New residual feed intake criterion for longitudinal data.

BACKGROUND: Residual feed intake (RFI) is one measure of feed efficiency, which is usually obtained by multiple regression of feed intake (FI) on measures of production, body weight gain and tissue composition. If phenotypic regression is used, the resulting RFI is generally not genetically independent of production traits, whereas if RFI is computed using genetic regression coefficients, RFI and production traits are independent at the genetic level. The corresponding regression coefficients can be easily derived from the result of a multiple trait model that includes FI and production traits. However, this approach is difficult to apply in the case of multiple repeated measurements of FI and production traits. To overcome this difficulty, we used a structured antedependence approach to account for the longitudinality of the data with a phenotypic regression model or with different genetic and environmental regression coefficients [multi- structured antedependence model (SAD) regression model]. RESULTS: After demonstrating the properties of RFI obtained by the multi-SAD regression model, we applied the two models to FI and production traits that were recorded for 2435 French Large White pigs over a 10-week period. Heritability estimates were moderate with both models. With the multi-SAD regression model, heritability estimates were quite stable over time, ranging from 0.14 ± 0.04 to 0.16 ± 0.05, while heritability estimates showed a U-shaped profile with the phenotypic regression model (ranging from 0.19 ± 0.06 to 0.28 ± 0.06). Estimates of genetic correlations between RFI at different time points followed the same pattern for the two models but higher estimates were obtained with the phenotypic regression model. Estimates of breeding values that can be used for selection were obtained by eigen-decomposition of the genetic covariance matrix. Correlations between these estimated breeding values obtained with the two models ranged from 0.66 to 0.83. CONCLUSIONS: The multi-SAD model is preferred for the genetic analysis of longitudinal RFI because, compared to the phenotypic regression model, it provides RFI that are genetically independent of production traits at all time points. Furthermore, it can be applied even when production records are missing at certain time points.

Identification of genomic regions affecting production traits in pigs divergently selected for feed efficiency.

BACKGROUND: Feed efficiency is a major driver of the sustainability of pig production systems. Understanding the biological mechanisms that underlie these agronomic traits is an important issue for environment questions and farms' economy. This study aimed at identifying genomic regions that affect residual feed intake (RFI) and other production traits in two pig lines divergently selected for RFI during nine generations (LRFI, low RFI; HRFI, high RFI). RESULTS: We built a whole dataset of 570,447 single nucleotide polymorphisms (SNPs) in 2426 pigs with records for 24 production traits after both imputation and prediction of genotypes using pedigree information. Genome-wide association studies (GWAS) were performed including both lines (global-GWAS) or each line independently (LRFI-GWAS and HRFI-GWAS). Forty-five chromosomal regions were detected in the global-GWAS, whereas 28 and 42 regions were detected in the HRFI-GWAS and LRFI-GWAS, respectively. Among these 45 regions, only 13 were shared between at least two analyses, and only one was common between the three GWAS but it affects different traits. Among the five quantitative trait loci (QTL) detected for RFI, two were close to QTL for meat quality traits and two pinpointed novel genomic regions that harbor candidate genes involved in cell proliferation and differentiation processes of gastrointestinal tissues or in lipid metabolism-related signaling pathways. In most cases, different QTL regions were detected between the three designs, which suggests a strong impact of the dataset structure on the detection power and could be due to the changes in allelic frequencies during the establishment of lines. CONCLUSIONS: In addition to efficiently detecting known and new QTL regions for feed efficiency, the combination of GWAS carried out per line or simultaneously using all individuals highlighted chromosomal regions that affect production traits and presented significant changes in allelic frequencies across generations. Further analyses are needed to estimate whether these regions correspond to traces of selection or result from genetic drift.

Assessment of trade-offs between feed efficiency, growth-related traits, and immune activity in experimental lines of layer chickens.

