resulted in higher cooking losses (24%) than cooking on a grill (12%). Cooking losses increased as the grill temperature increased. Numerous significant correlations were found among variables. Carcass weight is associated with all the collagen and texture variables. Correlation coefficients among texture and collagen variables were statistically significant and these correlation coefficients were in general higher for solubility percentage than for total collagen content, highlighting the importance of the solubility of collagen rather than total collagen in determining meat textural properties. PRACTICAL APPLICATIONS: To differentiate a product in the market, it is necessary to define its characteristics. Differentiation allows increasing the added value of products and, therefore, income of the farmers. In addition, it guarantees to the consumers that the product they purchase has the intrinsic and extrinsic quality features that they seek. For consumers, beef texture is one of the most important quality attributes sought, therefore, studying factors that can affect beef texture is a major interest for the industry.
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Colágeno/análise , Culinária , Carne Vermelha/análise , Animais , Cruzamento , Bovinos , Europa (Continente) , Qualidade dos Alimentos , MasculinoRESUMO
To identify new molecular markers of beef sensory quality, the transcriptomes of Longissimus thoracis muscle from 25 Charolais bull calves were analyzed using microarrays and compared between high and low meat quality groups; 215 genes were differentially expressed according to tenderness, juiciness, and/or flavor. Among these, 23 were up-regulated in the tenderest, juiciest, and tastiest meats, and 18 were highly correlated with both flavor and juiciness (e.g., PRKAG1), explaining up to 60% of their variability. Nine were down-regulated in the same meats, but only DNAJA1 [the results relating to DNAJA1 and its relationship with tenderness have been patented (Genomic marker for meat tenderness; Patent EP06300943.5, September 12, 2006)], which encodes a heat shock protein, showed a strong negative correlation with tenderness that alone explained 63% of its variability. This protein, known for its anti-apoptotic role, could be involved in meat aging. Thus, DNAJA1 could constitute a new marker of beef sensory quality.
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Bovinos/genética , Proteínas de Choque Térmico/genética , Carne/análise , Sensação , Animais , Expressão Gênica , Humanos , Masculino , Análise em Microsséries , Músculos/química , Controle de QualidadeRESUMO
Bidirectional promoters are regulatory regions co-regulating the expression of two neighbouring genes organized in a head-to-head orientation. In recent years, these regulatory regions have been studied in many organisms; however, no investigation to date has been done to analyse the genetic variation of the activity of this type of promoter regions. In our study, we conducted an investigation to first identify bidirectional promoters sharing genes expressed in bovine Longissimus thoracis and then to find genetic variants affecting the activity of some of these bidirectional promoters. Combining bovine gene information and expression data obtained using RNA-Seq, we identified 120 putative bidirectional promoters active in bovine muscle. We experimentally validated in vitro 16 of these bidirectional promoters. Finally, using gene expression and whole-genome genotyping data, we explored the variability of the activity in muscle of the identified bidirectional promoters and discovered genetic variants affecting their activity. We found that the expression level of 77 genes is correlated with the activity of 12 bidirectional promoters. We also identified 57 single nucleotide polymorphisms associated with the activity of 5 bidirectional promoters. To our knowledge, our study is the first analysis in any species of the genetic variability of the activity of bidirectional promoters.
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Músculos do Dorso/metabolismo , Regulação da Expressão Gênica , Polimorfismo de Nucleotídeo Único , Regiões Promotoras Genéticas , Proteínas/genética , Animais , Bovinos , Perfilação da Expressão Gênica , Masculino , Projetos PilotoRESUMO
This work aimed to investigate the consequences of muscle growth selection on muscle characteristics. An oxidative muscle (Rectus abdominis, RA) and a glycolytic one (Semitendinosus, ST) were studied in two groups of six extreme young Charolais bulls of high or low muscle growth. Mitochondrial activity was lower in muscles of bulls with high muscle growth. Transcriptomic studies allowed the identification of putatively differentially expressed genes. The differential expression between genetic types of two genes in RA (a heat shock protein and a thyroid receptor interacting protein) and of seven genes in ST (including LEU5, tropomyosin 2, and sarcosin) was confirmed by different statistical approaches or Northern blot analysis, as well as the differential expression of five genes (including PSMD4 and DPM synthase) between RA and ST. Both biochemical and transcriptomic results indicate that selection on muscle growth potential is associated with reduced slow-oxidative muscle characteristics. Further studies are required to understand the physiological importance of genes whose expression is changed by selection.
RESUMO
Myostatin is essential for proper regulation of myogenesis, and inactivation of Myostatin results in muscle hypertrophy. Here, we identified an unexpected mutation in the myostatin gene which is almost fixed in Blonde d'Aquitaine cattle. In skeletal muscle, the mutant allele was highly expressed leading to an abnormal transcript consisting of a 41-bp inclusion and premature termination codons and to residual levels of a correctly spliced transcript. This expression pattern, caused by a leaky intronic mutation with regard to spliceosome activity and its apparent stability with regard to surveillance mechanisms, could contribute to the moderate muscle hypertrophy in this cattle breed. This finding is of importance for genetic counseling for meat quantity and quality in livestock production and possibly to manipulate myostatin pre-mRNA in human muscle diseases.