scholarly journals Investigation of muscle transcriptomes using gradient boosting machine learning identifies molecular predictors of feed efficiency in growing pigs

2019 ◽  
Author(s):  
Farouk Messad ◽  
Isabelle Louveau ◽  
Basile Koffi ◽  
Hélène Gilbert ◽  
Florence Gondret
Keyword(s):  
Feed Efficiency ◽  
Conversion Ratio ◽  
Growing Pigs ◽  
Feed Conversion Ratio ◽  
Breeding Value ◽  
Gradient Boosting ◽  
Mrna Levels ◽  
Feed Conversion ◽  
Expression Levels ◽  
Muscle Genes

Abstract Background Improving feed efficiency (FE) is a major challenge in pig production. This complex trait is characterized by a high variability. Therefore, the identification of predictors of FE may be a relevant strategy to reduce phenotyping efforts in breeding and selection programs. The aim of this study was to investigate the suitability of expressed muscle genes in prediction of FE traits in growing pigs. The approach considered different transcriptomics experiments to cover a large range of FE values and identify reliable predictors. Results Microarrays data were obtained from longissimus muscles of two lines divergently selected for residual feed intake (RFI). Pigs (n = 71) from three experiments belonged to generations 6 to 8 of selection, were fed either a diet with a standard composition or a diet rich in fiber and lipids, received feed ad libitum or at restricted level, and weighed between 80 and 115 kg at slaughter. For each pig, breeding value for RFI was estimated (RFI-BV), and feed conversion ratio (FCR) and energy-based feed conversion ratio (FCRe) were calculated during the test periods. Gradient boosting algorithms were used on the merged muscle transcriptomes to identify very important predictors of FE traits. About 20,405 annotated molecular probes were commonly expressed in longissimus muscle across experiments. Six to 267 expressed muscle genes covering a variety of biological processes were found as important predictors for RFI-BV (R2=0.63-0.65), FCR (R2=0.61-0.70) and FCRe (R2=0.49-0.52). The error of prediction was less than 8% for FCR. Altogether, 56 predictors were common to RFI-BV and FCR. Expression levels of 24 target genes were further measured by qPCR. Linear regression confirmed the good accuracy of combining mRNA levels of these genes to fit FE traits (RFI-BV: R2=0.73, FRC: R2=0.76; FCRe: R2=0.75). Stepwise regression procedure highlighted 10 genes (FKBP5, MUM1, AKAP12, FYN, TMED3, PHKB, TGF, SOCS6, ILR4, and FRAS1) in a linear combination predicting FCR and FCRe. In addition, FKBP5 and expression levels of five other genes (IGF2, SERINC3, CSRNP3, EZR and RPL16) significantly contributed to RFI-BV. Conclusion It was possible to identify few genes expressed in muscle that might be reliable predictors of feed efficiency.

scholarly journals Investigation of muscle transcriptomes using gradient boosting machine learning identifies molecular predictors of feed efficiency in growing pigs

2019 ◽  
Author(s):  
Farouk Messad ◽  
Isabelle Louveau ◽  
Basile Koffi ◽  
Hélène Gilbert ◽  
Florence Gondret
Keyword(s):  
Feed Efficiency ◽  
Conversion Ratio ◽  
Growing Pigs ◽  
Feed Conversion Ratio ◽  
Breeding Value ◽  
Gradient Boosting ◽  
Mrna Levels ◽  
Feed Conversion ◽  
Expression Levels ◽  
Muscle Genes

