Review: optimizing genomic selection for crossbred performance by model improvement and data collection

Breeding programs aiming to improve the performance of crossbreds may benefit from genomic prediction of crossbred (CB) performance for purebred (PB) selection candidates. In this review, we compared genomic prediction strategies that differed in 1) the genomic prediction model used or 2) the data used in the reference population. We found 27 unique studies, two of which used deterministic simulation, 11 used stochastic simulation, and 14 real data. Differences in accuracy and response to selection between strategies depended on i) the value of the purebred crossbred genetic correlation (rpc), ii) the genetic distance between the parental lines, iii) the size of PB and CB reference populations, and iv) the relatedness of these reference populations to the selection candidates. In studies where a PB reference population was used, the use of a dominance model yielded accuracies that were equal to or higher than those of additive models. When rpc was lower than ~0.8, and was caused mainly by G × E, it was beneficial to create a reference population of PB animals that are tested in a CB environment. In general, the benefit of collecting CB information increased with decreasing rpc. For a given rpc, the benefit of collecting CB information increased with increasing size of the reference populations. Collecting CB information was not beneficial when rpc was higher than ~0.9, especially when the reference populations were small. Collecting only phenotypes of CB animals may slightly improve accuracy and response to selection, but requires that the pedigree is known. It is, therefore, advisable to genotype these CB animals as well. Finally, considering the breed-origin of alleles allows for modeling breed-specific effects in the CB, but this did not always lead to higher accuracies. Our review shows that the differences in accuracy and response to selection between strategies depend on several factors. One of the most important factors is rpc, and we, therefore, recommend to obtain accurate estimates of rpc of all breeding goal traits. Furthermore, knowledge about the importance of components of rpc (i.e., dominance, epistasis, and G × E) can help breeders to decide which model to use, and whether to collect data on animals in a CB environment. Future research should focus on the development of a tool that predicts accuracy and response to selection from scenario specific parameters.     

Impact of inclusion rates of crossbred phenotypes and genotypes in nucleus selection programs

Numerous methods have been suggested to incorporate crossbred (CB) phenotypes and genotypes into swine selection programs, yet little research has focused on the implicit trade-off decisions between generating data at the nucleus or commercial level. The aim of this study was to investigate the impact of altering the proportion of purebred (PB) and CB phenotypes and genotypes in genetic evaluations on the response to selection of CB performance. Assuming CB and PB performance with moderate heritabilities (h2=0.4), a three-breed swine crossbreeding scheme was simulated and selection was practiced for six generations, where the goal was to increase CB performance. Phenotypes, genotypes, and pedigrees for three PB breeds (25 and 175 mating males and females for each breed, respectively), F₁ crosses (400 mating females), and terminal cross progeny (2,500) were simulated. The genome consisted of 18 chromosomes with 1,800 quantitative trait loci and 72k single nucleotide polymorphism (SNP) markers. Selection was performed in PB breeds using estimated breeding value for each phenotyping/genotyping strategy. Strategies investigated were: 1) increasing the proportion of CB with genotypes, phenotypes, and sire pedigree relationships, 2) decreasing the proportion of PB phenotypes and genotypes, and 3) altering the genetic correlation between PB and CB performance (rpc). Each unique rpc scenario and data collection strategy was replicated 10 times. Results showed that including CB data improved the CB performance regardless of rpc or data collection strategy compared with when no CB data were included. Compared with using only PB information, including 10% of CB progeny per generation with sire pedigrees and phenotypes increased the response in CB phenotype by 134%, 55%, 33%, 23%, and 21% when rpc was 0.1, 0.3, 0.5, 0.7, and 0.9, respectively. When the same 10% of CB progeny were also genotyped, CB performance increased by 243%, 54%, 38%, 23%, and 20% when the rpc was 0.1, 0.3, 0.5, 0.7, and 0.9, respectively, compared with when no CB data were utilized. Minimal change was observed in the average CB phenotype when PB phenotypes were included or proportionally removed when CB were genotyped. Removal of both PB phenotypes and genotypes when CB were genotyped greatly reduced the response in CB performance. In practice, the optimal inclusion rate of CB and PB data depends upon the genetic correlation between CB and PB animals and the expense of additional CB data collection compared with the economic benefit associated with increased CB performance.     

