Comparison of two models to estimate genetic parameters for number of born alive in pigs

The performance of the two‐trait animal model that regards the first parity and later parities as two different traits in estimating genetic parameters for number of born alive (NBA) was examined using real and simulated data. Genetic parameters for NBA were estimated in purebred Landrace and Large White pigs using a single‐trait repeatability model (Model 1) that regards all parities as the same trait and a two‐trait animal model (Model 2) that regards the first and the later parities as different traits. For Model 2, the permanent environmental effect was fitted to only the records of the later parities. Heritability for NBA estimated using Model 1 was 0.12 for Landrace and 0.11 for Large White. Estimated heritability for NBA of the first parity and the later parities was 0.21 and 0.16, respectively, for Landrace; 0.18 and 0.16, respectively, for Large White obtained using Model 2, and higher than those in both breeds obtained using Model 1. Further results based on data simulated using the Monte Carlo method suggest that estimated additive genetic variance could be more biased using Model 2 than Model 1.     

荣昌猪初产繁殖性状的全基因组关联研究

旨在鉴定荣昌猪初产繁殖性状的重要变异位点和基因,为荣昌猪繁殖性状的遗传改良提供重要的分子标记和基因资源。本研究选取429头荣昌母猪进行猪50K芯片基因分型,经过质量控制和基因型填充后,保留35 046个SNPs用于分析。采用主成分分析法研究群体结构,利用混合线性模型(mixed-linear model, MLM)将出生年、出生月作为固定效应,将主成分值作为协变量对总产仔数、活产仔数、死胎数和初生窝重性状进行全基因组关联分析(GWAS)。结果显示,在全基因组显著水平上鉴定出2个影响荣昌猪初生窝重的SNPs和1个影响荣昌猪死胎数的SNP;在潜在显著水平上鉴定到5个影响荣昌猪总产仔数的SNPs, 3个影响荣昌猪活产仔数的SNPs和10个影响荣昌猪死胎数的SNPs。通过全基因组关联分析筛选到1个显著的SNP(SSC17:57 315 180 bp)同时影响荣昌猪总产仔数、活产仔数和初生窝重,1个显著的SNP(SSC1:279 214 647 bp)同时影响荣昌猪活产仔数和总产仔数,暗示基因在不同性状间具有一因多效性。本研究根据候选基因的相关分子生物学功能,确定BMP7基因为影响荣昌猪总产仔数...     

Growth rate of growing pigs is weakly correlated genetically with litter size,while the amount of genetic variation for growth rate changes with litter size

Abstract

We reasoned that if we assessed pigs for litter size and growth rate during the grow-out stage of production (25–100 kg body weight) we would find: 1) an unfavourable genetic correlation between litter size and growth rate; and 2) that the amount of additive genetic variation expressed for growth rate varies with litter size. We tested these premises by assessing 2212 litters from the Yorkshire breed for litter size, while 3038 growing pigs from 550 of these litters were assessed for growth rate during the grow-out stage of production. Genetic correlations were estimated using the additive genetic (co)variances obtained from a bivariate linear animal model fitted to litter size and growth rate. The amount of additive genetic variation expressed for growth rate as a function of litter size was estimated by fitting a univariate linear animal model with random regression on litter size. Our findings did not support the first of our premises as we found that the genetic correlation between litter size and growth rate was favourable (0.28±0.27), albeit not significantly different from zero. However, we were able to support our second premise as we found that the relationship between amount of additive genetic variation for growth rate and litter size was quadratic; the amount of additive genetic variation was highest in small and large litters (h²=0.60 and 0.65), and lowest in intermediate litter sizes (h²=0.29). These findings indicate that: 1) breeding for litter size would not reduce the growth rate of growing pigs; and 2) the amount of genetic variation for growth rate changes with litter size.     

