Efficiency Traits Research Articles

Transcriptome Analysis of Breast Muscle Reveals Pathways Related to Protein Deposition in High Feed Efficiency of Native Turkeys.

Simple SummaryDue to the high cost of feed in the poultry production system, improving feed efficiency can reduce production costs. This study aimed to investigate the transcriptome of breast muscle tissue of native male turkeys that have been phenotyped for high and low feed efficiency. After the rearing period, the most efficient and the least efficient male turkeys were selected and slaughtered for RNA-Seq. Genes with different expressions in muscle tissue were identified between high feed efficiency turkeys compared to low feed efficiency turkeys. The results showed that high feed efficiency birds increased the expression of genes related to amino acid biosynthesis and low feed efficiency birds increased the expression of genes related to the immune response. Eleven key genes associated with the phenotypic expression of feed efficiency were selected that may be good potential candidates for biomarkers of feed efficiency in genetic selection in turkeys. This study provides new insights into the differences in transcripts between breast muscle tissues between turkeys with high and low feeding efficiencies.Feed efficiency is important due to the high cost of food, which accounts for about 70% of the total cost of a turkey breeding system. Native poultry are an important genetic resource in poultry breeding programs. This study aimed to conduct a global transcriptome analysis of native male turkeys which have been phenotyped for high and low feed efficiency. Feed efficiency traits were recorded during the experimental period. After slaughter, the three most efficient and three least efficient male turkeys were selected for RNA-Seq analysis. A total of 365 genes with different expressions in muscle tissue were identified between turkeys with a high feed efficiency compared to turkeys with a low feed efficiency. In the pathway analysis of up-regulated genes, major pathways included the “metabolism of glycine, serine, and threonine”; the “adipocytokine signaling pathway” and the “biosynthesis of amino acids”. In the pathway analysis of down-regulated genes, the major pathways included “dorso-ventral axis formation” and “actin cytoskeleton regulation”. In addition, gene set enrichment analyses were performed, which showed that high feed efficiency birds exhibit an increased expression of genes related to the biosynthesis of amino acids and low feed efficiency birds an increased expression of genes related to the immune response. Furthermore, functional analysis and protein network interaction analysis revealed that genes including GATM, PSAT1, PSPH, PHGDH, VCAM1, CD44, KRAS, SRC, CAV3, NEDD9, and PTPRQ were key genes for feed efficiency. These key genes may be good potential candidates for biomarkers of feed efficiency in genetic selection in turkeys.

Estimates of variance components for feedlot traits of the Simmentaler breed in South Africa

Breeding of beef cattle is changing, with more emphasis on efficiency of production. Feed cost is the highest expense, and reducing it has the potential to increase profitability. Common measures of efficiency are ratio traits such as feed conversion (feed consumed/weight gain) and feed efficiency (weight gain / feed consumed). Feed conversion ratio is commonly used in South Africa in an attempt to improve feed efficiency. These ratio traits are associated with growth rate. Selection for them would result in higher growth as a correlated response and might also increase the mature size of the cows and their maintenance cost. Thus, alternative efficiency traits such as residual feed intake and residual daily gain have been proposed. In this study, variance components, and genetic parameters for feedlot traits for the South African Simmentaler breed were estimated, with emphasis on the efficiency traits. The focus was to evaluate the use of residual feed intake as an alternative trait. The results indicate non-significant correlations between residual feed intake and body weight and growth traits, implying that residual feed intake should have little effect on the other traits. This is in contrast to the moderate to strong correlations of feed conversion ratio with the same traits. The study demonstrates that considerable genetic variation exists for residual feed intake, which can be exploited. Selection for residual feed intake can reduce the carbon footprint of beef due to the associated lower methane emissions.

Unlocking the Nexus between Leaf-Level Water Use Efficiency and Root Traits Together with Gas Exchange Measurements in Rice (Oryza sativa L.).

