scholarly journals A combined GWAS approach reveals key loci for socially-affected traits in Yorkshire pigs

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Pingxian Wu ◽  
Kai Wang ◽  
Jie Zhou ◽  
Dejuan Chen ◽  
Anan Jiang ◽  
...  
Keyword(s):  
Feed Intake ◽  
Genetic Architecture ◽  
Average Daily Gain ◽  
Significant Snps ◽  
Genetic Effects ◽  
Single Locus ◽  
Yorkshire Pigs ◽  
Feeding Speed ◽  
Daily Gain ◽  
Gwas Approach

AbstractSocially affected traits in pigs are controlled by direct genetic effects and social genetic effects, which can make elucidation of their genetic architecture challenging. We evaluated the genetic basis of direct genetic effects and social genetic effects by combining single-locus and haplotype-based GWAS on imputed whole-genome sequences. Nineteen SNPs and 25 haplotype loci are identified for direct genetic effects on four traits: average daily feed intake, average daily gain, days to 100 kg and time in feeder per day. Nineteen SNPs and 11 haplotype loci are identified for social genetic effects on average daily feed intake, average daily gain, days to 100 kg and feeding speed. Two significant SNPs from single-locus GWAS (SSC6:18,635,874 and SSC6:18,635,895) are shared by a significant haplotype locus with haplotype alleles ‘GGG’ for both direct genetic effects and social genetic effects in average daily feed intake. A candidate gene, MT3, which is involved in growth, nervous, and immune processes, is identified. We demonstrate the genetic differences between direct genetic effects and social genetic effects and provide an anchor for investigating the genetic architecture underlying direct genetic effects and social genetic effects on socially affected traits in pigs.

PSXII-12 Partitioning direct and maternal genetic effects into additive and non-additive components for growth and maternal traits in Yorkshire pigs

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 251-252
Author(s):  
Jicai Jiang ◽  
Shauneen O’Neill ◽  
Christian Maltecca ◽  
Justin Fix ◽  
Tamar Crum ◽  
...  
Keyword(s):  
Birth Weight ◽  
Environmental Effect ◽  
Linear Mixed Model ◽  
Growth Traits ◽  
Average Daily Gain ◽  
Genetic Effects ◽  
Average Weight ◽  
Yorkshire Pigs ◽  
Direct Dominance ◽  
Daily Gain

Abstract This study investigates how much direct and maternal non-additive genetic effects contribute to growth and maternal traits in swine. We analyzed a sample of 19,475 genotyped Yorkshire pigs from Acuity Ag Solutions, LLC (Carlyle, IL). Approximately 50K SNPs were kept after quality control, and missing genotypes were then imputed using findhap.f90. The genotypes were used to construct genomic relationship matrices (GRMs) corresponding to additive (A), dominance (D), and additive-by-additive epistasis (E) effects for both direct and maternal effects. The GRMs were subsequently employed as covariance structure matrices in a linear mixed model consisting of eight random components, namely three direct genetic effects (Ad, Dd, and Ed), three maternal genetic effects (Am, Dm, and Em), maternal environmental effect, and common litter environmental effect. We estimated these variance components (VCs) for six growth traits (birth weight, average daily gain, back fat, and loin area) and six maternal traits of a sow (total number of piglets born, number of piglets born alive, average weight of piglets at birth, average weight of piglets weaned) using REML in MMAP (https://mmap.github.io/). As shown in Table 1, we found significant (P< 0.05) direct dominance and epistasis VCs for all six growth traits. Additionally, direct epistasis effects explained a larger proportion of phenotypic variation than direct dominance for all growth traits (0.04–0.12 vs. 0.01–0.04). In contrast, direct non-additive VCs were not significant for any maternal trait except for epistasis in average weight of piglets weaned. As for maternal non-additive effects, we only discovered significant additive VC in birth weight and average daily gain and significant epistasis VC in back fat (P< 0.05). Other maternal genetic VCs were largely negligible. In summary, direct dominance and epistasis effects play a prominent role in growth traits of Yorkshire pigs.

scholarly journals PROTEIN AND AMINO ACID LEVELS AND SEQUENCE IN SWINE DIETS: EFFECTS ON GAIN, FEED CONVERSION, AND CARCASS CHARACTERISTICS

1972 ◽  
Vol 52 (3) ◽  
pp. 531-541 ◽  
Author(s):  
A. B. PIERCE ◽  
J. P. BOWLAND
Keyword(s):  
Amino Acid ◽  
Feed Intake ◽  
Average Daily Gain ◽  
Growth Stages ◽  
Intake Rate ◽  
Feed Conversion ◽  
Yorkshire Pigs ◽  
Amino Acid Balance ◽  
Protein Diets ◽  
Daily Gain