BACKGROUND: In all organisms, life-history traits are constrained by trade-offs, which may represent physiological limitations or be related to energy resource management. To detect trade-offs within a population, one promising approach is the use of artificial selection, because intensive selection on one trait can induce unplanned changes in others. In chickens, the breeding industry has achieved remarkable genetic progress in production and feed efficiency over the last 60 years. However, this may have been accomplished at the expense of other important biological functions, such as immunity. In the present study, we used three experimental lines of layer chicken-two that have been divergently selected for feed efficiency and one that has been selected for increased antibody response to inactivated Newcastle disease virus (ND3)-to explore the impact of improved feed efficiency on animals' immunocompetence and, vice versa, the impact of improved antibody response on animals' growth and feed efficiency. RESULTS: There were detectable differences between the low (R+) and high (R-) feed-efficiency lines with respect to vaccine-specific antibody responses and counts of monocytes, heterophils, and/or T cell population. The ND3 line presented reduced body weight and feed intake compared to the control line. ND3 chickens also demonstrated an improved antibody response against a set of commercial viral vaccines, but lower blood leucocyte counts. CONCLUSIONS: This study demonstrates the value of using experimental chicken lines that are divergently selected for RFI or for a high antibody production, to investigate the modulation of immune parameters in relation to growth and feed efficiency. Our results provide further evidence that long-term selection for the improvement of one trait may have consequences on other important biological functions. Hence, strategies to ensure optimal trade-offs among competing functions will ultimately be required in multi-trait selection programs in livestock.

Genetic parameters and genomic prediction for feed intake recorded at the group and individual level in different production systems for growing pigs.

BACKGROUND: In breeding programs, recording large-scale feed intake (FI) data routinely at the individual level is costly and difficult compared with other production traits. An alternative approach could be to record FI at the group level since animals such as pigs are normally housed in groups and fed by a shared feeder. However, to date there have been few investigations about the difference between group- and individual-level FI recorded in different environments. We hypothesized that group- and individual-level FI are genetically correlated but different traits. This study, based on the experiment undertaken in purebred DanBred Landrace (L) boars, was set out to estimate the genetic variances and correlations between group- and individual-level FI using a bivariate random regression model, and to examine to what extent prediction accuracy can be improved by adding information of individual-level FI to group-level FI for animals recorded in groups. For both bivariate and univariate models, single-step genomic best linear unbiased prediction (ssGBLUP) and pedigree-based BLUP (PBLUP) were implemented and compared. RESULTS: The variance components from group-level records and from individual-level records were similar. Heritabilities estimated from group-level FI were lower than those from individual-level FI over the test period. The estimated genetic correlations between group- and individual-level FI based on each test day were on average equal to 0.32 (SD = 0.07), and the estimated genetic correlation for the whole test period was equal to 0.23. Our results demonstrate that by adding information from individual-level FI records to group-level FI records, prediction accuracy increased by 0.018 and 0.032 compared with using group-level FI records only (bivariate vs. univariate model) for PBLUP and ssGBLUP, respectively. CONCLUSIONS: Based on the current dataset, our findings support the hypothesis that group- and individual-level FI are different traits. Thus, the differences in FI traits under these two feeding systems need to be taken into consideration in pig breeding programs. Overall, adding information from individual records can improve prediction accuracy for animals with group records.

Research progress on the regulation of nutrition and immunity by microRNAs in fish.

MicroRNAs (miRNAs) are a class of highly conserved, endogenous non-coding single-stranded small RNA molecules with a length of 18-25 nucleotides. MiRNAs can negatively regulate the target gene through complementary pairing with the mRNA. It has been more than 20 years since the discovery of miRNA molecules, and many achievements have been made in fish research. This paper reviews the research progress in the regulation of fish nutrition and immunity by miRNAs in recent years. MiRNAs regulate the synthesis of long-chain polyunsaturated fatty acids, and are involved in the metabolism of glucose, lipids, as well as cholesterol in fish. Moreover, miRNAs play various roles in antibacterial and antiviral immunity of fish. They can promote the immune response of fish, but may also participate in the immune escape mechanism of bacteria or viruses. One important aspect of miRNAs regulation on fish immunity is mediated by targeting pattern recognition receptors and downstream signaling factors. Together, current results indicate that miRNAs are widely involved in the complex regulatory network of fish. Further studies on fish miRNAs may deepen our understanding of the regulatory network of fish nutrition and immunity, and have the potential to promote the development of microRNA-based products and detection reagents that can be applied in aquaculture industry.

Effects of dried natto diet on the transcript levels of the peroxisome proliferator-activated receptor-γ, coactivator-1α and -1ß, and nuclear receptor corepressor 1 genes in laying hens.