Drought stress severely affects plant growth and development, causing significant yield loss in rice. This study demonstrates the relevance of water use efficiency with deeper rooting along with other root traits and gas exchange parameters. Forty-nine rice genotypes were evaluated in the basket method to examine leaf-level water use efficiency (WUEi) variation and its relation to root traits. Significant variation in WUEi was observed (from 2.29 to 7.39 µmol CO2 mmol−1 H2O) under drought stress. Regression analysis revealed that high WUEi was associated with higher biomass accumulation, low transpiration rate, and deep rooting ratio. The ratio of deep rooting was also associated with low internal CO2 concentration. The association of deep rooting with lower root number and root dry weight suggests that an ideal drought-tolerant genotype with higher water use efficiency should have deeper rooting (>30% RDR) with moderate root number and root dry weight to be sustained under drought for a longer period. The study also revealed that, under drought stress conditions, landraces are more water-use efficient with superior root traits than improved genotypes.

Greenhouse gas emissions, dry matter intake and feed efficiency of young Holstein bulls

Livestock farming is directly responsible for greenhouse gas (GHG) emissions, mainly due to enteric fermentation. Feed efficiency in livestock species is generally evaluated through feed conversion ratio (FCR) and residual feed intake (RFI), which are associated to GHG emissions. The aim of this study was to characterise FCR and RFI in relation to body traits, feed intake, feeding behaviour and GHG emissions of Holstein bulls. Data were collected between May 2018 and July 2020 on 111 animals. Pearson correlations between studied traits were estimated on the residuals obtained from a linear mixed model which included the fixed effect of the linear covariate of age of bull on the dependent variable and the random effect of the bull. To assess the effect of RFI and FCR the same linear mixed model was implemented firstly by including the fixed effect of RFI (2 classes) and secondly the fixed effect of FCR (2 classes). Correlations between dry matter intake (DMI) and GHG ranged from 0.25 (CH4) to 0.36 (CO2). The strongest relationship was estimated between feed efficiency traits and DMI (0.86). RFI and FCR showed weak to moderate correlations with GHG (0.12–0.31). Animals belonging to the low classes of RFI and FCR had lower DMI and showed significant reduction of GHG emissions. Results of the present study highlighted significant differences in terms of feed efficiency and GHG emissions among tested animals; further research is needed on their progeny to investigate the genetic background of the same efficiency and emission-related traits. Highlights Feed efficiency and emission of greenhouse gases vary among Holstein bulls. Dry matter intake and feed efficiency traits were strongly positively associated. Animals endowed with greater feed efficiency had lower emissions and feed intake. Results of the present study will be useful to select animals for feed efficiency.

Microbiability and microbiome-wide association analyses of feed efficiency and performance traits in pigs

BackgroundThe objective of the present study was to investigate how variation in the faecal microbial composition is associated with variation in average daily gain (ADG), backfat thickness (BFT), daily feed intake (DFI), feed conversion ratio (FCR), and residual feed intake (RFI), using data from two experimental pig lines that were divergent for feed efficiency. Estimates of microbiability were obtained by a Bayesian approach using animal mixed models. Microbiome-wide association analyses (MWAS) were conducted by single-operational taxonomic units (OTU) regression and by back-solving solutions of best linear unbiased prediction using a microbiome covariance matrix. In addition, accuracy of microbiome predictions of phenotypes using the microbiome covariance matrix was evaluated.ResultsEstimates of heritability ranged from 0.31 ± 0.13 for FCR to 0.51 ± 0.10 for BFT. Estimates of microbiability were lower than those of heritability for all traits and were 0.11 ± 0.09 for RFI, 0.20 ± 0.11 for FCR, 0.04 ± 0.03 for DFI, 0.03 ± 0.03 for ADG, and 0.02 ± 0.03 for BFT. Bivariate analyses showed a high microbial correlation of 0.70 ± 0.34 between RFI and FCR. The two approaches used for MWAS showed similar results. Overall, eight OTU with significant or suggestive effects on the five traits were identified. They belonged to the genera and families that are mainly involved in producing short-chain fatty acids and digestive enzymes. Prediction accuracy of phenotypes using a full model including the genetic and microbiota components ranged from 0.60 ± 0.19 to 0.78 ± 0.05. Similar accuracies of predictions of the microbial component were observed using models that did or did not include an additive animal effect, suggesting no interaction with the genetic effect.ConclusionsOur results showed substantial associations of the faecal microbiome with feed efficiency related traits but negligible effects with growth traits. Microbiome data incorporated as a covariance matrix can be used to predict phenotypes of animals that do not (yet) have phenotypic information. Connecting breeding environment between training sets and predicted populations could be necessary to obtain reliable microbiome predictions.

