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Background Single nucleotide polymorphism (SNP) arrays for domestic cattle have catalyzed the identification of genetic markers associated with complex traits for inclusion in modern breeding and selection programs. Using actual and imputed Illumina 778K genotypes for 3887 U.S. beef cattle from 3 populations (Angus, Hereford, SimAngus), we performed genome-wide association analyses for feed efficiency and growth traits including average daily gain (ADG), dry matter intake (DMI), mid-test metabolic weight (MMWT), and residual feed intake (RFI), with marker-based heritability estimates produced for all traits and populations. Results Moderate and/or large-effect QTL were detected for all traits in all populations, as jointly defined by the estimated proportion of variance explained (PVE) by marker effects (PVE ≥ 1.0%) and a nominal P -value threshold ( P  ≤ 5e-05). Lead SNPs with PVE ≥ 2.0% were considered putative evidence of large-effect QTL ( n  = 52), whereas those with PVE ≥ 1.0% but < 2.0% were considered putative evidence for moderate-effect QTL ( n  = 35). Identical or proximal lead SNPs associated with ADG, DMI, MMWT, and RFI collectively supported the potential for either pleiotropic QTL, or independent but proximal causal mutations for multiple traits within and between the analyzed populations. Marker-based heritability estimates for all investigated traits ranged from 0.18 to 0.60 using 778K genotypes, or from 0.17 to 0.57 using 50K genotypes (reduced from Illumina 778K HD to Illumina Bovine SNP50). An investigation to determine if QTL detected by 778K analysis could also be detected using 50K genotypes produced variable results, suggesting that 50K analyses were generally insufficient for QTL detection in these populations, and that relevant breeding or selection programs should be based on higher density analyses (imputed or directly ascertained). Conclusions Fourteen moderate to large-effect QTL regions which ranged from being physically proximal (lead SNPs ≤ 3Mb) to fully overlapping for RFI, DMI, ADG, and MMWT were detected within and between populations, and included evidence for pleiotropy, proximal but independent causal mutations, and multi-breed QTL. Bovine positional candidate genes for these traits were functionally conserved across vertebrate species.

Background Wenchang chickens are one of the most popular local chicken breeds in the Chinese chicken industry. However, the low feed efficiency is the main shortcoming of this breed. Therefore, there is a need to find a more precise breeding method to improve the feed efficiency of Wenchang chickens. In this study, we explored important candidate genes and variants for feed efficiency and growth traits through genome-wide association study (GWAS) analysis. Results Estimates of genomic heritability for growth and feed efficiency traits, including residual feed intake (RFI) of 0.05, average daily food intake (ADFI) of 0.21, average daily weight gain (ADG) of 0.24, body weight (BW) at 87, 95, 104, 113 days of age (BW87, BW95, BW104 and BW113) ranged from 0.30 to 0.44. Important candidate genes related to feed efficiency and growth traits were identified, such as PLCE1, LAP3, MED28, QDPR, LDB2 and SEL1L3 genes. Conclusion The results identified important candidate genes for feed efficiency and growth traits in Wenchang chickens and provide a theoretical basis for the development of new molecular breeding technology.

Background Feed efficiency (FE) related traits play a key role in the economy and sustainability of beef cattle production systems. The accurate knowledge of the physiologic background for FE-related traits can help the development of more efficient selection strategies for them. Hence, multi-trait weighted GWAS (MTwGWAS) and meta-analyze were used to find genomic regions associated with average daily gain (ADG), dry matter intake (DMI), feed conversion ratio (FCR), feed efficiency (FE), and residual feed intake (RFI). The FE-related traits and genomic information belong to two breeding programs that perform the FE test at different ages: post-weaning (1,024 animals IZ population) and post-yearling (918 animals for the QLT population). Results The meta-analyze MTwGWAS identified 14 genomic regions (-log10( p  -value) > 5) regions mapped on BTA 1, 2, 3, 4, 7, 8, 11, 14, 15, 18, 21, and 29. These regions explained a large proportion of the total genetic variance for FE-related traits across-population ranging from 20% (FCR) to 36% (DMI) in the IZ population and from 22% (RFI) to 28% (ADG) in the QLT population. Relevant candidate genes within these regions (LIPE, LPL, IGF1R, IGF1, IGFBP5, IGF2, INS, INSR, LEPR, LEPROT, POMC, NPY, AGRP, TGFB1, GHSR, JAK1, LYN, MOS, PLAG1, CHCD7, LCAT , and PLA2G15 ) highlighted that the physiological mechanisms related to neuropeptides and the metabolic signals controlling the body's energy balance are responsible for leading to greater feed efficiency. Integrated meta-analysis results and functional pathway enrichment analysis highlighted the major effect of biological functions linked to energy, lipid metabolism, and hormone signaling that mediates the effects of peptide signals in the hypothalamus and whole-body energy homeostasis affecting the genetic control of FE-related traits in Nellore cattle. Conclusions Genes and pathways associated with common signals for feed efficiency-related traits provide better knowledge about regions with biological relevance in physiological mechanisms associated with differences in energy metabolism and hypothalamus signaling. These pleiotropic regions would support the selection for feed efficiency-related traits, incorporating and pondering causal variations assigning prior weights in genomic selection approaches.