Genetic parameters and purebred–crossbred genetic correlations for growth,meat quality,and carcass traits in pigs

Growth, meat quality, and carcass traits are of economic importance in swine breeding. Understanding their genetic basis in purebred (PB) and commercial crossbred (CB) pigs is necessary for a successful breeding program because, although the breeding goal is to improve CB performance, phenotype collection and selection are usually carried out in PB populations housed in biosecure nucleus herds. Thus, the selection is indirect, and the accuracy of selection depends on the genetic correlation between PB and CB performance (rpc). The objectives of this study were to 1) estimate genetic parameters for growth, meat quality, and carcass traits in a PB sire line and related commercial CB pigs and 2) estimate the corresponding genetic correlations between purebred and crossbred performance (rpc). Both objectives were investigated by using pedigree information only (PBLUP) and by combining pedigree and genomic information in a single-step genomic BLUP (ssGBLUP) procedure. Growth rate showed moderate estimates of heritability for both PB and CB based on PBLUP, while estimates were higher in CB based on ssGBLUP. Heritability estimates for meat quality traits were diverse and slightly different based on PB and CB data with both methods. Carcass traits had higher heritability estimates based on PB compared with CB data based on PBLUP and slightly higher estimates for CB data based on ssGBLUP. A wide range of estimates of genetic correlations were obtained among traits within the PB and CB data. In the PB population, estimates of heritabilities and genetic correlations were similar based on PBLUP and ssGBLUP for all traits, while based on the CB data, ssGBLUP resulted in different estimates of genetic parameters with lower SEs. With some exceptions, estimates of rpc were moderate to high. The SE on the rpc estimates was generally large when based on PBLUP due to limited sample size, especially for CBs. In contrast, estimates of rpc based on ssGBLUP were not only more precise but also more consistent among pairs of traits, considering their genetic correlations within the PB and CB data. The wide range of estimates of rpc (less than 0.70 for 7 out of 13 traits) indicates that the use of CB phenotypes recorded on commercial farms, along with genomic information, for selection in the PB population has potential to increase the genetic progress of CB performance.     

Inclusion of sire by herd interaction effect in the genomic evaluation for weaning weight of American Angus

A spurious negative genetic correlation between direct and maternal effects of weaning weight (WW) in beef cattle has historically been problematic for researchers and industry. Previous research has suggested the covariance between sires and herds may be contributing to this relationship. The objective of this study was to estimate the variance components (VC) for WW in American Angus with and without sire by herd (S×H) interaction effect when genomic information is used or not. Five subsets of ~100k animals for each subset were used. When genomic information was included, genotypes were added for 15,637 animals. Five replicates were performed. Four different models were tested, namely, M1: without S×H interaction effect and with covariance between direct and maternal effect (σam) ≠ 0; M2: with S×H interaction effect and σam ≠ 0; M3: without S×H interaction effect and with σam = 0; M4: with S×H interaction effect and σam = 0. VC were estimated using the restricted maximum likelihood (REML) and single-step genomic REML (ssGREML) with the average information algorithm. Breeding values were computed using single-step genomic BLUP for the models above and one additional model, which had the covariance zeroed after the estimation of VC (M5). The ability of each model to predict future breeding values was investigated with the linear regression method. Under REML, when the S×H interaction effect was added to the model, both direct and maternal genetic variances were greatly reduced, and the negative covariance became positive (i.e., when moving from M1 to M2). Similar patterns were observed under ssGREML, but with less reduction in the direct and maternal genetic variances and still a negative covariance. Models with the S×H interaction effect (M2 and M4) had a better fit according to the Akaike information criteria. Breeding values from those models were more accurate and had less bias than the other three models. The rankings and breeding values of artificial insemination sires (N = 1,977) greatly changed when the S×H interaction effect was fit in the model. Although the S×H interaction effect accounted for 3% to 5% of the total phenotypic variance and improved the model fit, this change in the evaluation model will cause severe reranking among animals.     

