scholarly journals Changes in genetic parameters for fitness and growth traits in pigs under genomic selection

2020 ◽  
Vol 98 (2) ◽  
Author(s):  
Jorge Hidalgo ◽  
Shogo Tsuruta ◽  
Daniela Lourenco ◽  
Yutaka Masuda ◽  
Yijian Huang ◽  
...  

Abstract Genomic selection increases accuracy and decreases generation interval, speeding up genetic changes in the populations. However, intensive changes caused by selection can reduce the genetic variation and can strengthen undesirable genetic correlations. The purpose of this study was to investigate changes in genetic parameters for fitness traits related with prolificacy (FT1) and litter survival (FT2 and FT3), and for growth (GT1 and GT2) traits in pigs over time. The data set contained 21,269 (FT1), 23,246 (FT2), 23,246 (FT3), 150,492 (GT1), and 150,493 (GT2) phenotypic records obtained from 2009 to 2018. The pedigree file included 369,776 animals born between 2001 and 2018, of which 39,103 were genotyped. Genetic parameters were estimated with bivariate models (FT1-GT1, FT1-GT2, FT2-GT1, FT2-GT2, FT3-GT1, and FT3-GT2) using 3-yr sliding subsets. With a Bayesian implementation using the GIBBS3F90 program computations were performed as genomic analysis (GEN) or pedigree-based analysis (PED), that is, with or without genotypes, respectively. For GEN (PED), the changes in heritability from the first to the last year interval, that is, from 2009–2011 to 2015–2018 were 8.6 to 5.6 (7.9 to 8.8) for FT1, 7.8 to 7.2 (7.7 to 10.8) for FT2, 11.4 to 7.6 (10.1 to 7.5) for FT3, 35.1 to 16.5 (32.5 to 23.7) for GT1, and 35.9 to 16.5 (32.6 to 24.1) for GT2. Differences were also observed for genetic correlations as they changed from −0.31 to −0.58 (−0.28 to −0.73) for FT1-GT1, −0.32 to −0.50 (−0.29 to −0.74) for FT1-GT2, −0.27 to −0.45 (−0.30 to −0.65) for FT2-GT1, −0.28 to −0.45 (−0.32 to −0.66) for FT2-GT2, 0.14 to 0.17 (0.11 to 0.04) for FT3-GT1, and 0.14 to 0.18 (0.11 to 0.05) for FT3-GT2. Strong selection in pigs reduced heritabilities and emphasized the antagonistic genetic relationships between fitness and growth traits. With genotypes considered, heritability estimates were smaller and genetic correlations were greater than estimates with only pedigree and phenotypes. When selection is based on genomic information, genetic parameters estimated without this information can be biased because preselection is not accounted for by the model.

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 41-41
Author(s):  
Jorge Hidalgo ◽  
Shogo Tsuruta ◽  
Daniela Lourenco ◽  
Yijian Huang ◽  
Kent Gray ◽  
...  

Abstract Genomic selection increases intensity of selection and decreases generation interval. However, intensive selection reduces genetic variation and can strengthen undesirable genetic correlations. The purpose of this study was to investigate changes in genetic parameters of litter size (LS), number born alive (NBA), number born dead (NBD) and average daily gain (ADG) and weight at off-test (WT) in pigs over time. The data set contained 20,086 (LS), 21,230 (NBA), 21,230 (NBD), 144,717 (ADG) and 144,718 (WT) phenotypic records. Pedigree file included 369,776 animals born between 2001 and 2018, of which 39,038 were genotyped. Two trait models were evaluated (LS-ADG, LS-WT, NBA-ADG, NBA-WT, NBD-ADG and NBD-WT) using 3-year sliding subsets starting from 2010. Variance components and genetic parameters were estimated using GIBBS2F90 program. Computations were performed with (BLUP) or without (ssGBLUP) genotypes. For BLUP (ssGBLUP), the changes in heritability from 2010–2012 to 2015–2018 were 0.08 to 0.09 (0.08 to 0.06) for LS, 0.33 to 0.24 (0.37 to 0.16) for ADG, 0.11 to 0.07 (0.10 to 0.07) for NBD, and 0.32 to 0.24 (0.38 to 0.17) for WT. Differences were also observed for genetic correlations as they were -0.23 to -0.73 (-0.31 to -0.58) for LS-ADG, -0.24 to -0.74 (-0.31 to -0.50) for LS-WT, -0.33 to -0.65 (-0.41 to -0.53) for NBA-ADG, -0.35 to -0.66 (-0.42 to -0.45) for NBA-WT, 0.12 to 0.04 (0.12 to 0.16) for NBD-ADG, and 0.11 to 0.05 (0.11 to 0.22) for NBD-WT. Genomic selection in pigs reduced heritabilities and emphasized the antagonistic relationship that are under strong selection. Heritabilities estimated from ssGBLUP declined more than those by BLUP while changes in the genetic correlations were smaller and more gradual by ssGBLUP. Differences between ssGBLUP and BLUP could be caused by genomic pre-selection unaccounted for by BLUP.