Long-term artificial selection of Hanwoo (Korean) cattle left genetic signatures for the breeding traits and has altered the genomic structure

Indigenous Korean breeds such as Hanwoo (Korean) cattle have adapted to their local environment during the past 5000 years. In the 1980s, the National Genetic Improvement Program was established to develop a modern economic breed for beef production in Korea through artificial selection. This process is thought to have altered the genomic structure of breeding traits over time. The detection of genetic variants under selection could help to elucidate the genetic mechanism of artificial selection in modern cattle breeds. Indigenous Hanwoo cattle have adapted in response to local natural and artificial selection during a 40-year breeding program. We analyzed genomic changes in the selection signatures of an unselected population (USP; n = 362) and a selected population (KPN; n = 667) of Hanwoo cattle. Genomic changes due to long-term artificial selection were identified using a genome-wide integrated haplotype score (iHS) and a genome-wide association study (GWAS). Signatures of recent selection were detected as positive (piHS > 6) or negative (piHS < –6) iHS scores spanning more than 46 related genes in KPN cattle, but none in USP cattle. A region adjacent to the PLAG1 gene was found to be under strong selection for carcass weight. The GWAS results also showed a selection signature on BTA14, but none on BTA13. Pathway and quantitative trait locus analysis results identified candidate genes related to energy metabolism, feed efficiency, and reproductive traits in Hanwoo cattle. Strong selection significantly altered Hanwoo cattle genome structural properties such as linkage disequilibrium (LD) and haplotypes through causal mutation for target traits. Haplotype changes of genome structure which are changes of ancestral allele to derived alleles due to selection were clearly identified on BTA13 and BTA14; however, the structure of the LD block was not clearly observed except BTA14. Thus, selection based on EBVs would be working very well in Hanwoo cattle breeding program appears to have been highly successful.

Genetic Modeling and Genomic Analyses of Yearling Temperament in American Angus Cattle and Its Relationship With Productive Efficiency and Resilience Traits.

Cattle temperament has been considered by farmers as a key breeding goal due to its relevance for cattlemen’s safety, animal welfare, resilience, and longevity and its association with many economically important traits (e.g., production and meat quality). The definition of proper statistical models, accurate variance component estimates, and knowledge on the genetic background of the indicator trait evaluated are of great importance for accurately predicting the genetic merit of breeding animals. Therefore, 266,029 American Angus cattle with yearling temperament records (1–6 score) were used to evaluate statistical models and estimate variance components; investigate the association of sex and farm management with temperament; assess the weighted correlation of estimated breeding values for temperament and productive, reproductive efficiency and resilience traits; and perform a weighted single-step genome-wide association analysis using 69,559 animals genotyped for 54,609 single-nucleotide polymorphisms. Sex and extrinsic factors were significantly associated with temperament, including conception type, age of dam, birth season, and additional animal–human interactions. Similar results were observed among models including only the direct additive genetic effect and when adding other maternal effects. Estimated heritability of temperament was equal to 0.39 on the liability scale. Favorable genetic correlations were observed between temperament and other relevant traits, including growth, feed efficiency, meat quality, and reproductive traits. The highest approximated genetic correlations were observed between temperament and growth traits (weaning weight, 0.28; yearling weight, 0.28). Altogether, we identified 11 genomic regions, located across nine chromosomes including BTAX, explaining 3.33% of the total additive genetic variance. The candidate genes identified were enriched in pathways related to vision, which could be associated with reception of stimulus and/or cognitive abilities. This study encompasses large and diverse phenotypic, genomic, and pedigree datasets of US Angus cattle. Yearling temperament is a highly heritable and polygenic trait that can be improved through genetic selection. Direct selection for temperament is not expected to result in unfavorable responses on other relevant traits due to the favorable or low genetic correlations observed. In summary, this study contributes to a better understanding of the impact of maternal effects, extrinsic factors, and various genomic regions associated with yearling temperament in North American Angus cattle.