Abstract We evaluated the genetic relationships (1) among feed efficiency traits with different fattening periods, (2) between feed efficiency traits and growth traits, and (3) between feed efficiency traits and carcass traits, to determine the influence of genetic factors on feed efficiency traits. In total, 4,578 Japanese Black cattle from a progeny testing program were used. Residual feed intake (RFI), residual BW gain (RG), and residual intake and BW gain (RIG) were defined as feed efficiency traits, and were measured for the first half (approximately 9 to 15 months of age), latter half (approximately 15 to 21 months of age), and total period of fattening (approximately 9 to 21 months of age). A single-trait animal model for estimating heritability and a two-trait animal model for estimating genetic and phenotypic correlations were used. The heritability estimates for RFI, RG, and RIG were different in each fattening period, ranging from 0.36 to 0.46, 0.19 to 0.28, and 0.28 to 0.34, respectively, and the heritability estimates for the total fattening period were greater than those for the first and latter halves separately. RIG showed the greatest preferred genetic correlation, with a greater feed conversion ratio than the other feed efficiency traits (ranging from −0.84 to −0.96). RG in the first and latter halves of the fattening period had different genetic correlations with the growth starting point (0.82 and −0.06, respectively) and maturity rate (0.49 and −0.51, respectively) of the Gompertz growth curve parameters, and is strongly dependent on the different fattening periods. Feed efficiency traits in different fattening periods had low genetic correlations with the carcass traits (from −0.05 to 0.19 for RFI; from 0.02 to 0.31 for RG; and from −0.11 to 0.20 for RIG). This study indicated the possibility for genetic improvement through the selection of high-RIG animals to decrease feed intake and increase BW gain without any unfavorable correlated responses affecting mature (asymptotic) weight and carcass grade.

The beef cattle industry represents a significant portion of the USA’s agricultural sect, with beef cattle accounting for the most red meat consumed in the USA. Feed represents the largest input cost in the beef industry, accounting for approximately 70% of total input cost. Given that, novel methods need to be employed to optimize feed efficiency in cattle to reduce monetary cost as well as environmental cost associated with livestock industries, such as methane production and nitrogen release into the environment. The rumen microbiome contributes to feed efficiency by breaking down low-quality feedstuffs into energy substrates that can subsequently be utilized by the host animal. Attempts to manipulate the rumen microbiome have been met with mixed success, though persistent changes have not yet been achieved beyond changing diet. Recent technological advances have made analyzing host-wide effects of the rumen microbiome possible, as well as provided finer resolution of those effects. This manuscript reviews contributing factors to the rumen microbiome establishment or re-establishment following rumen microbiome perturbation, as well as host-microbiome interactions that may be responsible for possible host specificity of the rumen microbiome. Understanding and accounting for the variety of factors contributing to rumen microbiome establishment or re-establishment in cattle will ultimately lead to identification of biomarkers of feed efficiency that will result in improved selection criteria, as well as aid to determine methods for persistent microbiome manipulation to optimize production phenotypes.