Optimal selection method for establishing an inbred strain of laboratory animals with high performance for litter size at weaning

The optimal selection method was investigated for establishing an inbred strain of laboratory animals with high performance for litter size at weaning (LSW). A Monte Carlo computer simulation was used to assess the effects of our selection methods on the genetic change of LSW under the continuous use of full‐sib mating for 20 generations. Smaller number of growing animals of each sex per litter and genetic evaluation for selection using a BLUP animal model increased LSW. Use of information on another trait genetically related to LSW, larger population size, and greater number of generations for random selection before starting full‐sib mating were useful for establishing an inbred strain of laboratory animals with high performance for LSW. It was concluded that LSW can be increased by directional selection when establishing inbred strains.     

Estimation of genetic parameters for farrowing traits in purebred Landrace and Large White pigs

Genetic parameters were estimated for six reproductive traits related to farrowing events in Landrace and Large White pigs; total number born (TNB), number born alive (NBA), number stillborn (NSB), total litter weight at birth (LWB), mean litter weight at birth (MWB), and gestation length (GL). We analyzed 62,534 farrowing records for 10,637 Landrace dams and 49,817 farrowing records for 8,649 Large White dams. Estimated heritabilities of TNB, NBA, NSB, LWB, MWB, and GL by single‐trait repeatability model analyses were 0.12, 0.12, 0.08, 0.18, 0.19, and 0.29, respectively, in Landrace, and 0.12, 0.10, 0.08, 0.18, 0.16, and 0.34, respectively, in Large White. Genetic correlation between NBA and NSB was unfavorable: 0.20 in Landrace and 0.33 in Large White. Genetic correlations of GL with the other five traits were weak: from ?0.18 with NSB to ?0.03 with NBA in Landrace, and from ?0.22 with NSB to ?0.07 with NBA in Large White. LWB had a highly favorable genetic correlation with NBA (0.74 in both breeds), indicating the possibility of using LWB for the genetic improvement of NBA.     

A comparison of accuracy validation methods for genomic and pedigree‐based predictions of swine litter size traits using Large White and simulated data

The objective of this study was to compare and determine the optimal validation method when comparing accuracy from single‐step GBLUP (ssGBLUP) to traditional pedigree‐based BLUP. Field data included six litter size traits. Simulated data included ten replicates designed to mimic the field data in order to determine the method that was closest to the true accuracy. Data were split into training and validation sets. The methods used were as follows: (i) theoretical accuracy derived from the prediction error variance (PEV) of the direct inverse (iLHS), (ii) approximated accuracies from the accf90(GS) program in the BLUPF90 family of programs (Approx), (iii) correlation between predictions and the single‐step GEBVs from the full data set (GEBV_Full), (iv) correlation between predictions and the corrected phenotypes of females from the full data set (Y_c), (v) correlation from method iv divided by the square root of the heritability (Y_ch) and (vi) correlation between sire predictions and the average of their daughters' corrected phenotypes (Y_cs). Accuracies from iLHS increased from 0.27 to 0.37 (37%) in the Large White. Approximation accuracies were very consistent and close in absolute value (0.41 to 0.43). Both iLHS and Approx were much less variable than the corrected phenotype methods (ranging from 0.04 to 0.27). On average, simulated data showed an increase in accuracy from 0.34 to 0.44 (29%) using ssGBLUP. Both iLHS and Y_ch approximated the increase well, 0.30 to 0.46 and 0.36 to 0.45, respectively. GEBV_Full performed poorly in both data sets and is not recommended. Results suggest that for within‐breed selection, theoretical accuracy using PEV was consistent and accurate. When direct inversion is infeasible to get the PEV, correlating predictions to the corrected phenotypes divided by the square root of heritability is adequate given a large enough validation data set.     