2000 ◽  
Vol 71 (1) ◽  
pp. 59-64 ◽  
Author(s):  
T. Oikawa ◽  
T. Sanehira ◽  
K. Sato ◽  
Y. Mizoguchi ◽  
H. Yamamoto ◽  
...  

AbstractRestricted maximum likelihood analyses fitting an animal model were conducted to estimate genetic parameters with a pooled-data set of performance tests (growth traits and food intake) on 661 bulls and progeny tests (growth traits and carcass traits) on 535 steers. Traits studied included concentrate intake (CONC), roughage intake (ROU), TDN conversion (TCNV), TDN intake (TINT) of bulls; rib eye area (REA), marbling score (MARB), dressing proportion (DRES) and subcutaneous fat depth (SCF) of steers. Body weight at start (BWS), body weight at finish (BWF) and average daily gain (ADG) of all animals were measured. Estimated heritabilities were 0·18 (CONC), 0·71 (ROU), 0·11 (TCNV) and 0·36 (TINT); 0·02 (REA), 0·49 (MARB), 0·15 (DRES), 0·15 (SCF), and from 0·20 to 0·38 for growth traits. Genetic correlations of ROU were different from those of CONC, probably due to inconsistent restrictions on concentrate intake; those of TINT with the weights, ADG and SCF were high. MARB showed positive genetic correlations with growth traits and low correlations with TINT and SCF. High potentiality for improvement of marbling score was suggested.


2019 ◽  
Vol 24 (4) ◽  
pp. 143
Author(s):  
Ibrahim Abu El- Naser

Data in this study were collected from live body weight records and milk yield for the first three lactations of Egyptian buffaloes maintained at the Mahallet Mousa Experimental Station of Animal Production Research Institute, relying on 987 records of Egyptian buffaloes spread over 16 years. These data were analyzed to estimate genetic parameters using animal model. Overall means in kilograms of BW, WW, W18, WFC, 1stMY, 2ndMY and 3rdMY were 36.56, 96.95, 322.02, 462.09, 1561.53, 1755 and 1837.71, respectively. Direct additive heritability (h2a) for mentioned traits were 0.31, 0.22, 0.24, 0.27, 0.23, 0.23 and 0.17, respectively. Corresponding computation of maternal heritability (h2m) for same traits were 0.39, 0.34, 0.22, 0.40, 0.29, 0.31 and 0.21, respectively. Evaluation of genetic correlations among different all studied traits were positive and ranged from 0.07 to 0.83, while phenotypic correlations were positive and ranged from 0.02 to 0.55. Accuracy of (PBV's) varying from 62 to 76, 62 to 83 and 41 to 77% for sires, cows and dams, successively; pointing out the genetic improvement could be achieved through any pathway of them. Higher direct and maternal heritability for BW and WFC and genetic correlations between first three lactations milk yield and each of BW and WFC higher than genetic correlations between first three lactations milk yield and WW and W18. Therefore, it is appropriate to select buffalo female calves for live body weight at birth than for live body weights at other ages.