Chromium (Cr) is a trace element and plays a significant role in fish nutrition and physiology. An experiment was designed to know the effects of Cr addition in the diets to growth and feed utilization in striped catfish (Pangasianodon hypophthalmus). Four diets with Cr (0, 2, 4, and 8 mg kg−1) were fed to striped catfish in aquaria with triplicate groups for 60 days. Survival, growth parameters (weight gain, WG; %WG; specific growth rate, SGR), and feed utilization (feed intake, FI; feed efficiency, FE; protein efficiency ratio, PER; feed conversion ratio, FCR) were calculated at the end of the feeding trial. Several hemato-biochemical parameters, such as hemoglobin (Hb), red blood cell (RBC), white blood cell (WBC) and glucose level, and frequency of micronucleus (MN) formation in erythrocytes, were analyzed. The growth parameters (WG, %WG, and SGR) and feed utilization (FE and PER) increased significantly in the fish fed with 2 and 4 mg kg−1 Cr supplemented diets. On the other hand, the growth parameters suppressed in the fish fed with 8 mg kg−1 Cr-based diet. The polynomial regression analysis based on WG showed that 2.82 mg kg−1 Cr supplementation in the diet is optimum for the tested fish species. The values of Hb (g/dL), RBC (×106/mm3) and blood glucose (mg/dL) significantly decreased in the fish fed with the highest (8 mg kg−1) Cr-based feed. Conversely, MN frequency was significantly increased in the fish fed with 8 mg kg−1 Cr-based diet. Overall, 2.82 mg Cr kg−1 can be added to the diets of striped catfish for its better growth with maximum utilization of feed.

Aquaculture activity is affected by various environmental factors, including water salinity and high temperatures. The present study investigated the impact of using varying water salinity (0, 5, 10, 15 and 20 ppt) on the growth behavior, immune responses and antioxidative responses of common carp. Fish were raised under optimal conditions except for water salinity for 8 weeks; fish were then subjected to high-temperature stress (32 °C) for 48 h. The results indicated a reduced final weight (FBW), weight gain (WG), specific growth rate (SGR), condition factor (CF), feed intake and feed efficiency ratio (FER) in common carp reared in 15 and 20 ppt (p < 0.05). The lowest FBW, WG, SGR, CF, feed intake and FER values were observed in fish reared in 20 ppt water salinity (p < 0.05). In gills, the superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GPx) were markedly decreased, but malondialdehyde (MDA) levels increased in fish challenged with 15 and 20 ppt before they were subjected to heat stress (p < 0.05). After heat stress, the SOD, CAT and GPx were decreased, and the MDA increased in fish reared in varying salinity levels (p < 0.05). Before heat stress, the intestinal SOD, CAT and GPx markers were decreased by 15 and 20 ppt, while the MDA level was increased by 15 and 20 ppt (p < 0.05). Generally, heat stress lowered the SOD, CAT and GPx activity in the intestines and liver tissues but increased MDA levels in common carp stressed by varying salinity levels (p < 0.05). The most decreased lysozyme activity, SOD, CAT and GPx and increased MDA levels were observed in common carp exposed to 20 ppt before and after heat stress (p < 0.05). After heat stress, fish exposed to 15 and 20 ppt had lower NBT than the remaining groups, and fish exposed to 20 ppt had the lowest values (p < 0.05). Overall, the heat stress markedly suppressed the antioxidant and immune responses of common carp reared in hypersalinity conditions.

In the current experiment the effects of brown seaweeds (Sargassum aquifolium, SA) on blood biochemical, antioxidant, innate immune, and mRNA gene expression responses of Tilapia (Oreochromis niloticus) under high stocking rate were examined. The fish were allocated into equal six experimental groups: low stocking density (LSD) (the fish reared at 10 g L−1 and fed an un-supplemented diet), High stocking density (HSD) (the fish reared at 20 g L−1 and fed an un-supplemented diet), HSD + SA50, HSD + SA100, HSD + SA150, and HSD + SA200 (the fish reared at 20 g L−1 and fed Sargassum-supplemented diet at level 50, 100, 150, 200 g kg−1, respectively). After 56 days of the feeding trial, the fish at the HSD treatment revealed remarkedly reduced growth and feed efficiency compared to those at the LSD treatment, but the HSD + SA50 and HSD + SA100 fish groups showed a marked enhancement in performance and efficiency of consumed diets comparable to the LSD treatment. Under overcrowded stress, the fish fed diets enriched with Sargassum significantly diminished ammonia releasing levels within the entire environment. Serum total protein, albumin, liver enzymes, and lipase levels had significantly improved in HSD + SA150 and HSD + SA200 fish groups compared to those in the HSD treatment. Superoxide dismutase, catalase, and glutathione peroxidase exhibited high values at HSD + SA200- and LSD-treated groups than the HSD-treated group. However, HSD suppressed all plasma antioxidant activity. The high stocking rate remarkedly recorded higher plasma malondialdehyde levels, and Sargassum treatments significantly alleviated such increases. The HSD and HSD + SA50 fish groups significantly reduced plasma lysozyme, complement C3, IgA, and IgM levels and revealed higher intestinal aerobic and anaerobic bacterial counts than those at the LSD treatment; however, enriched tilapia diets with a high level of Sargassum diminished these negative effects. The HSD fish group significantly upregulated the expression of tumor necrosis factor-alpha (TNF-a), and downregulated interleukin 10 (IL10), catalase (CAT), and glutathione (GST) genes. Sargassum dietary administration, specifically at 50 g kg−1 level notably alleviated the adverse effects of high stocking rate on the cytokines. In conclusion, enriched tilapia diets with Sargassum treatment at levels ranging from 50 up to 100 g kg−1 alleviated overcrowded stress, oxidative stress, and immunosuppression caused by high stocking rate in Tilapia (O. niloticus).