Components of heterosis for growth traits and litter size in line crosses of mice after long-term selection

Strains selected for 54 generations for large 8-week weight (N8, S8), for small weight (N6, S6), for high 3–5-week gain and low 8-week weight (N1) as well as unselected randomly mated control strains (N9, S9) were crossed, and F ₁, F ₂ and both back crosses created. N strains are derived from a NMRI base, S strains from a synthetic four-way cross among inbred lines. Heterosis for 8-week weight (8-ww) was some 6%, but 30% for 3–5-week gain and it was on average negative (22%) for 5–8-week gain. When epistatic effects were taken into account, it appeared that heterosis for 8-ww was largely due to beneficial effects of non-parental gene combinations, i.e. additive × additive epistatic effects were negative. These non-parental combinations neutralized the mostly negative dominance effects. The latter were mostly positive for early gain but in all 9 line crosses negative for late gain. The digenic effects of the non-parental origin were not large enough to balance the negative dominance effects for late gain, so that heterosis was negative. It appears therefore that early and late gain are affected by different sets of genes. Maternal additive effects on 8-ww and early gain are smaller than direct additive effects but mostly of similar sign. For late gain there appears to be no connection with direct additive effects. Direct litter heterosis was almost 50% but much of this was due to positively acting recombinational gene combinations, while direct litter dominance was mostly negative. Maternal additive effects on litter size differed depending on whether they were estimated from dams with crossbred or with purebred litter. Heterosis was small in crosses between control strains. Heterosis caused by recombinant gene pairs should be amenable to improvement by selection.     

Improving management for higher reproduction accelerates genetic improvement in closed herd of swine

The present study compared responses to selection at different conception rates and litter sizes at weaning in a simulated closed herd in a swine breeding program. The base population consisted of 10 males and 50 females, and 10 generations of selection was practiced by using individual phenotype or best linear unbiased prediction of breeding values for a trait with heritability (h²) of either 0.2 or 0.5. The probability of conception in a single mating was assumed to be 0.8, 0.9 or 1.0. Litter size at weaning was sampled randomly from a normal distribution with mean 8, 10 or 12 and variance 8.1225. Genetic response increased by approximately 6% for h² = 0.2 and approximately 5% for h² = 0.5 at generation 10 when conception rate was increased from 0.8 to 1.0. However, litter size at weaning did not affect response to selection. In conclusion, improving conception rate by environmental management increases genetic response indirectly in a breeding program of a closed swine herd.     

Effective population size and inbreeding depression on litter size in rabbits. A case study

The purpose of this study is to use demographic and litter size data on four Spanish maternal lines of rabbits (A, V, H and LP), as a case study, in order to: (i) estimate the effective population size of the lines, as a measure of the rate of increase of inbreeding, and (ii) study whether the inbreeding effect on litter size traits depends on the pattern of its accumulation over time. The lines are being selected for litter size at weaning and are kept closed at the same selection nucleus under the same selection and management programme. The study considered 47 794 l and a pedigree of 14 622 animals. Some practices in mating and selection management allow an increase of the inbreeding coefficient lower than 0.01 per generation in these lines of around 25 males and 125 females. Their effective population size (Ne) was around 57.3, showing that the effect of selection, increasing the inbreeding, was counterbalanced by the management practices, intended to reduce the rate of inbreeding increase. The inbreeding of each individual was broken down into three components: old, intermediate and new inbreeding. The coefficients of regression of the old, intermediate and new inbreeding on total born (TB), number born alive (NBA) and number weaned (NW) per litter showed a decreasing trend from positive to negative values. Regression coefficients significantly different from zero were those for the old inbreeding on TB (6.79 ± 2.37) and NBA (5.92 ± 2.37). The contrast between the coefficients of regression between the old and new inbreeding were significant for the three litter size traits: 7.57 ± 1.72 for TB; 6.66 ± 1.73 for NBA and 5.13 ± 1.67 for NW. These results have been interpreted as the combined action of purging unfavourable genes and artificial selection favoured by the inbreeding throughout the generations of selection.     