Effects of dried Portulaca oleracea supplementation to the laying hen diet on productive performance, egg physical traits, fatty acid composition, and cholesterol content

Portulaca oleracea is a widespread herbaceous plant particularly rich in polyunsaturated fatty acids (PUFA), antioxidant compounds and characterised by a healthy omega-6/omega-3 ratio. The focus of this research was to evaluate the effects of Portulaca oleracea supplementation to the diet of laying hens on productive performance, egg physical traits, fatty acid composition and cholesterol content. Twenty-six 24-week-old Warren strain layers were randomly assigned to two different groups of 18 and eight birds, respectively: one group received a commercial diet (C) whereas the other group was given the same control diet supplemented with 20% of dried Portulaca oleracea (PO). Hens were fed for 21 days. Feed and water were provided ad libitum. The poor palatability of the PO diet compromised the optimisation of the productive performance, with a significant reduction of the oviposition efficiency (0.69 vs 0.88 for PO and C, respectively; P &amp;lt; 0.05) and egg physical traits. Considering the egg nutritional traits, dietary PO significantly decreased the yolk proportion of saturated fatty acid (43.0% vs 44.1%, P &amp;lt; 0.05), while it increased the content of PUFA (19.4% vs 17.8%, P &amp;lt; 0.001), and within the latter, both omega-6 and omega-3 proportion significantly increased in comparison with C group (16.4% vs 17.6%, P &amp;lt; 0.001 and 1.46% vs 1.80%, P &amp;lt; 0.001, for n-6 and n-3, respectively). This resulted in an improvement of the omega-6/omega-3 ratio (10.4 vs 11.3 for PO and C, respectively; P &amp;lt; 0.05). Egg yolk cholesterol content did not vary between dietary treatments. It could be concluded that the use of Portulaca oleracea for producing omega-3-enriched eggs is feasible once the problem of palatability has been overcome and the energy requirements of the hens have been covered.

Harnessing the Potential of Wheat-Pea Species Mixtures: Evaluation of Multifunctional Performance and Wheat Diversity.

Species mixtures and heterogeneous crop populations are two promising approaches for diversified ecological cropping systems with increased resilience and reduced dependency on external inputs. Inter- and intraspecific diversity were evaluated in combination using 15 wheat (Triticum aestivum) entries, including line cultivars and heterogeneous populations (HPs), from central Europe and Hungary and one winter pea cultivar under organic conditions. Monocultures and wheat mixtures were evaluated multi-functionally for yield, quality, land use efficiency, crop protection, and wheat entry traits. Mixtures increased cereal grain quality, weed suppression, resource use efficiency, yield gain, and reduced lodging. Effects were stronger in 2018/19, which were characterized by dry and nutrient-poor conditions than in 2019/20 when nutrient levels were higher. Wheat entries varied considerably in protein content and yield in both mixtures and monocultures. Under higher nutrient availability, entry-based variation was reduced in both systems, and peas were suppressed. Because of low disease pressure, the wheat entries varied little in terms of disease protection services, and mixture effects on the disease were low. The multi-criteria framework identified stability of yield, yield gains, and quality under high environmental variability of mixtures as clear agronomic advantages with HPs being considerably more stable than line cultivars. Some line cultivars outperformed the HPs in either protein content or yield across environments but not both simultaneously. Trait analysis revealed a possible link between harvest index and reduced competition in mixtures, which can increase yield performance in specific line cultivars. System cultivar interactions were generally very low and highly dependent on environmental conditions. We conclude that while cultivar breeding for mixtures can be successful in monocultures, high environmental variation highlights the necessity of evaluating cultivars in mixtures. In addition, use of intraspecific diversity within interspecific mixed cropping systems can be a valuable addition to further improve mixture performance and its stability under increasing environmental stresses due to climate change.

Evaluation of Post-weaning Efficiency in Nellore-Angus Crossbred Steers through Model Predicted Residual Consumption