The effects of natto, a fermented soybean food, on transcript levels of hen peroxisome proliferator-activated receptor-γ (PPARG), PPARG coactivator-1α and -1ß (PPARGC1A and PPARGC1B), and nuclear receptor corepressor 1 (NCOR1) were investigated using real-time polymerase chain reaction in white leghorn (Julia strain) hens. Twenty-one- and 34-week-old hens were fed a basic or 3% dried natto-supplemented diet for 8 weeks. In the 21- and 34-week-old hens fed the natto-supplemented diet, hepatic PPARGC1B and NCOR1 transcript levels and adipose and hepatic PPARG transcript levels were significantly lower, respectively, than those in the control group. Furthermore, 34- and 42-week-old hens were fed a basic diet supplemented with 3% of the protein/fiber-enriched fraction (PFB) or 0.6% of the fat-enriched fraction (FAT) of natto, respectively, for 8 weeks. Adipose PPARG transcript levels were higher in the FAT diet group and significantly lower in the PFB diet group than in the control group. However, both FAT and PFB diet groups showed significantly lower hepatic PPARG transcript levels than did the control group. These results suggest that dried natto influences the transcript levels of PPARG, PPARGC1B, and NCOR1, and the FAT and PFB of natto influence the adipose and hepatic PPARG transcript levels in hens.

Chronic Effects of a High Sucrose Diet on Murine Gastrointestinal Nutrient Sensor Gene and Protein Expression Levels and Lipid Metabolism.

The gastrointestinal tract (GIT) plays a key role in regulating nutrient metabolism and appetite responses. This study aimed to identify changes in the GIT that are important in the development of diet related obesity and diabetes. GIT samples were obtained from C57BL/6J male mice chronically fed a control diet or a high sucrose diet (HSD) and analysed for changes in gene, protein and metabolite levels. In HSD mice, GIT expression levels of fat oxidation genes were reduced, and increased de novo lipogenesis was evident in ileum. Gene expression levels of the putative sugar sensor, slc5a4a and slc5a4b, and fat sensor, cd36, were downregulated in the small intestines of HSD mice. In HSD mice, there was also evidence of bacterial overgrowth and a lipopolysaccharide activated inflammatory pathway involving inducible nitric oxide synthase (iNOS). In Caco-2 cells, sucrose significantly increased the expression levels of the nos2, iNOS and nitric oxide (NO) gas levels. In conclusion, sucrose fed induced obesity/diabetes is associated with changes in GI macronutrient sensing, appetite regulation and nutrient metabolism and intestinal microflora. These may be important drivers, and thus therapeutic targets, of diet-related metabolic disease.

Gene networks for three feed efficiency criteria reveal shared and specific biological processes.

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.

Genomic regions and signaling pathways associated with indicator traits for feed efficiency in juvenile Atlantic salmon (Salmo salar).

BACKGROUND: One objective of this study was to identify putative quantitative trait loci (QTL) that affect indicator phenotypes for growth, nitrogen, and carbon metabolism in muscle, liver, and adipose tissue, and for feed efficiency. Another objective was to perform an RNAseq analysis (184 fish from all families), to identify genes that are associated with carbon and nitrogen metabolism in the liver. The material consisted of a family experiment that was performed in freshwater and included 2281 individuals from 23 full-sib families. During the 12-day feed conversion test, families were randomly allocated to family tanks (50 fish per tank and 2 tanks per family) and fed a fishmeal-based diet labeled with the stable isotopes 15N and 13C at inclusion levels of 2 and 1%, respectively. RESULTS: Using a linear mixed-model algorithm, a QTL for pre-smolt growth was identified on chromosome 9 and a QTL for carbon metabolism in the liver was identified on chromosome 12 that was closely related to feed conversion ratio on a tank level. For the indicators of feed efficiency traits that were derived from the stable isotope ratios (15N and 13C) of muscle tissue and growth, no convincing QTL was detected, which suggests that these traits are polygenic. The transcriptomic analysis showed that high carbon and nitrogen metabolism was associated with individuals that convert protein from the feed more efficiently, primarily due to higher expression of the proteasome, lipid, and carbon metabolic pathways in liver. In addition, we identified seven transcription factors that were associated with carbon and nitrogen metabolism and located in the identified QTL regions. CONCLUSIONS: Analyses revealed one QTL associated with pre-smolt growth and one QTL for carbon metabolism in the liver. Both of these traits are associated with feed efficiency. However, more accurate mapping of the putative QTL will require a more diverse family material. In this experiment, fish that have a high carbon and nitrogen metabolism in the liver converted protein from the feed more efficiently, potentially because of a higher expression of the proteasome, lipid, and carbon metabolic pathways in liver. Within the QTL regions, we detected seven transcription factors that were associated with carbon and nitrogen metabolism.