Two experiments with a total of 176 pigs were conducted to assess the effects of dietary protein level and amino acid balance on performance of starting, growing, and finishing pigs and carcass quality at market weight. Diets offered in the three stages of growth contained 20, 17, or 14% protein, 14% protein + 0.2% L-lysine HCl (L), or 14% protein + L + 0.1% DL-methionine (M). Feed intake, average daily gain, and feed conversion were inferior in the starting period for pigs fed the 14% protein diet, with less effect as the pigs aged. A compensatory feed conversion effect in later growth stages was observed in pigs fed 14% protein diets throughout. However, age to market averaged 2–3 weeks longer for pigs fed the 14% protein sequence throughout compared with other treatments. L or L plus M supplements improved feed intake, rate of gain, and feed conversion, with less effect as the pigs aged. The sequences of 20, 17, 14; 20, 14, 14; or 17, 17, 17% protein resulted in an average overall daily gain of 0.70 kg. Digestible energy and nitrogen coefficients were not influenced by diet, breed, or sex. In experiment 1, treatment had no effect on carcass measurements but in experiment 2, loin area was reduced in pigs fed 14% protein diets throughout and was improved with amino acid supplements. Although gilts generally had lower feed intakes and slower gains than barrows, they had equal feed conversion and superior carcasses. Hampshire × Yorkshire pigs gained more slowly but had superior carcasses in comparison with Landrace × Yorkshire pigs in experiment 2. The experiments demonstrate that there is considerable flexibility allowable in levels and sequence of protein that may be fed during starting, growing, and finishing periods to allow similar performance of market pigs.

scholarly journals A meta-analysis of genome-wide association studies for average daily gain and lean meat percentage in two Duroc pig populations

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Shenping Zhou ◽  
Rongrong Ding ◽  
Fanming Meng ◽  
Xingwang Wang ◽  
Zhanwei Zhuang ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Growth And Development ◽  
Genetic Architecture ◽  
Association Studies ◽  
Meta Analysis ◽  
Average Daily Gain ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Daily Gain

Abstract Background Average daily gain (ADG) and lean meat percentage (LMP) are the main production performance indicators of pigs. Nevertheless, the genetic architecture of ADG and LMP is still elusive. Here, we conducted genome-wide association studies (GWAS) and meta-analysis for ADG and LMP in 3770 American and 2090 Canadian Duroc pigs. Results In the American Duroc pigs, one novel pleiotropic quantitative trait locus (QTL) on Sus scrofa chromosome 1 (SSC1) was identified to be associated with ADG and LMP, which spans 2.53 Mb (from 159.66 to 162.19 Mb). In the Canadian Duroc pigs, two novel QTLs on SSC1 were detected for LMP, which were situated in 3.86 Mb (from 157.99 to 161.85 Mb) and 555 kb (from 37.63 to 38.19 Mb) regions. The meta-analysis identified ten and 20 additional SNPs for ADG and LMP, respectively. Finally, four genes (PHLPP1, STC1, DYRK1B, and PIK3C2A) were detected to be associated with ADG and/or LMP. Further bioinformatics analysis showed that the candidate genes for ADG are mainly involved in bone growth and development, whereas the candidate genes for LMP mainly participated in adipose tissue and muscle tissue growth and development. Conclusions We performed GWAS and meta-analysis for ADG and LMP based on a large sample size consisting of two Duroc pig populations. One pleiotropic QTL that shared a 2.19 Mb haplotype block from 159.66 to 161.85 Mb on SSC1 was found to affect ADG and LMP in the two Duroc pig populations. Furthermore, the combination of single-population and meta-analysis of GWAS improved the efficiency of detecting additional SNPs for the analyzed traits. Our results provide new insights into the genetic architecture of ADG and LMP traits in pigs. Moreover, some significant SNPs associated with ADG and/or LMP in this study may be useful for marker-assisted selection in pig breeding.

scholarly journals 268 Administering an appeasing substance to optimize welfare and performance of receiving cattle

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 193-193
Author(s):  
Eduardo Colombo ◽  
Reinaldo F Cooke ◽  
Alice Brandão ◽  
Jacob Wiegand ◽  
Kelsey Schubach ◽  
...  
Keyword(s):  
Feed Intake ◽  
Feed Efficiency ◽  
Treatment Effects ◽  
Average Daily Gain ◽  
Plasma Concentrations ◽  
Feedlot Cattle ◽  
Skin Area ◽  
And Performance ◽  
Antimicrobial Treatments ◽  
Daily Gain