A combination of Lactobacillus buchneri and Pediococcus pentosaceus extended the aerobic stability of conventional and brown midrib mutants–corn hybrids ensiled at low dry matter concentrations by causing a major shift in their bacterial and fungal community

We evaluated the effects of applying a combination inoculant to four corn hybrids harvested at high moisture on their nutritive value and microbial populations. The treatment design was the factorial combination of corn hybrids ensiled with (INO) and without (CON) inoculant. The hybrids were TMF2R737 (MCN), F2F817 (MBR), P2089YHR (PCN), and PI144XR (PBR), ensiled at dry matter (DM) concentrations of 30.5%, 26.3%, 31.1%, and 31.5%, respectively; MBR and PBR were brown midrib mutants (BMR). The inoculant contained Lactobacillus buchneri and Pediococcus pentosaceus (4 × 10⁵ and 1 × 10⁵ cfu/g of fresh corn). The experiment had a complete randomized design with treatments replicated six times. Corn was treated or not with inoculant, packed into 7.6 L bucket silos, and stored for 100 d. At d 0, the relative abundance (RA, %) of Enterobacteriaceae was lower in PBR vs. the other hybrids [51.3 vs. x¯ = (average of) 58.4] and in the case of fungi, incertae sedis (i.s.) Tremellales and Mucoraceae were more and less abundant, respectively, in conventional hybrids vs. BMRs (x¯= 25.8 vs. x¯ = 13.9 and x¯ = 3.64 vs. x¯ = 7.52; P < 0.04). After ensiling, INO had higher LAB (9.3 vs. 7.1 log cfu/g of fresh corn) and acetic acid (3.44% vs. 1.32% of DM) and lower yeast (3.1 vs. 4.6) and molds (1.5 vs. 3.0), and also extended the aerobic stability (582 vs. 111 h) but decreased DM recovery (95.6% vs. 97.4%) vs. CON (P < 0.02). Inoculation reduced bacterial phylogenetic diversity (6.75 vs. 14.4) but increased fungal observed taxonomical units (46 vs. 20) vs. CON (P < 0.01). Also, a higher relative abundance (RA) for Lactobacillaceae (99.2% vs. 75.7%) and lower for Enterobacteriaceae (0.28 vs. 9.93) was observed due to inoculation (P < 0.001). For fungi, INO had a lower RA compared to CON for Monascaceae (12.6 vs. 44.7) and increased i.s. Tremellales (8.0 vs. 1.2) and i.s. Saccharomycetales (6.4% vs. 0.3%; P < 0.006). Inoculation changed the diverse bacterial community found in the phyllosphere across hybrids to a taxonomically uneven one dominated by Lactobacillaceae. In the case of fungi, INO application increased the fungal diversity at d 100 mainly by reducing the dominance of Monascaceae vs. CON. In conclusion, the INO treatment overwhelmed the disparate microbial populations found across BMR and conventional hybrids ensiled at low DM concentrations and ensured a significant concentration of acetic acid that modified fungal populations and in turn extended the aerobic stability of all hybrids.     