Development and comparison of RNA-sequencing pipelines for more accurate SNP identification: practical example of functional SNP detection associated with feed efficiency in Nellore beef cattle.

BACKGROUND: Optimization of an RNA-Sequencing (RNA-Seq) pipeline is critical to maximize power and accuracy to identify genetic variants, including SNPs, which may serve as genetic markers to select for feed efficiency, leading to economic benefits for beef production. This study used RNA-Seq data (GEO Accession ID: PRJEB7696 and PRJEB15314) from muscle and liver tissue, respectively, from 12 Nellore beef steers selected from 585 steers with residual feed intake measures (RFI; n = 6 low-RFI, n = 6 high-RFI). Three RNA-Seq pipelines were compared including multi-sample calling from i) non-merged samples; ii) merged samples by RFI group, iii) merged samples by RFI and tissue group. The RNA-Seq reads were aligned against the UMD3.1 bovine reference genome (release 94) assembly using STAR aligner. Variants were called using BCFtools and variant effect prediction (VeP) and functional annotation (ToppGene) analyses were performed. RESULTS: On average, total reads detected for Approach i) non-merged samples for liver and muscle, were 18,362,086.3 and 35,645,898.7, respectively. For Approach ii), merging samples by RFI group, total reads detected for each merged group was 162,030,705, and for Approach iii), merging samples by RFI group and tissues, was 324,061,410, revealing the highest read depth for Approach iii). Additionally, Approach iii) merging samples by RFI group and tissues, revealed the highest read depth per variant coverage (572.59 ± 3993.11) and encompassed the majority of localized positional genes detected by each approach. This suggests Approach iii) had optimized detection power, read depth, and accuracy of SNP calling, therefore increasing confidence of variant detection and reducing false positive detection. Approach iii) was then used to detect unique SNPs fixed within low- (12,145) and high-RFI (14,663) groups. Functional annotation of SNPs revealed positional candidate genes, for each RFI group (2886 for low-RFI, 3075 for high-RFI), which were significantly (P < 0.05) associated with immune and metabolic pathways. CONCLUSION: The most optimized RNA-Seq pipeline allowed for more accurate identification of SNPs, associated positional candidate genes, and significantly associated metabolic pathways in muscle and liver tissues, providing insight on the underlying genetic architecture of feed efficiency in beef cattle.

Transcriptome sequencing of Coccinella septempunctata adults (Coleoptera: Coccinellidae) feeding on artificial diet and Aphis craccivora.

BACKGROUND: The insect predator Coccinella septempunctata can effectively control many types of pests, such as aphids, whiteflies, and small lepidopteran larvae. We previously found that C. septempunctata fed an artificial diet showed diminished biological properties(e.g. fecundity, egg hatching rate, survival rate, etc.) compared with those fed natural prey (Aphis craccivora), likely due to different nutritional characteristics of the diet. In this study, we used transcriptome sequencing analysis to identify nutrition- and metabolism-related genes of C. septempunctata that were differentially expressed depending on diet. METHODOLOGY/PRINCIPAL FINDINGS: The Illumina HiSeq2000 was used to sequence 691,942,058 total clean reads from artificial diet-fed and A. craccivora-fed C. septempunctata libraries, and the clean reads were assembled using Trinity de novo software (Tabel 2). Comparison of transcriptome sequences revealed that expression of 38,315 genes was affected by the artificial diet, and 1,182 of these genes showed a significant change in expression levels (FDR ≤ 0.05,|log2FC|≥1, "FC" stands for "fold change"). These differentially expressed genes (DEGs) were likely associated with the decreased egg laying capacity, hatching rate, longevity, and increased sex ratio (♀:♂) of adult C. septempunctata observed in the group fed the artificial diet. Furthermore, in the most DEGs metabolic pathways for C. septempunctata feeding on the artificial diet accumulated amino acid metabolic pathways, lipid metabolic pathways, and starch and glucose metabolism were down-regulated. CONCLUSIONS/SIGNIFICANCE: We found some differentially expressed genes and metabolic pathways are related to nutrition, from which a more informative feedback for diet formulation was obtained and the artificial diet could be more efficiently optimized.