Genetic parameter estimation for number born alive at different parities in Landrace and Large White pigs

We estimated genetic parameters for number born alive (NBA) from the first to the seventh parities in Landrace and Large White pigs using three models. Analyzing 55,160 farrowing records for 12,677 Landrace dams and 43,839 for 10,405 Large White dams, we used a single‐trait animal model to estimate the heritability of NBA at each parity and a two‐trait animal model and a single‐trait random regression model to estimate the genetic correlations between parities. Heritability estimates of NBA at each parity ranged from 0.08 to 0.13 for Landrace and from 0.05 to 0.16 for Large White. Estimated genetic correlations between parities in all cases were positive. Genetic correlations between the first and second parities were slightly lower than those between other neighboring parities. Genetic correlations between more distant parities tended to be lower, in some cases <0.8. The results indicate the necessity to investigate the applicability of evaluating NBA at different parities as different traits (e.g., the first and later parities), although a repeatability model might still be reasonable.     

台系杜洛克猪产仔数重复力的评定

为了解台系杜洛克母猪重复力遗传参数在国内的适应性,充实完善台系杜洛克猪产仔数的重复力,继续选育提高杜洛克猪育种水平及经济效益。通过采用组内相关的方法,对某大型种猪企业的台系杜洛克猪1~8胎次产仔数的重复力进行估测。结果表明:台系杜洛克猪1~8胎次的平均产仔数分别为8.6头、9.65头、9.35头、9.00头、8.30头、8.80头、7.65头;台系杜洛克猪8个胎次平均产仔数为8.44头;台系杜洛克猪产仔数的重复力为0.42。     

Relationships among steroid hormone levels in newborn piglets,birth weight,placental weight,vitality of offspring and litter size

Blood estrone sulfate (E₁S), estrone (E₁), estradiol (E₂) and progesterone (P₄) in newborn piglets were measured to clarify the relationships among birth and placental weight, vitality of offspring and litter size. First, the association between vital status (normal, weak and stillborn) from 165 newborn piglets of 18 litters and steroid concentrations; second, steroid concentrations from 152 newborn normal piglets and litter size; and third, steroid content in fetal placenta from 50 newborn normal piglets of six litters and litter size, were investigated. In the normal group, the birth and placental weight were significantly higher than those in the other groups. Blood E₁S levels in the stillborn group were significantly lower, whereas E₁, E₂ and P₄ were significantly higher compared to the normal group. Blood and placental E₁S levels in the small litter group were significantly higher than those in the other groups. However, there was no significant difference among the three litter size groups in the levels of steroid hormones in maternal blood. These results indicate that vitality of newborn piglets is related to E₁S concentration of neonate, to birth weight and placental weight. However, steroid hormone concentrations of newborn piglets were greatly affected by the number of littermates.     

Short communication: investigation of the feasibility of genomic selection in Icelandic Cattle

Icelandic Cattle is a local dairy cattle breed in Iceland. With about 26,000 breeding females, it is by far the largest among the indigenous Nordic cattle breeds. The objective of this study was to investigate the feasibility of genomic selection in Icelandic Cattle. Pedigree-based best linear unbiased prediction (PBLUP) and single-step genomic best linear unbiased prediction (ssGBLUP) were compared. Accuracy, bias, and dispersion of estimated breeding values (EBV) for milk yield (MY), fat yield (FY), protein yield (PY), and somatic cell score (SCS) were estimated in a cross validation-based design. Accuracy (r^) was estimated by the correlation between EBV and corrected phenotype in a validation set. The accuracy (r^) of predictions using ssGBLUP increased by 13, 23, 19, and 20 percentage points for MY, FY, PY, and SCS for genotyped animals, compared with PBLUP. The accuracy of nongenotyped animals was not improved for MY and PY, but increased by 0.9 and 3.5 percentage points for FY and SCS. We used the linear regression (LR) method to quantify relative improvements in accuracy, bias (Δ^), and dispersion (b^) of EBV. Using the LR method, the relative improvements in accuracy of validation from PBLUP to ssGBLUP were 43%, 60%, 50%, and 48% for genotyped animals for MY, FY, PY, and SCS. Single-step GBLUP EBV were less underestimated (Δ^), and less overdispersed (b^) than PBLUP EBV for FY and PY. Pedigree-based BLUP EBV were close to unbiased for MY and SCS. Single-step GBLUP underestimated MY EBV but overestimated SCS EBV. Based on the average accuracy of 0.45 for ssGBLUP EBV obtained in this study, selection intensities according to the breeding scheme of Icelandic Cattle, and assuming a generation interval of 2.0 yr for sires of bulls, sires of dams and dams of bulls, genetic gain in Icelandic Cattle could be increased by about 50% relative to the current breeding scheme.     