Abstract This experiment evaluated the impacts of bovine appeasing substance (BAS) administration on performance, health, and physiological responses of feedlot cattle during a 45-d receiving period. A total of 342 recently-weaned Angus-influenced steers, originating from 16 cow-calf operations, were obtained from an auction yard on d -1 and road-transported (12 h) to the feedlot. Upon arrival on d 0, body weight (BW) was recorded and steers were ranked by BW and source and assigned to receive BAS (Nutricorp, Araras, SP, Brazil; n = 171) or placebo (diethylene glycol monoethyl ether; CON; n = 171). Treatments (5 mL) were topically applied to the nuchal skin area of each animal. Within treatment, calves were allocated to 1 of 24 drylot pens (12 pens/treatment) and received a free choice total-mixed ration from d 1 to 45. Calves were assessed for bovine respiratory disease (BRD) signs and feed intake was recorded from each pen daily. Steer BW was again recorded on d 1, 7, 17, 31, and 45, whereas blood samples were collected from 5 steers/pen concurrently with each BW assessment. Average daily gain was greater (P = 0.05) in BAS vs. CON calves, although final BW did not differ (P = 0.36) between treatments. No treatment effects were detected for feed intake (P = 0.95), resulting in greater (P = 0.05) feed efficiency in BAS vs. CON steers. No treatment effects were detected (P ≥ 0.37) for plasma concentrations of haptoglobin, whereas plasma cortisol concentrations were greater (P = 0.05) in CON vs. BAS steers on d 7 (treatment × day; P = 0.07). Incidence of BRD was greater (P ≤ 0.05) in BAS vs. CON on d 6 to 10 and d 18 to 21 (treatment × day; P < 0.01), although overall BRD incidence did not differ (P = 0.24) between treatments. The number of antimicrobial treatments required per steer diagnosed with BRD symptoms to recover from sickness was greater (P = 0.04) in CON vs. BAS calves. No treatment differences were detected (P ≥ 0.41) for mortality incidence, or proportion of steers removed from the experiment due to extreme sickness. Results from this experiment indicate BAS administration upon feedlot entry improved average daily gain by enhancing feed efficiency. Administration of BAS facilitated earlier detection of BRD and reduced the need for antimicrobial treatments. Collectively, these results suggest BAS administration as a promising strategy to benefit performance and immunocompetence of feedlot receiving cattle.

scholarly journals THE EFFECTS OF LEVELS OF ISOLATION, OR VARIETAL DIFFERENCES IN, HIGH FIBRE HULL FRACTION OF LOW GLUCOSINOLATE RAPESEED MEALS ON RAT OR PIG PERFORMANCE

1978 ◽  
Vol 58 (4) ◽  
pp. 743-752 ◽  
Author(s):  
J. J. KENNELLY ◽  
F. X. AHERNE ◽  
A. J. LEWIS
Keyword(s):  
Feed Intake ◽  
Average Daily Gain ◽  
Rapeseed Meal ◽  
Sprague Dawley ◽  
Crude Fibre ◽  
Gain Ratio ◽  
Sprague Dawley Rats ◽  
Significant Difference ◽  
Pig Performance ◽  
Daily Gain

Forty-eight crossbred pigs of average initial weight 21 kg were fed 10% Tower rapeseed meal (RSM) and 10% Candle RSM as partial replacements for soybean meal (SBM). Diets were formulated to be isocaloric. Pigs fed the SBM diet consumed less feed, gained significantly (P < 0.01) faster and were more efficient at converting feed to gain than those fed the RSM diets. Performance of pigs fed Candle RSM was not significantly different to that obtained with Tower RSM. In a second experiment, dehulled Tower RSM and Tower RSM hulls were mixed in amounts to produce RSM with crude fibre levels of 6.8, 10.8, 13.5 and 15.8%. The simulated RSM and Tower and Candle RSM were used to completely replace SBM in the diets of weanling (75 g) Sprague-Dawley rats. Rats fed SBM had significantly (P < 0.05) higher average daily gain (ADG) than those fed Tower or Candle RSM, or diets containing the rapeseed meats. There was no significant (P < 0.05) difference in ADG, feed intake or feed to gain ratio of rats fed either Tower or Candle RSM. Feed intake, feed to gain ratio and fecal volatile fatty acid concentrations increased while average daily gain decreased with increasing level of hulls in simulated RSM diets. There was no significant difference (P < 0.05) in thyroid weight between rats fed SBM, Tower RSM or Candle RSM.