Quantification of transmission of foot-and-mouth disease virus caused by an environment contaminated with secretions and excretions from infected calves

Foot-and-mouth disease virus (FMDV) infected animals can contaminate the environment with their secretions and excretions. To quantify the contribution of a contaminated environment to the transmission of FMDV, this study used calves that were not vaccinated and calves that were vaccinated 1 week prior to inoculation with the virus in direct and indirect contact experiments. In direct contact experiments, contact calves were exposed to inoculated calves in the same room. In indirect contact experiments, contact calves were housed in rooms that previously had held inoculated calves for three days (either from 0 to 3 or from 3 to 6 days post inoculation). Secretions and excretions from all calves were tested for the presence of FMDV by virus isolation; the results were used to quantify FMDV transmission. This was done using a generalized linear model based on a 2 route (2R, i.e. direct contact and environment) SIR model that included information on FMDV survival in the environment. The study shows that roughly 44% of transmission occurs via the environment, as indicated by the reproduction ratio R^02Renvironment that equalled 2.0, whereas the sum of R^02Rcontact and R^02Renvironment equalled 4.6. Because vaccination 1 week prior to inoculation of the calves conferred protective immunity against FMDV infection, no transmission rate parameters could be estimated from the experiments with vaccinated calves. We conclude that a contaminated environment contributes considerably to the transmission of FMDV therefore that hygiene measures can play a crucial role in FMD control.

Electronic supplementary material

The online version of this article (doi:10.1186/s13567-015-0156-5) contains supplementary material, which is available to authorized users.     

大白猪、长白猪和杜洛克猪RBP4基因多态性及其与繁殖性能的相关分析

本试验通过PCR-RFLP技术对大白猪、长白猪和杜洛克猪的视黄醇结合蛋白4(retinol binding protein 4,RBP4)基因第4外显子Msp Ⅰ酶切位点进行多态性分析,并对各基因型母猪的第2、3胎次产仔数、产活仔数、断奶仔猪数、初生窝重、21日龄的窝重及断奶成活率进行测定,进而分析RBP4基因多态性与繁殖性能的关系。结果表明,RBP4基因在3个品种中均存在多态位点;χ²适合性检验表明大白猪在该位点偏离Hardy-Weinberg平衡状态(P<0.05),而长白猪和杜洛克猪在该位点处于Hardy-Weinberg平衡状态(P>0.05)。其中,大白猪中优势基因型为BB基因型,而长白猪和杜洛克猪中优势基因型为AA基因型。在繁殖性能上,长白猪BB基因型群体第2胎总产仔数、产活仔数、断奶仔猪数、初生窝重、21日龄断奶窝重分别高于AA基因型0.97头、1.28头、0.92头、1.74 kg和4.42 kg,高于AB基因型0.92头、1.02头、0.98头、1.43 kg和4.98 kg;第3胎次中总体上BB基因型也为有利基因型。     

Effect of RNF4-SacII gene polymorphism on reproductive traits of Landrace × Large White crossbred sows

The aim of the present study was to investigate whether and to what extent the RNF4-SacII gene polymorphism influences reproduction performances in hyperprolific sow lines. The study involved 101 Landrace x Large White crossbred sows, with 461 records collected on the following reproductive traits: Total Number of piglets Born per litter (TNB), Number of piglets Born Alive per litter (NBA), Number of StillBorn piglets per litter (NSB), piglet Pre-Weaning Mortality (PWM) and Number of piglets at Weaning per litter (NW). The least square method with the GLM procedure in SAS with eight effects was used to pursue the data analysis. Study results revealed that TT homozygotes and TC heterozygotes had a significantly higher (p < .05) NW than CC homozygotes for the life-span performance in all parities and first parity analysed. In the fourth parity analysed, TNB and NBA in TC genotype were significantly higher (p < .05) as compared with TT genotype. Based on the life-span performance, significant effect (p < .05) was recorded for order of parity on TNB, NBA and NW, for farrowing season on TNB and NSB, and for lactation length on PWM. In the second parity, significant effect (p < .05) was recorded for sire of boar on NSB and for gestation length on TNB. Only in the fourth parity, significant effect (p < .05) of RNF4 gene was observed on NBA. There was significant additive effect (p < .05) of the RNF4 gene polymorphism identified on NW in all parities analysed, and significant additive and dominance effects (p < .05) on NSB in the third parity analysed. In conclusion, additional research on related production pig genotypes is necessary to elucidate the effect of RNF4 gene mutation on reproductive traits.     