Feed accounts for the greatest proportion of egg production costs and there is substantial variation in feed to egg conversion ratio (FCR) efficiency between individual hens. Despite this understanding, there is a paucity of information regarding layer hen feeding behaviour, diet selection and its impact on feed efficiency. It was hypothesised that variation in feed to egg conversion efficiency between hens may be influenced by feeding behaviour. For this experiment, two 35-bird groups of ISA Brown layers were selected from 450 individually caged hens at 25-30 weeks of age for either low FCR < 1.8 ± 0.02 (high feed efficiency (HFE) or high FCR > 2.1 ± 0.02 (low feed efficiency (LFE)). For each of these 70 hens, intake of an ad-libitum mash diet at 2-minute time intervals, 24 h a day, for 7 days was determined alongside behavioural assessment and estimation of the selection of components of the mash. The group selected for HFE had a lower feed intake, similar egg mass and associated lower FCR when compared with the LFE group. Whilst feed intake patterns were similar between HFE and LFE hens, there was a distinct intake pattern for all layer hens with intake rate increasing from 0300 to 1700 h with a sharp decline to 2200 h. High feed efficiency hens selected a diet with 25% more ash and 4% less gross energy than LFE hens. The LFE hens also spent more time eating with more walking events, but less time spent resting, drinking, preening and cage pecking events as compared with HFE hens. In summary, there was no contrasting diurnal pattern of feed consumption behaviour between the groups ranked on feed efficiency, however high feed efficiency hens consumed less feed and selected a diet with greater ash content and lower gross energy as compared with LFE hens. Our work is now focused on individual hen diet selection from mash diets with an aim of formulating precision, targeted diets for greater feed efficiency.

Microalgae and live yeast have gained interest in improving animal performance. This study evaluated the effect of supplementation with Spirulina platensis , Saccharomyces cerevisiae , or their combination on the in vitro and in vivo rumen fermentation, rumen microbiota, and milk yield and composition of lactating Shami goats. The in vitro experiment included four diets: non-supplemented basal diet consisted of Alfalfa hay and a concentrate feed mixture (C); basal diet supplemented with 1% Saccharomyces (Y) based on dry matter; basal diet supplemented with 1% Spirulina (A); and basal diet supplemented with 1% of a mixture of Saccharomyces and Spirulina (AY). In the in vivo experiment, twenty-one lactating goats were divided into three groups (n = 7) to receive one of three diets: C, A, and AY. Group AY had higher in vitro gas production, dry matter digestion (DMD), and volatile fatty acids (VFA) ( p  < 0.05). Milk yield and feed efficiency were higher in groups A and AY compared to group C. Group AY goats exhibited higher rumen total VFA, acetic, and propionic, while group A showed higher butyric acid. Lower predicted methane was observed in group AY. Groups A and AY showed distinctive microbial communities. The bacterial community was dominated by phylum Bacteroidota, and genera Prevotella and Rikenellaceae RC9 gut group, which were higher in the AY group. The archaeal community was dominated by the genus Methanobrevibacter , which had a lower prevalence in group AY. The combination of live yeast and Spirulina improved rumen fermentation and the milk yield; therefore, it could be used as a feed additive for lactating goats.