Effects of in ovo feeding of vitamin C on post-hatch performance, immune status and DNA methylation-related gene expression in broiler chickens.

This study aimed to evaluate the effect of in ovo feeding (IOF) of vitamin C at embryonic age 11 (E11) on post-hatch performance, immune status and DNA methylation-related gene expression in broiler chickens. A total of 240 Arbor Acres breeder eggs (63 (sem 0·5) g) were randomly divided into two groups: normal saline and vitamin C (VC) groups. After incubation, newly hatched chicks from each group were randomly divided into six replicates with ten chicks per replicate. Hatchability, average daily feed intake (D21-42 and D1-42), and average daily gain and feed conversion ratio (D1-21) were improved by vitamin C treatment (P < 0·05). IOF of vitamin C increased vitamin C content (D1), total antioxidant capacity (D42), IgA (D1), IgM (D1 and D21), stimulation index for T lymphocyte (D35) and lysozyme activity (D21) in plasma (P < 0·05). On D21, vitamin C increased the splenic expression of IL-4 and DNMT1 and decreased IL-1ß, Tet2, Tet3 and Gadd45ß expression (P < 0·05). On D42, vitamin C increased the splenic expression of IL-4 and DNMT3A and decreased IFN-γ, Tet3, MBD4 and TDG expression (P < 0·05). In conclusion, the vitamin C via in ovo injection can be absorbed by broiler's embryo and IOF of vitamin C at E11 improves the post-hatch performance and immune status and, to some extent, the antioxidant capacity of broiler chickens. The expression of enzyme-related DNA methylation and demethylation indicates that the level of DNA methylation may increase in spleen in the VC group and whether the fluctuating expression of pro- and anti-inflammatory cytokines is related to DNA methylation change remained to be further investigated.

Effects of 25-hydroxycholecalciferol supplementation in maternal diets on reproductive performance and the expression of genes that regulate lactation in sows.

One hundred Yorkshire × Landrace sows were randomly assigned to one of two dietary treatments (diet ND: 6,000 IU vitamin D3 /d feed; diet 25-D: 200 µg/day 25OHD3 feed). The experiment began on d 90 of gestation and continued until weaning on day 21 of lactation. In sows that received 25OHD3 , the growth rate of the piglets before weaning was significantly accelerated (0.266 kg/day, p < .05). Sow serum was collected after weaning, and those in the 25OHD3 group were found to have significantly higher serum calcium (CA) and phosphorus (PI) levels (p < .05). Interestingly, the oestrus cycle of sows fed 25OHD3 was significantly shortened (p < .05), the oestrus time was concentrated on the fifth day after weaning, and the piglets were born with a higher degree of uniformity (p < .05). Colostrum was collected on the day of delivery, and the colostrum of sows fed 25OHD3 contained higher milk fat content than the control group (p < .05). 25OHD3 supplementation increased the mRNA and protein expression of INSIG1 and SREBP1, which regulate milk fat synthesis, in the mammary gland of lactating sows (p < .05). In conclusion, 25OHD3 supplementation in maternal diets improved reproductive performance, milk fat content and the mRNA and protein levels of genes regulating milk fat synthesis in lactating sows.

GWAS for Lifespan and Decline in Climbing Ability in Flies upon Dietary Restriction Reveal decima as a Mediator of Insulin-like Peptide Production.