Pharmacokinetics of IV Ketorolac in Horses Undergoing Orchiectomy

Ketorolac (KET) is a nonsteroidal anti-inflammatory drug for human use, with a potent analgesic activity, that is used in the relief of moderate-to-severe postoperative pain. The pharmacokinetics of KET tromethamine was evaluated after single IV injection at 0.5 mg/kg body weight, after intubation and 10 minutes before surgery, to six Arabian colts undergoing orchiectomy. Intraoperative cardiorespiratory variables were monitored. Blood samples were collected for 36 hours, and serum samples were analyzed by high performance liquid chromotography with ultraviolet-visible detection. During surgery, all monitored physiological parameters were stable. Intermittent positive pressure ventilation, and normocapnia were maintained throughout the procedure in all animals. No adverse effects were observed. The kinetics of KET was described by a two-compartment models, and also a noncompartmental analysis was performed. The distribution and elimination half-lives were t_1/2λ1$t_{1/2{\lambda }_1}$ 0.06 ± 0.02 and t_1/2λ2$t_{1/2{\lambda }_2}$ 0.59 ± 0.21 hours, respectively. Body clearance and mean residence time were 339.99 ± 120.19 mL/h/kg and 0.49 ± 0.22 hours, respectively. The volume of distribution at steady state and volume of distribution based on the terminal phase were 218.83 ± 134.26 mL/kg and 522.5 ± 529.3 mL/kg, respectively. The serum protein binding was 75.8 ± 2.9%. The results indicate that KET at 0.5 mg/kg IV was very rapidly eliminated and thus was likely not effective in the postoperative period. However, further studies including a control group and at higher doses are suggested to investigate the KET kinetics and the analgesic efficacy in horse and define the most appropriate dosage scheme.     

Comparison of different methods to calculate venous admixture in anaesthetized horses

Objective

The aim of this study was to compare different methods to determine venous admixture (${\dot{Q}}_{\text{s}}/{\dot{Q}}_{\text{t}}$) in anaesthetized horses. The first objective was to estimate ${\dot{Q}}_{\text{s}}/{\dot{Q}}_{\text{t}}$ using jugular venous blood oxygen content (${\dot{Q}}_{\text{s}}/{\dot{Q}}_{\text{t}\text{jugular}}$), and a fixed value for the oxygen extraction (F-shunt). The second objective was to assess the influence of blood pressure and positioning on oxygen extraction. The third objective was to perform regression analysis between jugular and mixed venous blood oxygen tensions.

胎次、产仔月份及纯繁/杂交对母猪产仔性能的影响

本研究统计分析了部分非遗传因素(胎次、产仔月份及纯繁/杂交)对长白、大白和杜洛克母猪产仔性能(总产仔数、产活仔数及初生窝重)的影响,旨在为后备母猪的选种提供指导。结果表明,2~5胎仔猪的初生窝重较重;其中2、3胎的初生窝重极显著高于头胎及6胎之后的仔猪初生窝重(P<0.01)。3月份总产仔数、产活仔数及初生窝重极显著高于其他月份(P<0.01),且11月份初生窝重显著低于其他月份(P<0.05)。长白纯繁母猪在产活仔数方面极显著优于大白纯繁母猪和长白×大白杂交母猪(P<0.01);在初生窝重方面,大白×长白杂交母猪的初生窝重极显著高于大白纯繁母猪和长白×大白杂交母猪(P<0.01)。第2胎与3~4胎、第3胎与第4胎的总产仔数呈极显著正相关(P<0.01)。综上所述,该猪场母猪3~6胎的产仔性能较好,且以1~4月份的产仔性能为佳;配种方式以长白纯繁和大白×长白杂交为宜;第2胎产仔性能可作为后备母猪选留的重要依据。     

Selection for litter size at day five to improve litter size at weaning and piglet survival rate