The objective of this work was to evaluate efficiency traits of Nellore-Angus crossbred steers (n = 349) on feed. Steers were fed a grain-based diet beginning at approximately 12 months of age for an average of 140 days. Contemporary groups were born in the fall or spring of 2003 through 2007 in full-sibling embryo transfer families or half-sibling families all sired by the same bulls. Individual intake was measured and weights were recorded to permit calculation of average daily gain. Residual feed intake (RFI) was estimated as the residual of models employing regressions on metabolic mid-test weight and ADG. An additional efficiency metric was also constructed and evaluated: model predicted residual consumption (MPRC). Mixed linear models were used to analyze daily dry matter intake, average daily gain (ADG), metabolic mid-test weight, RFI, and MPRC. Large positive associations of DMI with MPRC and RFI were identified along with low positive associations between metabolic mid-weight with ADG and MPRC. Genome wide association analysis revealed 5 regions associated with DMI, but none for the other traits analyzed. Residual feed intake values varied greatly between the contemporary group value and the overall value for the steers, showing the calculation&amp;rsquo;s dependency on the reference population. However, MPRC as based upon a standardized population, did not fluctuate. More selection phenotypes and strategies are needed for large-scale improvements in global beef cattle production sustainability. The stability of the MPRC metric could be beneficial for future feed efficiency research across multiple and diverse contemporary groups, and diverse production environments.

Rumen and lower gut microbiomes relationship with feed efficiency and production traits throughout the lactation of Holstein dairy cows

Fermentation of dietary nutrients in ruminants' gastrointestinal (GI) tract is an essential mechanism utilized to meet daily energy requirements. Especially in lactating dairy cows, the GI microbiome plays a pivotal role in the breakdown of indigestible plant polysaccharides and supply most AAs, fatty acids, and gluconeogenic precursors for milk synthesis. Although the contribution of the rumen microbiome to production efficiency in dairy cows has been widely researched over the years, variations throughout the lactation and the lower gut microbiome contribution to these traits remain poorly characterized. Therefore, we investigated throughout lactation the relationship between the rumen and lower gut microbiomes with production efficiency traits in Holstein cows. We found that the microbiome from both locations has temporal stability throughout lactation, yet factors such as feed intake levels played a significant role in shaping microbiome diversity. The composition of the rumen microbiome was dependent on feed intake. In contrast, the lower gut microbiome was less dependent on feed intake and associated with a potentially enhanced ability to digest dietary nutrients. Therefore, milk production traits may be more correlated with microorganisms present in the lower gut than previously expected. The current study's findings advance our understanding of the temporal relationship of the rumen and lower gut microbiomes by enabling a broader overview of the gut microbiome and production efficiency towards more sustainable livestock production.

Composition of the ileum microbiota is a mediator between the host genome and phosphorus utilization and other efficiency traits in Japanese quail (Coturnix japonica)

BackgroundPhosphorus is an essential nutrient in all living organisms and, currently, it is the focus of much attention due to its global scarcity, the environmental impact of phosphorus from excreta, and its low digestibility due to its storage in the form of phytates in plants. In poultry, phosphorus utilization is influenced by composition of the ileum microbiota and host genetics. In our study, we analyzed the impact of host genetics on composition of the ileum microbiota and the relationship of the relative abundance of ileal bacterial genera with phosphorus utilization and related quantitative traits in Japanese quail. An F2 cross of 758 quails was genotyped with 4k genome-wide single nucleotide polymorphisms (SNPs) and composition of the ileum microbiota was characterized using target amplicon sequencing. Heritabilities of the relative abundance of bacterial genera were estimated and quantitative trait locus (QTL) linkage mapping for the host was conducted for the heritable genera. Phenotypic and genetic correlations and recursive relationships between bacterial genera and quantitative traits were estimated using structural equation models. A genomic best linear unbiased prediction (GBLUP) and microbial (M)BLUP hologenomic selection approach was applied to assess the feasibility of breeding for improved phosphorus utilization based on the host genome and the heritable part of composition of the ileum microbiota.ResultsAmong the 59 bacterial genera examined, 24 showed a significant heritability (nominal p ≤ 0.05), ranging from 0.04 to 0.17. For these genera, six genome-wide significant QTL were mapped. Significant recursive effects were found, which support the indirect host genetic effects on the host’s quantitative traits via microbiota composition in the ileum of quail. Cross-validated microbial and genomic prediction accuracies confirmed the strong impact of microbial composition and host genetics on the host’s quantitative traits, as the GBLUP accuracies based on the heritable microbiota-mediated components of the traits were similar to the accuracies of conventional GBLUP based on genome-wide SNPs.ConclusionsOur results revealed a significant effect of host genetics on composition of the ileal microbiota and confirmed that host genetics and composition of the ileum microbiota have an impact on the host’s quantitative traits. This offers the possibility to breed for improved phosphorus utilization based on the host genome and the heritable part of composition of the ileum microbiota.