Dietary restriction (DR) is the most robust means to extend lifespan and delay age-related diseases across species. An underlying assumption in the aging field is that DR enhances both lifespan and physical activity through similar mechanisms, but this has not been rigorously tested in different genetic backgrounds. Furthermore, nutrient response genes responsible for lifespan extension or age-related decline in functionality remain underexplored in natural populations. To address this, we measured nutrient-dependent changes in lifespan and age-related decline in climbing ability in the Drosophila Genetic Reference Panel fly strains. On average, DR extended lifespan and delayed decline in climbing ability, but there was a lack of correlation between these traits across individual strains, suggesting that distinct genetic factors modulate these traits independently and that genotype determines response to diet. Only 50% of strains showed positive response to DR for both lifespan and climbing ability, 14% showed a negative response for one trait but not both, and 35% showed no change in one or both traits. Through GWAS, we uncovered a number of genes previously not known to be diet responsive nor to influence lifespan or climbing ability. We validated decima as a gene that alters lifespan and daedalus as one that influences age-related decline in climbing ability. We found that decima influences insulin-like peptide transcription in the GABA receptor neurons downstream of short neuropeptide F precursor (sNPF) signaling. Modulating these genes produced independent effects on lifespan and physical activity decline, which suggests that these age-related traits can be regulated through distinct mechanisms.

Effects of rice feeding and carnitine addition on growth performance and mRNA expression of protein metabolism-related genes in broiler grower chicks.

This study was carried out to evaluate the nutritional effects of rice feeding and carnitine addition to a diet for broiler chicks. Thirty-six male 10-day-old broiler chicks were assigned to one of the following four treatment groups: corn-based diet (corn group), rice-based diet (rice group), and each diet with added carnitine (100 ppm). The experimental period was 2 weeks. Rice feeding resulted in significantly higher growth performance (body weight gain and feed efficiency) compared to corn feeding. Carnitine addition also resulted in higher growth performance. Breast muscle and thigh muscle weight (g) were significantly higher in broiler chicks fed rice and those fed diets with added carnitine. Liver mRNA expression of IGF-I was significantly higher in broiler chicks fed rice compared to those fed corn. There was no significant difference in mRNA expression of muscle atrogin-1 or liver CPT-I between broiler chicks fed rice and those fed corn, not between broilers chicks fed diets containing carnitine or not. Overall, these results show that rice feeding and carnitine addition improve the growth performance of broiler chicks by increasing mRNA expression of liver IGF-I. In addition, carnitine action is not affected by different cereals (corn and rice).

Identification and Annotation of Potential Function of Regulatory Antisense Long Non-Coding RNAs Related to Feed Efficiency in Bos taurus Bulls.

Long non-coding RNAs (lncRNAs) can influence transcriptional and translational processes in mammalian cells and are associated with various developmental, physiological and phenotypic conditions. However, they remain poorly understood and annotated in livestock species. We combined phenotypic, metabolomics and liver transcriptomic data of bulls divergent for residual feed intake (RFI) and fat accretion. Based on a project-specific transcriptome annotation for the bovine reference genome ARS-UCD.1.2 and multiple-tissue total RNA sequencing data, we predicted 3590 loci to be lncRNAs. To identify lncRNAs with potential regulatory influence on phenotype and gene expression, we applied the regulatory impact factor algorithm on a functionally prioritized set of loci (n = 4666). Applying the algorithm of partial correlation and information theory, significant and independent pairwise correlations were calculated and co-expression networks were established, including plasma metabolites correlated with lncRNAs. The network hub lncRNAs were assessed for potential cis-actions and subjected to biological pathway enrichment analyses. Our results reveal a prevalence of antisense lncRNAs positively correlated with adjacent protein-coding genes and suggest their participation in mitochondrial function, acute phase response signalling, TCA-cycle, fatty acid ß-oxidation and presumably gluconeogenesis. These antisense lncRNAs indicate a stabilizing function for their cis-correlated genes and a putative regulatory role in gene expression.

Genetic and genomic analyses for predicted methane-related traits in Japanese Black steers.

The objectives of this study were to estimate genetic parameters and to perform a genome-wide association study (GWAS) for predicted methane-related traits in Japanese Black steers. The methane production and yield traits were predicted using on-farm measurable traits, such as dry matter intake and average daily gain. A total of 4,578 Japanese Black steers, which were progenies of 362 sires genotyped with imputed 551,995 single nucleotide polymorphisms (SNPs), had phenotypes of predicted methane-related traits during the total fattening period (52 weeks). For the estimation of genetic parameters, the estimated heritabilities were moderate (ranged from 0.57 to 0.60). In addition, the estimated genetic correlations of methane production traits with most of carcass traits and feed-efficiency traits were unfavorable, but those of methane yield traits were favorable or low. For the GWAS, no genome-wide significant SNP was detected, but a total of four quantitative trait locus (QTL) regions that explained more than 5.0% of genetic variance were localized on the genome, and some candidate genes associated with growth and feed-efficiency traits were located on the regions. Our results suggest that the predicted methane-related traits are heritable and some QTL regions for the traits are localized on the genome in Japanese Black steers.