Abstract Background Improving feed efficiency (FE) is a major challenge in pig production. This complex trait is characterized by a high variability. Therefore, the identification of predictors of FE may be a relevant strategy to reduce phenotyping efforts in breeding and selection programs. The aim of this study was to investigate the suitability of expressed muscle genes in prediction of FE traits in growing pigs. The approach considered different transcriptomics experiments to cover a large range of FE values and identify reliable predictors. Results Microarrays data were obtained from longissimus muscles of two lines divergently selected for residual feed intake (RFI). Pigs (n = 71) from three experiments belonged to generations 6 to 8 of selection, were fed either a diet with a standard composition or a diet rich in fiber and lipids, received feed ad libitum or at restricted level, and weighed between 80 and 115 kg at slaughter. For each pig, breeding value for RFI was estimated (RFI-BV), and feed conversion ratio (FCR) and energy-based feed conversion ratio (FCRe) were calculated during the test periods. Gradient boosting algorithms were used on the merged muscle transcriptomes to identify very important predictors of FE traits. About 20,405 annotated molecular probes were commonly expressed in longissimus muscle across experiments. Six to 267 expressed muscle genes covering a variety of biological processes were found as important predictors for RFI-BV (R2=0.63-0.65), FCR (R2=0.61-0.70) and FCRe (R2=0.49-0.52). The error of prediction was less than 8% for FCR. Altogether, 56 predictors were common to RFI-BV and FCR. Expression levels of 24 target genes were further measured by qPCR. Linear regression confirmed the good accuracy of combining mRNA levels of these genes to fit FE traits (RFI-BV: R2=0.73, FRC: R2=0.76; FCRe: R2=0.75). Stepwise regression procedure highlighted 10 genes (FKBP5, MUM1, AKAP12, FYN, TMED3, PHKB, TGF, SOCS6, ILR4, and FRAS1) in a linear combination predicting FCR and FCRe. In addition, FKBP5 and expression levels of five other genes (IGF2, SERINC3, CSRNP3, EZR and RPL16) significantly contributed to RFI-BV. Conclusion It was possible to identify few genes expressed in muscle that might be reliable predictors of feed efficiency.

scholarly journals Investigation of muscle transcriptomes using gradient boosting machine learning identifies molecular predictors of feed efficiency in growing pigs

2019 ◽  
Author(s):  
Farouk Messad ◽  
Isabelle Louveau ◽  
Basile Koffi ◽  
Hélène Gilbert ◽  
Florence Gondret
Keyword(s):  
Feed Efficiency ◽  
Conversion Ratio ◽  
Growing Pigs ◽  
Feed Conversion Ratio ◽  
Breeding Value ◽  
Gradient Boosting ◽  
Mrna Levels ◽  
Feed Conversion ◽  
Expression Levels ◽  
Muscle Genes

Abstract Background Improving feed efficiency (FE) is a major challenge in pig production. This complex trait is characterized by a high variability. Therefore, the identification of predictors of FE may be a relevant strategy to reduce phenotyping efforts in breeding and selection programs. The aim of this study was to investigate the suitability of expressed muscle genes in prediction of FE traits in growing pigs. The approach considered different transcriptomics experiments to cover a large range of FE values and identify reliable predictors. Results Microarrays data were obtained from longissimus muscles of two lines divergently selected for residual feed intake (RFI). Pigs (n = 71) from three experiments belonged to generations 6 to 8 of selection, were fed either a diet with a standard composition or a diet rich in fiber and lipids, received feed ad libitum or at restricted level, and weighed between 80 and 115 kg at slaughter. For each pig, breeding value for RFI (RFI-BV) was estimated, and feed conversion ratio (FCR) and energy-based feed conversion ratio (FCRe) were calculated during the test periods. Gradient boosting algorithms were used on the merged muscle transcriptomes to identify very important predictors of FE traits. About 20,405 annotated molecular probes were commonly expressed in longissimus muscle across experiments. Six to 267 expressed muscle genes covering a variety of biological processes were found as important predictors for RFI-BV (R2=0.63-0.65), FCR (R2=0.61-0.70) and FCRe (R2=0.49-0.52). The error of prediction was less than 8% for FCR. Altogether, 56 predictors were common to RFI-BV and FCR. Expression levels of 24 target genes were further measured by qPCR. Linear regression confirmed the good accuracy of combining mRNA levels of these genes to fit FE traits (RFI-BV: R2=0.73, FRC: R2=0.76; FCRe: R2=0.75). Stepwise regression procedure highlighted 10 genes (FKBP5, MUM1, AKAP12, FYN, TMED3, PHKB, TGF, SOCS6, ILR4, and FRAS1) in a linear combination predicting FCR and FCRe. In addition, FKBP5 and expression levels of five other genes (IGF2, SERINC3, CSRNP3, EZR and RPL16) significantly contributed to RFI-BV. Conclusion It was possible to identify few genes expressed in muscle that might be reliable predictors of feed efficiency.

scholarly journals Copy number variation of amylase alpha 2B gene is associated with feed efficiency traits in Large White pigs--title not given--

2021 ◽  
Author(s):  
Tsukasa Yoshidomi ◽  
Kazuaki Tanaka ◽  
Tatsuya Takizawa ◽  
Satoshi Nikaido ◽  
Tetsuya Ito ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Feed Intake ◽  
Feed Efficiency ◽  
Copy Number ◽  
Conversion Ratio ◽  
Growing Pigs ◽  
Feed Conversion Ratio ◽  
Feed Conversion ◽  
Large White ◽  
Number Variation