Developments in prediction theories of the effective size of populations under selection

The effective population size is a key parameter in the definition of selection programs, because the magnitude of this parameter determines both the rate of inbreeding and the amount of genetic drift in the population. Prediction of the effective size of selected populations is complicated by the fact that selection has a cumulative effect on the effective size. In the present article, two basic approaches to predict the effective size of populations under selection were summarized, and the interrelation among them was clarified. Several extensions to practical situations relevant to animal breeding, such as non‐random mating, index selection and marker‐assisted selection, were also reviewed.     

Characterization of a line of pigs previously selected for increased litter size for RBP4 and follistatin

The objective of this study was to determine if selection response for increased litter size in pigs could be partially attributed to three type 1 marker loci coding for genes known to affect litter size: oestrogen receptor (ESR), retinol‐binding protein 4 (RBP4) and follistatin (FS). In the high litter size line (LS), pigs from the largest litters, based on number of pigs born alive (NBA), were retained to parent the next generation. A randomly selected control line (LC) was maintained. Gilts were reared in litters of 10 pigs or less to minimize maternal effects. Pigs were measured at generations 10–12. Additional traits scored were number of fully formed pigs (NFF) and number of mummified fetuses (MUM). Breeding values for NFF and NBA were greater (p < 0.05) in LS than LC in generations 11 and 12, but no significant line differences were found for MUM. The A allele of the ESR locus was fixed in both lines. After adjustment for effects of genetic drift, frequency of the two alleles segregating for the FS and RBP4 loci did not differ significantly between lines. No significant additive or dominance effects of the FS markers were detected for NFF, NBA and MUM in either LS or LC. Response to selection for increased litter size could not be attributed to effects at the ESR, RBP4 or FS loci.     

Estimation of direct and maternal genetic variance for litter size in Canadian Yorkshire and Landrace swine using an animal model

Estimates of additive direct heritability (h2a) for traits such as litter size may be biased by maternal effects. The size of these effects was estimated using a derivative-free restricted maximum likelihood procedure under an animal model. First-parity records from Yorkshire (Y) and Landrace (L) gilts were obtained from the Quebec Record of Performance sow productivity program for 21,127 litters born between 1977 and 1987. Direct (sigma 2a) and maternal (sigma 2m) additive genetic variances, their covariance (sigma am) and error variance (sigma 2e) were estimated for total numbers born (NOBN), born alive (NOBA) and weaned (NOWN). Analysis of purebred Y and crossbred litters indicated that estimates of sigma 2a were of similar magnitude for all traits, with h2a ranging from .06 to .13. Except for L litters, estimates of sigma 2m were relatively low for NOBN and NOBA, and increased in size for NOWN, with h2m ranging from 0 to .08. Also, estimates of sigma am were negative, except for NOBN and NOBA with crossbred litters, and became increasingly negative for NOWN. Results from purebred L litters indicated there was a stronger negative correlation between direct and maternal genetic effects for NOBN and NOBA than for NOWN.     