2001 ◽  
Vol 72 (3) ◽  
pp. 449-456 ◽  
Author(s):  
A. Albera ◽  
R. Mantovani ◽  
G. Bittante ◽  
A. F. Groen ◽  
P. Carnier

AbstractEstimates of genetic parameters for beef production traits were obtained for Piemontese cattle. Data were from 988 young bulls station-tested from 1989 till 1998. Bulls entered the station at 6 to 8 weeks of age and, after an adaptation period of 3 months, were tested for growth, live fleshiness and bone thinness. Length of test was 196 days. Growth traits considered were gain at farm, gain during the adaptation period, gain on test and total gain at the station. Six different fleshiness traits and bone thinness were scored on live animals at the end of the test using a linear system. Live evaluations of fleshiness were adjusted for the weight at scoring in order to provide an assessment of conformation independent of body size. Genetic parameters were estimated using animal models. Heritability of live-weight gain ranged from 0·20 in the adaptation period to 0·60 for total gain at the station. Genetic correlations between gains at station in different periods were high (from 0·63 to 0·97). Residual correlation between gain during the adaptation period and gain during test was negative, probably due to the occurrence of compensatory growth of the animals.Live fleshiness traits and bone thinness were of moderate to high heritability (from 0·34 to 0·55) and highly correlated indicating that heavy muscled bulls also have thin bones. Accuracy of breeding values and therefore response to selection were improved by multiple trait analysis of the live fleshiness traits and bone thinness. Overall weight gain at the station had a moderate negative genetic correlation with all live fleshiness traits and bone thinness (from –0·11 to –0·39).


2011 ◽  
Vol 56 (No. 9) ◽  
pp. 381-389 ◽  
Author(s):  
K. Rzewuska ◽  
J. Jamrozik ◽  
A. Żarnecki ◽  
T. Strabel

 Genetic parameters for somatic cell score in the first three lactations of Polish Holstein-Friesian cattle were estimated. A multiple-lactation model was applied with random herd-test-day effect, fixed regressions for herd-year and age-season of calving, and random regressions for the additive genetic and permanent environmental effects. The large data set was used that included over one million test-day records and more than 58 000 cows. Estimates of covariance components and genetic parameters were obtained by Bayesian methods using the Gibbs sampler. Average daily heritabilities of somatic cell score (SCS) in the first three lactations were 0.11, 0.12 and 0.14 for the first, second and third lactation, respectively. Estimates of daily heritabilities were rather independent of days in milk (DIM), with no serious abnormalities at the beginning or the end of lactation. Average genetic correlations between SCS on the same DIM were 0.68, 0.62 and 0.70 for first and second, first and third, and second and third parities, respectively, and did not exceed 0.77. The low level of heritability estimates and relatively low genetic correlations between lactations would suggest that selection based on the first lactation only could limit a response in mastitis resistance for later lactations.


Animals ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 779 ◽  
Author(s):  
Hannah E. Willson ◽  
Hinayah Rojas de Oliveira ◽  
Allan P. Schinckel ◽  
Daniela Grossi ◽  
Luiz F. Brito

More recently, swine breeding programs have aimed to include pork quality and novel carcass (e.g., specific primal cuts such as the Boston butt or belly that are not commonly used in selection indexes) and belly traits together with growth, feed efficiency and carcass leanness in the selection indexes of terminal-sire lines, in order to efficiently produce pork with improved quality at a low cost to consumers. In this context, the success of genetic selection for such traits relies on accurate estimates of heritabilities and genetic correlations between traits. The objective of this study was to estimate genetic parameters for 39 traits in Duroc pigs (three growth, eight conventional carcass (commonly measured production traits; e.g., backfat depth), 10 pork quality and 18 novel carcass traits). Phenotypic measurements were collected on 2583 purebred Duroc gilts, and the variance components were estimated using both univariate and bivariate models and REML procedures. Moderate to high heritability estimates were found for most traits, while genetic correlations tended to be low to moderate overall. Moderate to high genetic correlations were found between growth, primal-cuts and novel carcass traits, while low to moderate correlations were found between pork quality and growth and carcass traits. Some genetic antagonisms were observed, but they are of low to moderate magnitude. This indicates that genetic progress can be achieved for all traits when using an adequate selection index.