Copy number variation (CNV) of the AMY gene in humans has been enthusiastically studied for its association with starch digestibility and obesity. The alpha-amylase (AMY) is a major starch digestive enzyme in mammals. This study aimed to determine the association between CNV of the porcine pancreatic amylase (AMY2B) gene and feed efficiency. Improvement of feed efficiency in growing pigs is of great economic interest. We assayed the copy number of AMY2B by using real-time quantitative PCR (qPCR) in a Large White pig population. We identified three genotypes for AMY2B CNVs, namely I/I (homozygotes of haplotype I; a chromosome with one copy of AMY2B), I/II (heterozygotes of haplotype I and II; a chromosome with two copies) and II/II (homozygotes of haplotype II). We tested the genotypes of the parental generation consisting of six males, 21 females and 265 offspring piglets to validate the AMY2B CNV genotyping. With very few mistyping exceptions, copy numbers of AMY2B were transmitted to piglets in segregation ratios following Mendelian inheritance. Finally, we performed an association analysis between the CNV of the AMY2B gene and feed efficiency traits in 207 uncastrated male pigs. The generalised linear model analysis showed the significant effects of AMY2B CNV genotype on average daily feed intake, total feed intake and feed conversion ratio during growth from 30 kg to 100 kg body weight. However, it was not associated with average daily gain, backfat thickness and loin eye muscle area. Individuals with the genotype I/I had about 76.6 ± 27.1 g lower average daily feed intake, 5.35 ± 1.90 kg lower total feed intake and 0.089 8 ± 0.026 5 lower feed conversion ratio than individuals with I/II and II/II genotypes. Thus, AMY2B CNV has the potential to be an effective genetic marker that could reduce feed costs for pig farming.  

Daily methane emissions and emission intensity of grazing beef cattle genetically divergent for residual feed intake

2017 ◽  
Vol 57 (4) ◽  
pp. 627 ◽  
Author(s):  
J. I. Velazco ◽  
R. M. Herd ◽  
D. J. Cottle ◽  
R. S. Hegarty
Keyword(s):  
Feed Intake ◽  
Emission Intensity ◽  
Dry Matter ◽  
Average Daily Gain ◽  
Residual Feed Intake ◽  
Conversion Ratio ◽  
Feed Conversion Ratio ◽  
Breeding Value ◽  
Dry Matter Intake ◽  
Feed Conversion

As daily methane production (DMP; g CH4/day) is strongly correlated with dry matter intake (DMI), the breeding of cattle that require less feed to achieve a desired rate of average daily gain (ADG) by selection for a low residual feed intake (RFI) can be expected to reduce DMP and also emission intensity (EI; g CH4/kg ADG). An experiment was conducted to compare DMP and EI of Angus cattle genetically divergent for RFI and 400-day weight (400dWT). In a 6-week grazing study, 64 yearling-age cattle (30 steers, 34 heifers) were grazed on temperate pastures, with heifers and steers grazing separate paddocks. Liveweight (LW) was monitored weekly and DMP of individual cattle was measured by a GreenFeed emission monitoring unit in each paddock. Thirty-nine of the possible 64 animals had emission data recorded for 15 or more days, and only data for these animals were analysed. For these cattle, regression against their mid-parent estimated breeding value (EBV) for post-weaning RFI (RFI-EBV) showed that a lower RFI-EBV was associated with higher LW at the start of experiment. Predicted dry matter intake (pDMI), predicted DMP (pDMP) and measured DMP (mDMP) were all negatively correlated with RFI-EBV (P < 0.05), whereas ADG, EI, predicted CH4 yield (pMY; g CH4/kg DMI) were not correlated with RFI-EBV (P > 0.1). Daily CH4 production was positively correlated with animal LW and ADG (P < 0.05). The associations between ADG and its dependent traits EI and pMY and predicted feed conversion ratio (kg pDMI/kg ADG) were strongly negative (r = –0.82, –0.57 and –0.85, P < 0.001) implying that faster daily growth by cattle was accompanied by lower EI, MY and feed conversion ratio. These results show that cattle genetically divergent for RFI do not necessarily differ in ADG, EI or pMY on pasture and that, if heavier, cattle with lower RFI-EBV can actually have higher DMP while grazing moderate quality pastures.