Signatures of selection in Nelore cattle revealed by whole-genome sequencing data.

Nelore cattle breed was farmed worldwide due to its economic importance in the beef market and adaptation to the tropics. In Brazil, purebred Nelore animals (PO) receive a certificate from the breeders' association based on the animal's genealogy and morphological characterization. The top 20 to 30% of the superior animals are eligible to receive the Special Certificate of Identification and Production (CEIP), meaning animals from this category were selected and evaluated in a breeding program to improve economically important traits. We used whole-genome sequencing and approaches based on haplotype differentiation and allelic differentiation to detect regions of selection signatures in Nelore cattle by comparing animals from PO and CEIP categories. From a total of 150 animals, a hierarchical clustering analysis was performed to choose the more unrelated animals from each category (16 PO and 40 CEIP). The hapFLK statistic was performed, and extensions of hapFLK values were investigated considering continuous regions with significant q-values. The Weir and Cockerham's Fst estimator (wcFst) was computed using the GPAT++ software library. The total of 82,326 SNPs with hapFLK values passed the FDR control (q-value<0.05), and 718 segments were target as signatures of selection. A total of 1713 highly differentiated genomic regions were identified based on the segmentFst approach. The signatures of selection were spread across the genome. Annotation of overlapping selection signature regions between the two methods revealed 118 genes in common. A variant located within the 3' region of the BOLA-DRB3 gene was found as a promising candidate polymorphism. Within genomic regions that deserves attention, we found genes previously associated with adaptation to tropical environments (HELB), growth and navel size (HMGA2), fat deposition and domestication (IRAK3), and feed efficiency and postmortem carcass traits (GABRG3). The genes BOLA-DQA2, BOLA-DQB, BOLA-DQA5, BOLA-DQA1, BOLA-DRB3, ENSBTAG00000038397 on chromosome 23 are part of the Bovine Major Histocompatibility Complex (MHC) Class II gene family, representing good candidates for immune response and adaptation to tropical conditions. The BoLA family genes and the interaction of ROBO1 with SLIT genes appeared in the enrichment results. Genomic regions located in intronic regions were also identified and might play a regulatory role in traits under selection in PO and CEIP subpopulations. The regions here identified contribute to our knowledge regarding genes and variants that have an important role in complex traits selected in this breed.

Integration of rumen and lower gut microbiomes throughout lactation improve the prediction of feed efficiency and production traits in dairy cows (Supplemental Table 1)

Integration of rumen and lower gut microbiomes throughout lactation improve the prediction of feed efficiency and production traits in dairy cows (Supplemental Table 1)

CNV detection and their association with growth, efficiency and carcass traits in Santa Inês sheep.

Copy number variations (CNV) are an important source of genetic variation. CNV has been increasingly studied and frequently associated with diseases and productive traits in livestock animals. However, CNV-based genome-wide association studies (GWAS) in Santa Inês sheep, one of the principal sheep breeds in Brazil, have not yet been reported. Thus, the aim of this study was to investigate the association between CNV and growth, efficiency and carcass traits in sheep. The Illumina OvineSNP50 BeadChip array was used to detect CNV in 491 Santa Inês individuals. Then, CNV-based GWAS was performed with a linear mixed model approach considering a genomic relationship matrix, for ten traits: (1) growth: body weight at three (W3) and six (W6) months of age; (2) efficiency: residual feed intake (RFI) and feed efficiency (FE) and (3) carcass: external carcass length (ECL), leg length (LL), carcass yield (CY), commercial cuts weight (CCW), loin eye area (LEA) and subcutaneous fat thickness (SFT). We identified 1,167 autosomal CNV in 438 sheep, with 294 non-redundant CNV, ranging from 21.8 to 861.9kb, merged into 216 distinct copy number variation regions (CNVRs). One significant CNV segment (pFDR -value<0.05) in OAR3 was associated with CY, while another significant CNV in OAR6 was associated with RFI. Additionally, another 5 CNV segments were considered relevant for investigation in the future studies. The significant segments overlapped 4 QTLs and spanned 8 genes, including the SPAST,TGFA and ADGRL3 genes, involved in cell differentiation and energy metabolism. Therefore, the results of the present study increase knowledge about CNV in sheep, their possible impacts on productive traits, and provide information for future investigations, being especially useful for those interested in structural variations in the sheep genome.