Selection for total number of piglets born (TNB) since 1992 has led to a significant increase in this trait in Danish Landrace and Danish Yorkshire but has also been accompanied by an increase in piglet mortality. The objective of this study was to estimate the genetic and phenotypic parameters for litter size and survival to find alternative selection criteria to improve litter size at weaning. Data from Landrace (9,300 litters) and Yorkshire (6,861 litters) were analyzed using REML based on a linear model including genetic effects of sow and service-sire. The estimates of heritability (based on the sow component) for TNB, number born alive (NBA), and number alive at d 5 after birth (N5D) and at weaning (about 3 wk, N3W) ranged from 0.066 to 0.090 in Landrace and 0.050 to 0.070 in Yorkshire. Genetic correlations between TNB and N3W were 0.289 in Landrace and 0.561 in Yorkshire, but between N5D and N3W the estimated genetic correlation was 0.995 in both populations. The approximate estimates of heritability for survival rate per litter at birth (SVB = NBA/TNB), from birth to d 5 (SV5 = N5D/NBA), and from d 5 to weaning (SVW = N3W/N5D) were 0.130, 0.131, and 0.023, respectively, in Landrace, and 0.095, 0.043, and 0.009, respectively, in Yorkshire. Genetic correlations between TNB and survival rates at different stages were negative. On the other hand, genetic correlations between N5D and survival rates and between N3W and survival rates were strongly or moderately positive, except for the correlations with SVW in Yorkshire. The results suggest that selection for N5D could be an interesting alternative to improve litter size at weaning and piglet survival for Danish Landrace and Danish Yorkshire.     

不同配种模式对二元母猪繁殖性能的影响

为探讨不同配种方式对二元母猪产仔数的影响,以杜洛克猪、长白猪、大白猪、皮特兰猪四个品种公猪精液采用人工授精的方法对11654头长大二元母猪配种,对所产11654窝总产仔数、窝产活仔数、窝损失等进行统计和分析,分析不同配种模式对二元母猪繁殖性能的影响。结果表明,配种次数、不同品种公猪组合配种对二元母猪总产仔数、产活仔数以及窝损失均无显著影响（P〉0.05）,但杜洛克公猪所配二元母猪的总产仔数和窝产仔数均高于大白和长白猪（P〈0.05）;采用长×杜×大组合配种的二元母猪总产仔数和窝产活仔数均高于其它三种组合。试验结果表明,在生产中,可在长白、大白、杜洛克猪中任选两个品种,通过二次配种的方式提高母猪的产仔数。     

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.     

Genetic parameters and trends for production traits and their relationship with litter traits in Landrace and Yorkshire pigs

Genetic parameters and trends in the average daily gain (ADG), backfat thickness (BF), loin muscle area (LMA), lean percentage (LP), and age at 90 kg (D90) were estimated for populations of Landrace and Yorkshire pigs. Additionally, the correlations between these production traits and litter traits were estimated. Litter traits included total born (TB) and number born alive (NBA). The data used for this study were obtained from eight farms during 1999 to 2016. Analyses were carried out with a multivariate animal model to estimate genetic parameters for production traits while bivariate analyses were performed to estimate the correlations between production and litter traits. The heritability estimates were 0.52 and 0.43 for ADG; 0.54 and 0.45 for BF; 0.25 and 0.26 for LMA; 0.54 and 0.48 for LP; and 0.56 and 0.46 for D90 in the Landrace and Yorkshire breeds, respectively. The ADG and D90 showed low genetic correlation with BF and LP. The LMA had ?0.40, ?0.32, 0.49, and 0.39 genetic correlations with ADG, BF, LP, and D90, respectively. Genetic correlations between production and litter traits were generally low, except for the correlations between LMA and TB (?0.23) in Landrace and ADG and TB (?0.16), ADG and NBA (?0.18), D90 and TB (0.19), and D90 and NBA (0.20) in Yorkshire. Genetic trends in production traits were all favorable except for LMA.     