Genetic parameters for litter size,piglet growth and sow's early growth and body composition in the Chinese–European line Tai Zumu

Genetics of piglet growth in association with sow's early growth and body composition were estimated in the Tai Zumu line. Piglet and sow's litter growth traits were calculated from individual weights collected at birth and at 3 weeks of age. Sow's litter traits included the number of piglets born alive (NBA), the mean piglet weight (MW) and the standard deviation of weights within the litter (SDW). Sow's early growth was measured by the age at 100 kg (A₁₀₀), and body composition included backfat thickness (BF₁₀₀). A main objective of this study was to estimate separately the direct genetic effect (d) and the maternal genetic effect (m) on piglet weight and daily weight gain during lactation. Variance components were estimated using the restricted maximum likelihood methodology based on animal models. The heritability estimates were 0.19 for NBA, 0.15 and 0.26 for SDW and MW at 3 weeks and 0.42 and 0.70 for A₁₀₀ and BF₁₀₀. The NBA was almost independent from SDW. Conversely, the A₁₀₀ and BF₁₀₀ were correlated unfavourably with SDW (r_g<−0.24, SE<0.12). A stronger selection for litter size should have little effect on litter homogeneity in weights. Selection for lean growth rate tends to favour heterogeneity in weights. The direct effect on piglet weight at birth and daily weight gain accounted for 12% (h² (d) = 0.02) and 50% (h² (d) = 0.11) of the genetic variance, respectively. The association between d and m for piglet weight was not different from zero at birth (r_g = 0.19, SE = 0.27), but a strong antagonism between d and m for daily weight gain from birth to 3 weeks was found (r_g = −0.41, SE = 0.17). Substantial direct and maternal genetic effects influenced piglet growth until weaning in opposite way.     

Genetic determination of individual birth weight, litter weight and litter size in Mukota pigs

Genetic parameters for individual birth weight (IBWT), total number of pigs born (NBT), number of pigs born alive (NBA), number of pigs born dead (NBD) and litter weight at birth (LBWT) were estimated using 1961 Mukota pigs kept at the University of Zimbabwe Farm, Harare, Zimbabwe. Variance components were estimated for IBWT based on a direct-maternal genetic effects model. The genetic relationships among NBT, NBA, NBD and LBWT were assessed using a multi-trait direct effects model. For LBWT, the direct, maternal and common environmental litter proportions on the phenotypic variance were 0.090, 0.033 and 0.009, respectively. After adjustment of IBWT for NBA, phenotypic fractions were 0.091, 0.034 and 0.011 for direct, maternal and litter effects. The correlation between the direct and maternal genetic effects of IBWT was − 0.354 and − 0.295, with and without adjustment for NBT. Heritabilities for NBT, NBA, NBD and LBWT were 0.020, 0.030, 0.088 and 0.196, respectively. Differences in the maternal heritability and the heritability for LBWT, a trait of the dam, are different due to accumulation of observations per litter. Maternal genetic effects are, therefore, of less importance than in highly selected European breeds.     

BMPR-IB基因多态性与河北肉用绵羊产羔数及羔羊生长发育的相关性研究

为了研究BMPR-IB基因单核苷酸多态性及其对绵羊产羔数和羔羊生长发育的影响,试验采用PCR-RFLP方法对小尾寒羊、杜泊、德克赛尔及河北肉用绵羊的BMPR-IB基因单核苷酸多态性进行了测定,并对BMPR-IB基因多态性与河北肉用绵羊产羔数和生长发育的关系进行了研究。结果表明:基因型频率在各品种间分布极不平衡,BB基因型河北肉用绵羊群体的总体平均产羔数显著高于B+基因型(P<0.05),极显著高于++基因型群体(P<0.01);90日龄时,++基因型河北肉用绵羊的胸宽和腰角宽显著高于B+基因型群体(P<0.05)。说明BMPR-IB基因的基因型对河北肉用绵羊羔羊的生长发育有一定影响。