The Potency of Bifidobacterium spp. as an Alternative to Antibiotic Growth Promoters on Feed Conversion Ratio, Feed Efficiency, and Nutrient Intake in Laying Hens

2021 ◽  
Vol 56 (2) ◽  
pp. 281-290
Author(s):  
Andreas Berny Yulianto ◽  
Anam Al Arif ◽  
Widya Paramita Lokapirnasari
Keyword(s):  
Feed Efficiency ◽  
Protein Intake ◽  
Crude Protein ◽  
Laying Hens ◽  
Conversion Ratio ◽  
Feed Conversion Ratio ◽  
Crude Fiber ◽  
Fiber Intake ◽  
Feed Conversion ◽  
Growth Promoters

This article describes a new idea about using Bifidobacteriumsp isolates as an alternative to antibiotic growth promoters, based on the ability of Bifidobacteriumsp isolates, which have the potential as a probiotic in laying hens. This study aims to prove that Bifobacteriumsp could improve production performance, including feed conversion ratio, feed efficiency, and nutrient intake (feed intake, crude protein intake, crude fiber intake, lipid intake, and organic matter). A total of 150 laying hens at 25 weeks of age were divided into three groups (P0: control, P1: 0.1% antibiotic growth promoters, P1: 0.05% Bifidobacterium spp. probiotic) and fed on a basal diet containing 2750 kcal/kg metabolizable energy and 18% crude protein for four weeks. The different supplementation to the basal diets showed significant differences (p<0.05) on feed conversion ratio, feed efficiency, feed intake, crude protein intake, crude fiber intake, lipid intake, and organic matter intake among the treatments. However, feed intake, feed conversion ratio, crude protein intake, crude fiber intake, lipid intake, and organic matter intake were lowest in the group fed with 0.5% of Bifidobacterium spp. The highest feed efficiency was obtained from the groups fed with 0.5% of Bifidobacterium spp, compared with the control and supplemented antibiotics growth promoters group. 0.5% of Bifidobacterium spp. supplementation to the diet of laying hens is beneficial for increasing feed efficiency and improving feed conversion ratio. The practical and theoretical significance of the results is that Bifidobacterium spp. can be used to improve production performance in laying hens.

scholarly journals Results of selection for breast muscle percentage and feed conversion ratio in Pekin ducks

2011 ◽  
Vol 27 (3) ◽  
pp. 769-776 ◽  
Author(s):  
H. Pingel
Keyword(s):  
Feed Efficiency ◽  
Conversion Ratio ◽  
Feed Conversion Ratio ◽  
Breast Muscle ◽  
Feed Consumption ◽  
Direct Selection ◽  
Meat Production ◽  
Feed Conversion ◽  
Nitrogen And Phosphorus ◽  
Selection For

Increasing breast muscle percentage by selection for breast layer thickness (muscle and skin) of living ducks by needle probe improves carcass quality as could be demonstrated by experiments and by applied breeding programs. In addition direct selection for individual feed conversion ratio can increase the efficiency of duck meat production. Divergent selection for feed conversion ratio from the age of 4 - 7 weeks over 11 generations has differentiated the feed efficiency by about 25 %. Causes for the reduction in feed conversion ratio are lower fat content of carcass, lower locomotor activity, higher enzymatic activity (alkaline phosphatase and creatinkinase in blood plasma) and better feed protein utilization. Because of lower feed consumption in the line selected for lower feed conversion ratio the emission of nitrogen and phosphorus via manure was reduced by about 39 and 26 %, respectively. That means, selection for better feed efficiency is not only an important economical but also an important ecological factor.

Reducing the cost of beef production through the genetic improvement of net feed efficiency

1998 ◽  
Vol 1998 ◽  
pp. 45-45
Author(s):  
R.M. Herd ◽  
J.A. Archer ◽  
P.F. Arthur ◽  
E.C. Richardson
Keyword(s):  
Feed Efficiency ◽  
Genetic Improvement ◽  
Production Systems ◽  
Growth Efficiency ◽  
Conversion Ratio ◽  
Feed Conversion Ratio ◽  
Feed Conversion ◽  
Selection For ◽  
The Cost ◽  
Animal Production Systems

Feed is the single largest cost in most animal production systems. Feed conversion ratio (FCR) is a commonly used measure of growth efficiency. Previous research has shown that FCR is moderately heritable and highly related to growth rate. While selection for FCR is beneficial to those feeding growing cattle for slaughter, any associated increase in the size of breeding females will mean this benefit will be at a cost to the calf breeder, as larger breeding cows require more feed.