2019 ◽  
Vol 97 (9) ◽  
pp. 3669-3683 ◽  
Author(s):  
Piush Khanal ◽  
Christian Maltecca ◽  
Clint Schwab ◽  
Kent Gray ◽  
Francesco Tiezzi

Abstract Swine industry breeding goals are mostly directed towards meat quality and carcass traits due to their high economic value. Yet, studies on meat quality and carcass traits including both phenotypic and genotypic information remain limited, particularly in commercial crossbred swine. The objectives of this study were to estimate the heritabilities for different carcass composition traits and meat quality traits and to estimate the genetic and phenotypic correlations between meat quality, carcass composition, and growth traits in 2 large commercial swine populations: The Maschhoffs LLC (TML) and Smithfield Premium Genetics (SPG), using genotypes and phenotypes data. The TML data set consists of 1,254 crossbred pigs genotyped with 60K SNP chip and phenotyped for meat quality, carcass composition, and growth traits. The SPG population included over 35,000 crossbred pigs phenotyped for meat quality, carcass composition, and growth traits. For TML data sets, the model included fixed effects of dam line, contemporary group (CG), gender, as well as random additive genetic effect and pen nested within CG. For the SPG data set, fixed effects included parity, gender, and CG, as well as random additive genetic effect and harvest group. Analyses were conducted using BLUPF90 suite of programs. Univariate and bivariate analyses were implemented to estimate heritabilities and correlations among traits. Primal yield traits were uniquely created in this study. Heritabilities [high posterior density interval] of meat quality traits ranged from 0.08 [0.03, 0.16] for pH and 0.08 [0.03, 0.1] for Minolta b* to 0.27 [0.22, 0.32] for marbling score, except intramuscular fat with the highest estimate of 0.52 [0.40, 0.62]. Heritabilities of primal yield traits were higher than that of primal weight traits and ranged from 0.17 [0.13, 0.25] for butt yield to 0.45 [0.36, 0.55] for ham yield. The genetic correlations of meat quality and carcass composition traits with growth traits ranged from moderate to high in both directions. High genetic correlations were observed for male and female for all traits except pH. The genetic parameter estimates of this study indicate that a multitrait approach should be considered for selection programs aimed at meat quality and carcass composition in commercial swine populations.


2019 ◽  
Vol 97 (10) ◽  
pp. 4076-4084
Author(s):  
Tiphaine Macé ◽  
Dominique Hazard ◽  
Fabien Carrière ◽  
Sebastien Douls ◽  
Didier Foulquié ◽  
...  

Abstract The main objective of this work was to study the relationships between body reserve (BR) dynamics and rearing performance (PERF) traits in ewes from a Romane meat sheep flock managed extensively on “Causse” rangelands in the south of France. Flock records were used to generate data sets covering 14 lambing years (YR). The data set included 1,146 ewes with 2 ages of first lambing (AGE), 3 parities (PAR), and 4 litter sizes (LS). Repeated measurements of the BW and BCS were used as indicators of BR. The ewe PERF traits recorded were indirect measurements for maternal abilities and included prolificacy, litter weight and lamb BW at lambing and weaning, ADG at 1, 2, and 3 mo after lambing, and litter survival from lambing to weaning. The effects of different BW and BCS trajectories (e.g., changes in BW and BCS across the production cycle), previously been characterized in the same animals, on PERF traits were investigated. Such trajectories reflected different profiles at the intraflock level in the dynamics of BR mobilization–accretion cycles. Genetic relationships between BR and PERF traits were assessed. All the fixed variables considered (i.e., YR, AGE, PAR, LS, and SEX ratio of the litter) have significant effects on the PERF traits. Similarly, BW trajectories had an effect on the PERF traits across the 3 PARs studied, particularly during the first cycle (PAR 1). The BCS trajectories only affected prolificacy, lamb BW at birth, and litter survival. Most of the PERF traits considered here showed moderate heritabilities (0.17–0.23) except for prolificacy, the lamb growth rate during the third month and litter survival which showed very low heritabilities. With exception of litter survival and prolificacy, ewe PERF traits were genetically, strongly, and positively correlated with BW whatever the physiological stage. A few weak genetic correlations were found between BCS and PERF traits. As illustrated by BW and BCS changes over time, favorable genetic correlations were found, even if few and moderate, between BR accretion or mobilization and PERF traits, particularly for prolificacy and litter weight at birth. In conclusion, our results show significant relationships between BR dynamics and PERF traits in ewes, which could be considered in future sheep selection programs aiming to improve robustness.