Regulation of growth-related genes by nutrition in paralarvae of the common octopus (Octopus vulgaris).

The common octopus (Octopus vulgaris) is a species of great interest to the aquaculture industry. However, the high mortalities registered during different phases of the octopus lifecycle, particularly the paralarvae stage, present a challenge for commercial aquaculture. Improvement of diet formulation is seen as one way to reduce mortality and improve growth. Molecular growth-markers could help to improve rearing protocols and increase survival and growth performance; therefore, over a hundred orthologous genes related to protein balance and muscle growth in vertebrates were identified for the common octopus and their suitability as molecular markers for growth in octopus paralarvae explored. We successfully amplified 14 of those genes and studied their transcription in paralarvae either fed with artemia, artemia + zoea diets or submitted to a short fasting-refeeding procedure. Paralarvae fed with artemia + zoea had higher growth rates compared to those fed only with artemia, as well as a significant increase in octopus mtor (mtor-L) and hsp90 (hsp90-L) transcription, with both genes also up-regulated during refeeding. Our results suggest that at least mtor-L and hsp90-L are likely linked to somatic growth in octopus paralarvae. Conversely, ckip1-L, crk-L, src-L and srf-L had expression patterns that did not match to periods of growth as would be expected based on similar studies in vertebrates, indicating that further research is needed to understand their function during growth and in a muscle specific context.

DNA metabarcoding and spatial modelling link diet diversification with distribution homogeneity in European bats.

Inferences of the interactions between species' ecological niches and spatial distribution have been historically based on simple metrics such as low-resolution dietary breadth and range size, which might have impeded the identification of meaningful links between niche features and spatial patterns. We analysed the relationship between dietary niche breadth and spatial distribution features of European bats, by combining continent-wide DNA metabarcoding of faecal samples with species distribution modelling. Our results show that while range size is not correlated with dietary features of bats, the homogeneity of the spatial distribution of species exhibits a strong correlation with dietary breadth. We also found that dietary breadth is correlated with bats' hunting flexibility. However, these two patterns only stand when the phylogenetic relations between prey are accounted for when measuring dietary breadth. Our results suggest that the capacity to exploit different prey types enables species to thrive in more distinct environments and therefore exhibit more homogeneous distributions within their ranges.

The spatio-temporal features of chicken mitochondrial ND2 gene heteroplasmy and the effects of nutrition factors on this gene.

Mitochondrial heterogeneity is the presence of two or more types of mitochondrial (mt)DNA in the same individual/tissue/cell. It is closely related to animal health and disease. ND2 is a protein-coding gene in mtDNA, which participates in mitochondrial respiratory chain and oxidative phosphorylation. In previous studies, we observed that the mt.A5703T and mt.T5727G sites in the ND2 gene were the heteroplasmic variation sites. We used pyrophosphate sequencing technology to examine chicken mt.A5703T and mt.T5727G heteroplasmic sites in the ND2 gene, in different tissues and at different development stages in chickens. We also investigated whether nutritional factors could affect the mt.A5703T and mt.T5727G heteroplasmy. Our results showed that chicken mt.A5703T and mt.T5727G heteroplasmy had clear spatio-temporal specificities, which varied between tissues/development stages. The mtDNA heterogeneity was relatively stable upon nutrition intervention, 30% dietary energy restriction (from 18 to 48 days old) and different types of dietary fats (at 5% concentration, from 1 to 42 days old) did not change the breast muscle heteroplasmy of broilers at the mt.A5703T and mt.T5727G sites. In addition, multiple potential heteroplasmic sites were detected by clone sequencing in the ND2 region, which potentially reflected abundant heteroplasmy in the chicken mitochondrial genome. These results provide an important reference for further research on heteroplasmy in chicken mitochondria.