scholarly journals 434 Late-Breaking: Expression of Growth hormone Gene (GH) and Insulin-like growth factor (IGF-2) in metabolic tissues of pigs are affected by unconventional dietary feed sources

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 42-43
Author(s):  
Ufuoma G Sorhue ◽  
Ikenna Omeje ◽  
Ifeanyichukwu udeh ◽  
Adimabua M Moemeka ◽  
Raphael E Onainor
Keyword(s):  
Growth Hormone ◽  
Body Weight ◽  
Weight Gain ◽  
Growth Factor ◽  
Feed Intake ◽  
Feed Efficiency ◽  
Conversion Ratio ◽  
Feed Conversion Ratio ◽  
Growth Hormone Gene ◽  
Feed Conversion

Abstract This study was conducted to examine the growth performance and expression patterns of growth hormone gene and insulin-like growth factor in metabolic tissues of pigs fed different unconventional feed sources. A total of 45 growing pigs were randomly assigned to 5 dietary treatments at 9 animals per treatment and 3 animals per replicate. Treatment one (T1) comprise of whole maize (WM) which served as the control, T2: brewers dried grain (BDG), T3: cassava peel meal (CPM), T4: plantain peel meal (PPM) and T5: corn husk meal (CHM) at 35% inclusion in the diet. Data collected and analyzed includes; initial body weight (IBW), final body weight (FBW), average daily feed intake (ADFI), average daily weight gain (ADG), feed conversion ratio (FCR) and feed efficiency (FE). At the end of the feeding trial, three animals per treatment (one animal per replicate) were slaughtered; the duodenum and liver were collected and stored using RNALater prior to RNA extraction. Real-time qPCR was performed in 40cycles using the PowerUp SYBR Green reagent and analysed using the Delta-Delta Ct method. All data were subjected to analysis of variance in a completely randomized design. The results showed that the treatment diets had effect on growth performance with significant differences (P &lt; 0.05) observed for average final weight, average total weight gain, average daily feed intake, feed conversion ratio and feed efficiency while the initial weight were not significantly different (P &gt; 0.05). IGF-2 was differentially expressed in the liver and duodenum across treatments while significant differences were not observed in the expression pattern of the growth hormone gene in both tissues. This study showed promise for the use of unconventional feeding stuffs in pig feeding and reveals that genes influencing performance characters are differentially expressed in relation to the source of unconventional feeds used in compounding pig diet.

Nutritional value of chickpea (Cicer arietinum) and pigeonpea (Cajanus cajan) meals for growing pigs and rats. 2. Effect of autoclaving and alkali treatment

1985 ◽  
Vol 36 (2) ◽  
pp. 337 ◽  
Author(s):  
T Visitpanich ◽  
ES Batterham ◽  
BW Norton
Keyword(s):  
Trypsin Inhibitor ◽  
Soybean Meal ◽  
Alkali Treatment ◽  
Conversion Ratio ◽  
Growing Pigs ◽  
Feed Conversion Ratio ◽  
Trypsin Inhibitor Activity ◽  
Growth Responses ◽  
Feed Conversion ◽  
Inhibitor Activity

Four experiments were conducted with rats to investigate the effects of autoclaving and alkali treatment on the growth-promoting ability of pigeonpea meal. In the fifth experiment, the effect of autoclaving pigeonpea meal was evaluated with pigs. With rats, there was a quadratic response (P < 0.05) in growth and feed conversion ratio to autoclaving pigeonpea seed for 15 min at 100-140�C, with maximum response occurring at c. 124�C. However, growth rate was still lower and feed conversion ratio higher than those of rats fed soybean meal (P < 0.05). Imbibing pigeonpea seed in alkali and subsequently drying it to original weight did not reduce tannin content but did reduce the trypsin-inhibitor activity from 10.3 to 5.1 units mg-1. Although both alkali treatment and autoclaving of the alkali-treated seed improved the growth and feed conversion ratios of rats, these treatments did not overcome the differences in protein quality between the pigeonpea and soybean meal diets. Autoclaving pigeonpea seed for 15 min at 110, 124 and 140�C reduced the trypsin-inhibitor activity of the meals from 11.2 to 0.7 units mg-'. Compared to pigs fed on unheated pigeonpea meal, pigs given autoclaved meal had higher (P < 0.05) growth rates and improved feed conversion ratios. These improved growth responses were similar to those produced by soybean meal.

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