1980 ◽  
Vol 30 (2) ◽  
pp. 271-276 ◽  
Author(s):  
A. P. Mavrogenis ◽  
A. Louca ◽  
O. W. Robison

ABSTRACTData on 792 Chios lambs born during the 1972/73 and 1973/74 lambing seasons were used to estimate genetic and phenotypic parameters for birth weight, weaning weight, age at weaning, pre-weaning daily gain, body weight at 5, 10, 15 and 20 weeks of age, and postweaning daily gain. Body weight at 15 weeks of age had the highest heritability estimate (0·73 ± 0·17) and that of post-weaning daily gain was also high (0·56 ± 0·15). Selection for either weight at 15 weeks or post-weaning daily gain would be expected to yield a greater response than selection for pre-weaning daily gain or weaning weight. Genetic correlations among weights and/or gains were positive (approximately 0·20). Phenotypic correlations among weights and gains were generally higher than genetic correlations. However, the correlation between pre— and post-weaning daily gain was small (0·08). Likewise, post-weaning daily gain had low correlations with all weights before 10 weeks. Age at weaning had moderate negative associations with all weights but a very low positive correlation with post-weaning daily gain.


2005 ◽  
Vol 81 (1) ◽  
pp. 11-21 ◽  
Author(s):  
N. R. Lambe ◽  
S. Brotherstone ◽  
M. J. Young ◽  
J. Conington ◽  
G. Simm

AbstractScottish Blackface ewes (no. = 308) were scanned four times per year using X-ray computed tomography (CT scanning) (pre-mating, pre-lambing, mid lactation and weaning), from 18 months to 5 years of age, giving a maximum of 16 scanning events per ewe. Total weights of carcass fat, internal fat and carcass muscle were estimated from the CT images at each scanning event. Lambs produced by these ewes were weighed at birth, mid lactation and weaning to calculate litter growth traits: litter birth weight; litter weight gain from birth until mid lactation; and litter weight gain from birth until weaning. Genetic (rg) and phenotypic (rp) correlations were estimated between ewe CT tissue traits and litter growth traits. Correlations between ewe CT tissue traits and litter size (LS) were also estimated. Ewe CT tissue traits were either unadjusted or adjusted for total soft tissue weight (sum of weights of carcass fat, internal fat and carcass muscle) to investigate relationships with either absolute tissue weights of carcass fat (CFWT), internal fat (IFWT), and carcass muscle (CMWT), or relative proportions of carcass fat (CFP), internal fat (IFP), and carcass muscle (CMP). Litter growth traits were either unadjusted or adjusted for litter size, to investigate relationships with total lamb burden (total litter birth weight (TBW), total litter weight gain from birth until mid lactation (TWGM), total litter weight gain from birth until weaning (TWGW)) or average lamb performance (average lamb birth weight (ABW), average lamb weight gain from birth until mid lactation (AWGM), average lamb weight gain from birth until weaning (AWGW)).Moderate to large positive genetic correlations were estimated between absolute weights of all three ewe tissues (CFWT, IFWT, CMWT), or muscle proportion (CMP), and litter size (LS). Significant positive genetic correlations were also estimated between weight (CMWT) or proportion (CMP) of muscle carried by the ewe pre-mating and total birth weight (TBW) and weight gains (TWGM, TWGW) of her litter, largely due to the associated increase in litter size. Muscle proportion (CMP) was not significantly correlated to average lamb weights or weight gains (ABW, AWGM, AWGW). Pre-lambing carcass fat weight (CFWT) and proportion (CFP) in the ewe showed positive genetic correlations with average lamb weights and weight gains (ABW, AWGM, AWGW), whereas, after lambing, CFP was negatively correlated with these lamb traits. Internal fat weight (IFWT) pre-mating showed positive genetic correlations with all litter growth traits (TBW, TWGM, TWGW, ABW, AWGM, AWGW). Average lamb growth traits were negatively correlated with pre-lambing internal fat proportion (IFP), but positively correlated to IFP at mid lactation and weaning.Correlations were also estimated between each pair of CT traits. Total internal fat weight and total carcass fat weight were very highly correlated (rp= 0·75,rg= 0·96). Correlations with total carcass muscle weight were smaller and positive for both carcass fat weight (rp= 0·48,rg= 0·12) and internal fat weight (rp= 0·42,rg= 0·20).The results suggest that selection for increased carcass muscle weight or proportion in a Scottish Blackface hill flock would have a positive effect on total weights of litters reared, but that selection against carcass fat weight or proportion in a breeding programme for Blackface sheep may have an impact on the maternal ability of the ewe. However, maintaining fat in internal depots may reduce the depletion of carcass fat during pregnancy, allowing this depot to provide energy for lactation, and may have a positive impact on lamb growth.


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