PSIV-2 A comparison of feedlot growth and performance of beef x Holstein crossbred steers and Holstein steers

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 298-299
Author(s):  
Bailey L Basiel ◽  
Chad D Dechow ◽  
Tara L Felix
Keyword(s):  
Feed Intake ◽  
Feed Efficiency ◽  
Average Daily Gain ◽  
Corn Silage ◽  
Department Of Agriculture ◽  
Feedlot Performance ◽  
Performance Variables ◽  
Dried Distillers Grains ◽  
And Performance ◽  
Daily Gain

Abstract Objectives were to compare feedlot performance and carcass traits of F1 beef × Holstein steers and Holstein steers. Angus or Limousin × Holstein crossbred [n = 27; age = 12 ± 3 months; body weight (BW) = 435 ± 8 kg] and Holstein (n = 20; age = 11 ± 2 months; BW = 400 ± 9 kg) steers were fed at the Pennsylvania Department of Agriculture Livestock Evaluation Center for 111 days. Feed intake was recorded using the GrowSafe Feed Intake Monitoring System (Model 4000E, GrowSafe Systems Ltd., Calgary AB, Canada). The diet contained corn silage, dried distillers grains, soybean meal, and cracked corn and was formulated to meet or exceed the requirements of beef cattle (NASEM, 2016). Growth performance variables of interest and carcass measurements were analyzed with the Mixed procedure of SAS (SAS 9.4; SAS Institute Inc., Cary, NC). USDA assigned quality grades (QG) and yield grades (YG) were analyzed the with GLIMMIX procedure of SAS. Breed was a fixed effect in all models. There were no differences (P &gt; 0.05) between breeds in average daily gain or feed efficiency. Crossbreds exceeded Holsteins in initial (P &lt; 0.01) and final BW (P = 0.01), dry matter intake (P = 0.03), hot carcass weight (P &lt; 0.01), backfat (P = 0.03), and ribeye area (REA; P &lt; 0.01). Thirty-five percent (35%) of the Holsteins received a QG of Choice or above while 74% of crossbreds graded USDA Choice or above (P = 0.01). However, 75% of Holsteins were YG 2 or lower while only 45% of crossbreds achieved YG 2 or less (P = 0.05). There was no improvement in efficiency when crossbreds were compared to Holsteins; however, carcasses from crossbreds were more likely to grade USDA Choice or above while yielding greater REA and backfat than Holsteins.

scholarly journals Residual feed intake and relationships with performance of Nellore cattle selected for post weaning weight

2011 ◽  
Vol 40 (4) ◽  
pp. 929-937 ◽  
Author(s):  
T. Lucila Sobrinho ◽  
R.H. Branco ◽  
S.F.M. Bonilha ◽  
A.M. Castilhos ◽  
L.A. Figueiredo ◽  
...  
Keyword(s):  
Body Weight ◽  
Standard Deviation ◽  
Feed Intake ◽  
Average Daily Gain ◽  
Residual Feed Intake ◽  
Feed Conversion ◽  
Relative Growth ◽  
Kleiber Ratio ◽  
Nellore Cattle ◽  
Daily Gain

The objective of this work was to evaluate performance, efficiency parameters and phenotypic correlations among measurements of energy efficiency of Nellore cattle selected for post weaning weight and classified according to residual feed intake, calculated by the difference between observed and predicted intake, based on average metabolic body weight and average daily gain. Thus, animals were classified within three groups: high (> mean + 0.5 standard deviation, less efficient); medium (±0.5 standard deviation of the mean); and low (< mean - 0.5 standard deviation, more efficient) residual feed intake. No differences were observed at initial and final body weights, average daily gain and dry matter intake among groups. Animals with low residual feed intake also had greater feed efficiency, feed conversion and partial efficiency of growth and did not differ from the other animals regarding to relative growth rate and Kleiber ratio. Residual feed intake was significantly correlated to feed efficiency (-0.25), feed conversion (0.25), partial efficiency of growth (-0.37) and dry matter intake (0.16) but it did not present significant correlation with body weight (0.04), average daily gain (-0.02), relative growth rate (-0.03) and Kleiber ratio (-0.05). Significant correlations were found between feed conversion and initial body weight (0.34) and average daily gain (-0.46). Partial efficiency of growth presented significant correlation with all other efficiency parameters analyzed. Residual feed intake has high potential in productive efficiency, when compared to the other energy efficiency measurements, being independent of growth and size of the animals.