Dietary Administration of L-Carnitine During the Fattening Period of Early Feed Restricted Lambs Modifies Ruminal Fermentation but Does Not Improve Feed Efficiency.

Early feed restriction of lambs may program animals to achieve reduced feed efficiency traits as a consequence of permanent mitochondrial dysfunction. The hypothesis at the background of the present study is that dietary administration of L-Carnitine (a compound that promotes the activation and transportation of fatty acids into the mitochondria) during the fattening period of early feed restricted lambs can: (a) improve the biochemical profile of early feed restricted lambs, (b) improve feed efficiency, (c) modulate the ruminal and intestinal microbiota, and (d) induce changes in the gastrointestinal mucosa, including the immune status. Twenty-two newborn male Merino lambs were raised under natural conditions but separated from the dams for 9 h daily to allow feed restriction during the suckling period. At weaning, lambs were assigned to a control group being fed ad libitum a complete pelleted diet during the fattening phase (CTRL, n = 11), whereas the second group (CARN, n = 11) received the same diet supplemented with 3 g of L-Carnitine/kg diet. The results revealed that even though L-Carnitine was absorbed, feed efficiency was not modified by dietary L-Carnitine during the fattening period (residual feed intake, p > 0.05), whereas ruminal fermentation was improved [total short-chain fatty acids (SCFAs), 113 vs. 154 mmol/l; p = 0.036]. Moreover, a trend toward increased concentration of butyrate in the ileal content (0.568 vs. 1.194 mmol/100 ml SCFA; p = 0.074) was observed. Other effects, such as reduced heart weight, lower levels of markers related to muscle metabolism or damage, improved renal function, and increased ureagenesis, were detected in the CARN group. Limited changes in the microbiota were also detected. These findings suggest that L-Carnitine may improve ruminal fermentation parameters and maintain both the balance of gut microbiota and the health of the animals. However, the improved ruminal fermentation and the consequent greater accumulation of intramuscular fat might have hidden the effects caused by the ability of dietary L-Carnitine to increase fatty acid oxidation at the mitochondrial level. This would explain the lack of effects of L-Carnitine supplementation on feed efficiency and points toward the need of testing lower doses, probably in the context of animals being fed in excess non-protein nitrogen.

LOW-N TOLERANCE, N-USE EFFICIENCY AND RESPONSIVENESS OF 37 Chenopodium quinoa GENOTYPES UNDER ORGANIC AND MINERAL FERTILIZER CONDITIONS

Low nitrogen (N) fertilizer rate causes negative effects on quinoa productivity; such effects differ from genotype to genotype and from fertilizer type to another. The objectives of the present investigation were: (i) to assess the low-N stress tolerance index (STI) of 37 quinoa genotypes under organic and inorganic fertilizers, (ii) to estimate the superiority of tolerant (T) to sensitive (S) genotypes for studied traits and (iii) to identify high yielding, low-N tolerant, N-efficient and N-responsive genotypes under each fertilizer type. A two-year field experiment was conducted, using a split split-plot design with three replications. Main plots were devoted to two fertilizer types, namely organic (compost) and inorganic (ammonium nitrate), sub-plots to three N rates, namely LN (71.4), MN (142.8) and HN (214.2 kg N/ha), and sub sub-plots to 37 quinoa genotypes. Seed yield/ha (SYPH) of T genotypes was significantly (P≤0.01) superior to S genotypes by 308.8, 123.8, and 152.6 % under organic fertilizer and 100.6, 123.6, and 212.6 % under mineral fertilizer, for LN, MN, and LN, respectively. Superiority in SYPH was associated with significant (P≤0.01) superiority in seed yield/plant (SYPP) and its components, economic (NUEe) and biological (NUEb) N-use efficiency traits under both fertilizer types. Based on STI and seed yield under HN and LN, the genotypes Nat-1, R-103 and Sekam-Bitter, under LN and HN organic fertilizer, Misr1 Improved, R-103 and Giza-1 under LN mineral fertilizer and Agritec-Beige, Egyptian White and, CICA-17, under HN mineral fertilizer conditions, were the most N efficient, most low-N tolerant and the highest seed yielders under respective environments. These genotypes should be recommended to quinoa breeding programs to develop high-yielding varieties for growing under respective low-N as well as high-N organic and inorganic fertilizer conditions.