HERITABILITIES AND GENETIC CORRELATIONS FOR ULTRASONIC BACKFAT MEASUREMENTS, GROWTH AND CARCASS TRAITS IN SWINE

1982 ◽  
Vol 62 (3) ◽  
pp. 665-670 ◽  
Author(s):  
D. C. JEFFRIES ◽  
R. G. PETERSON
Keyword(s):  
Key Words ◽  
Genetic Correlation ◽  
Genetic Parameters ◽  
Average Daily Gain ◽  
Genetic Correlations ◽  
Phenotypic Correlation ◽  
Ultrasonic Measurements ◽  
Yorkshire Pigs ◽  
Daily Gain ◽  
Season Interaction

Genetic parameters were estimated for 2403 purebred Yorkshire pigs over a 2-yr period, representing 21 sires. The traits studied included average daily gain, age adjusted to 90 kg, ultrasonic measurements of backfat at the mid-back and loin positions, total and adjusted total ultrasonic backfat and corresponding carcass backfat measurements. Least squares analyses were used to estimate and adjust for the effects of sex, year-season and sex by year-season interaction. Heritabilities and genetic correlations were calculated for all traits using both half- and full-sib estimates. Adjusted age and adjusted total ultrasonic backfat measurements were found to have the highest heritabilities of the live traits in this study. Estimates of heritability for adjusted age and adjusted total ultrasonic backfat were 0.24 ± 0.10 and 0.26 ± 0.10 based on half-sib and 0.56 ± 0.07 and 0.41 ± 0.06 from full-sib analyses. The genetic correlation between these two traits was −0.07 ± 0.28 based on the half-sib method. The total phenotypic correlation was −0.01 ± 0.02. Key words: Swine, ultrasonic backfat, heritabilities, genetic correlations

Relationships between the activity of respiratory-chain complexes in pre- (biopsy) or post-slaughter muscle samples and feed efficiency in random-bred Ghezel lambs

2017 ◽  
Vol 57 (8) ◽  
pp. 1674
Author(s):  
M. J. Zamiri ◽  
R. Mehrabi ◽  
G. R. Kavoosi ◽  
H. Rajaei Sharifabadi
Keyword(s):  
Respiratory Chain ◽  
Feed Intake ◽  
Enzyme Activities ◽  
Feed Efficiency ◽  
Average Daily Gain ◽  
Chain Complex ◽  
Respiratory Chain Complex ◽  
Respiratory Chain Complexes ◽  
Chain Complexes ◽  
Daily Gain

The present study was conducted to determine the relationship between the activity of mitochondrial respiratory chain complexes in pre- and post-slaughter muscle samples and residual feed intake (RFI) in Ghezel male lambs born as a result of random mating. The study was based on the hypothesis that random-bred lambs with lower feed (or higher) RFI have lower (or higher) respiratory chain-complex activity in muscle samples. Lambs (n = 30) were fed a diet consisting of 70% concentrate and 30% alfalfa hay during a 70-day period. Individual feed intake and average daily gain were recorded to calculate the RFI, feed-conversion ratio (FCR) and adjusted FCR (aFCR). On the basis of these calculations, the lambs were classified into low and high groups for RFI, with FCR and aFCR (n = 22) being one standard deviation above or below the means; this was corroborated by Student’s t-test (P &lt; 0.01). At the end of the experiment, a 10-g biopsy sample was taken from the posterior side of the left femoral biceps. After 24 h, the lambs were slaughtered, and a sample from the posterior side of the right femoral biceps was dissected for determination of mitochondrial protein and respiratory chain-complex activities (Complexes I–V). The RFI was not correlated with the metabolic bodyweight and average daily gain, but was positively correlated (r = 0.56) with the average daily feed intake (P &lt; 0.01); mean daily feed intake in the low-RFI group was 200 g less than that in the high-RFI group. The FCR and aFCR were not significantly (P &gt; 0.05) correlated with average daily feed intake (r = 0.39 and r = 0.36 respectively), but showed a negative correlation (P &lt; 0.01) with average daily gain (r = –0.73 and r = –0.76 respectively). Although very high negative correlations were recorded between the activities of all five respiratory-chain complexes and RFI in muscle samples obtained before (–0.91 to –0.97) and after (–0.92 to –0.97) slaughter, Complexes I and V showed small negative correlations (–0.40) with FCR or aFCR (P &lt; 0.05). Enzyme activities of the respiratory-chain Complexes I, III and V were not significantly different between the pre- and post-slaughter biopsy samples; however, the enzyme activities of respiratory-chain Complexes II and IV were slightly higher in post-slaughter samples (P &lt; 0.01). These results suggested that it may be possible to use the enzymatic activity of respiratory-chain complexes in muscle biopsy samples for screening of lambs for RFI, providing a useful procedure for genetic selection of lambs for this component of feed efficiency. These encouraging results need to be verified in further experiments using other sheep breeds and a larger number of lambs.

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