Heritability and genetic correlation for residual feed intake of Pacific abalone Haliotis discus hannai

Pacific abalone (Haliotis discus hannai) is the dominant farmed abalone species in China. Feed efficiency is an important economic trait for abalone, but little attention has been paid to this trait in breeding programs of Pacific abalone. In this study, the growth and feed efficiency traits of 648 abalone were measured during two time periods (days 1–36 and days 37–72), while an individual-based accurate measurement method of feed efficiency for abalone was established. The residual feed intake (RFI) was first evaluated in abalone; this was significantly correlated between the two periods, while the feed efficiency ratio (FER) was not significantly correlated between the two periods. Genetic analysis showed that RFI exhibited moderate or high heritability, with respective scores of 0.32 and 0.40 in the two periods, and there was a strong positive genetic correlation between the two periods (0.892 ± 0.042). RFI showed weak negative genetic correlations with average daily gain (ADG) during the two growth periods (−0.144 and − 0.008), and a positive genetic correlation with daily feed intake (DFI) (0.901 and 0.794). In addition, a group-feeding experiment were carried out on 12 families. It was found that the body growth and feed intake of abalone were highly correlated with the results of individual-feeding experiment. The results demonstrated that RFI could be used as a suitable trait for indicating the feed efficiency of abalone in future breeding programs.

Distinctive carbon repression effects in the carbohydrate-selective wood decay fungus Rhodonia placenta

Brown rot fungi dominate the carbon degradation of northern terrestrial conifers. These fungi adapted unique genetic inventories to degrade lignocellulose and to rapidly release a large quantity of carbohydrates for fungal catabolism. We know that brown rot involves “two-step” gene regulation to delay most hydrolytic enzyme expression until after harsh oxidative pretreatments. This implies the crucial role of concise gene regulation to brown rot efficacy, but the underlying regulatory mechanisms remain uncharacterized. Here, using the combined transcriptomic and enzyme analyses we investigated the roles of carbon catabolites in controlling gene expression in model brown rot fungus Rhodonia placenta. We identified co-regulated gene regulons as shared transcriptional responses to no-carbon controls, glucose, cellobiose, or aspen wood (Populus sp.). We found that cellobiose, a common inducing catabolite for fungi, induced expression of main chain-cleaving cellulases in GH5 and GH12 families (cellobiose vs. no-carbon > 4-fold, Padj < 0.05), whereas complex aspen was a universal inducer for Carbohydrate Active Enzymes (CAZymes) expression. Importantly, we observed the attenuated glucose-mediated repression effects on cellulases expression, but not on hemicellulases and lignin oxidoreductases, suggesting fungi might have adapted diverged regulatory routes to boost cellulase production for the fast carbohydrate release. Using carbon regulons, we further predicted the cis- and trans-regulatory elements and assembled a network model of the distinctive regulatory machinery of brown rot. These results offer mechanistic insights into the energy efficiency traits of a common group of decomposer fungi with enormous influence on the carbon cycle.

Hydraulic tradeoffs underlie local variation in tropical forest functional diversity and sensitivity to drought.

Tropical forests are important to the regulation of climate and the maintenance of biodiversity on Earth. However, these ecosystems are threatened by climate change, as temperatures rise and droughts' frequency and duration increase. Xylem anatomical traits are an essential component in understanding and predicting forest responses to changes in water availability. We calculated the community-weighted means and variances of xylem anatomical traits of hydraulic and structural importance (plot-level trait values weighted by species abundance) to assess their linkages to local adaptation and community assembly in response to varying soil water conditions in an environmentally diverse Brazilian Atlantic Forest habitat. Scaling approaches revealed community-level tradeoffs in xylem traits not observed at the species level. Towards drier sites, xylem structural reinforcement and integration balanced against hydraulic efficiency and capacitance xylem traits, leading to changes in plant community diversity. We show how general community assembly rules are reflected in persistent fiber-parenchyma and xylem hydraulic tradeoffs. Trait variation across a moisture gradient is larger between species than within species and is realized mainly through changes in species composition and abundance, suggesting habitat specialization. Modeling efforts to predict tropical forest diversity and drought sensitivity may benefit from adding hydraulic architecture traits into the analysis.