Estimation of genetic parameters for reproductive traits in connectedness groups of Duroc,Landrace and Yorkshire pigs in China

The objective of this study was to estimate group- and breed-specific genetic parameters for reproductive traits in Chinese Duroc, Landrace, and Yorkshire populations. Records for reproductive traits between April 1998 and December 2017 from 92 nucleus pig breeding farms, which were involved in the China Swine Genetic Improvement Program, were analysed. Due to weak genetic connectedness across all farms, connectedness groups consisting of related farms were used. Three, two and four connectedness groups for Duroc, Landrace and Yorkshire were firstly established according to the genetic connectedness rating among farms. For each connectedness group a five-trait animal model was implemented, and via restricted maximum likelihood procedure the genetic parameters were estimated for five reproductive traits i.e., total number born (TNB), number born alive (NBA), litter weight at farrowing (LWF), farrowing interval (FI) and age at first farrowing (AFF). The average of heritabilities among connectedness groups ranged from .01 (for FI in Yorkshire) to .30 (for AFF in Duroc). Estimates of repeatability for litter traits ranged from .14 to .20 and were consistent for each breed, and for FI, the estimates varied from .01 to .11 across breeds and groups. The estimated genetic correlations among litter traits (i.e., TNB, NBA and LWF) were all significantly high (>.56) and similar across breeds. Averaged genetic correlations over three breeds were −.25, −.27, −.18, −.04, −.10, −.02, and .28 for FI-TNB, FI-NBA, FI-LWF, AFF-TNB, AFF-NBA, AFF-LWF and FI-AFF, respectively. The standard errors of the estimates were all very low (<0.01) in most situations. Results from this study suggest that selection based on TNB which is currently used in dam line selection index can improve NBA and LWF simultaneously. However, care should be taken on FI and AFF as they are both greatly influenced by non-genetic factors such as management and measurement.     

Is single-step genomic REML with the algorithm for proven and young more computationally efficient when less generations of data are present?

Efficient computing techniques allow the estimation of variance components for virtually any traditional dataset. When genomic information is available, variance components can be estimated using genomic REML (GREML). If only a portion of the animals have genotypes, single-step GREML (ssGREML) is the method of choice. The genomic relationship matrix (G) used in both cases is dense, limiting computations depending on the number of genotyped animals. The algorithm for proven and young (APY) can be used to create a sparse inverse of G (GAPY~-1) with close to linear memory and computing requirements. In ssGREML, the inverse of the realized relationship matrix (H⁻¹) also includes the inverse of the pedigree relationship matrix, which can be dense with a long pedigree, but sparser with short. The main purpose of this study was to investigate whether costs of ssGREML can be reduced using APY with truncated pedigree and phenotypes. We also investigated the impact of truncation on variance components estimation when different numbers of core animals are used in APY. Simulations included 150K animals from 10 generations, with selection. Phenotypes (h² = 0.3) were available for all animals in generations 1–9. A total of 30K animals in generations 8 and 9, and 15K validation animals in generation 10 were genotyped for 52,890 SNP. Average information REML and ssGREML with G⁻¹ and GAPY~-1 using 1K, 5K, 9K, and 14K core animals were compared. Variance components are impacted when the core group in APY represents the number of eigenvalues explaining a small fraction of the total variation in G. The most time-consuming operation was the inversion of G, with more than 50% of the total time. Next, numerical factorization consumed nearly 30% of the total computing time. On average, a 7% decrease in the computing time for ordering was observed by removing each generation of data. APY can be successfully applied to create the inverse of the genomic relationship matrix used in ssGREML for estimating variance components. To ensure reliable variance component estimation, it is important to use a core size that corresponds to the number of largest eigenvalues explaining around 98% of total variation in G. When APY is used, pedigrees can be truncated to increase the sparsity of H and slightly reduce computing time for ordering and symbolic factorization, with no impact on the estimates.     

Number of ovulations in culled Landrace × Yorkshire gilts in the tropics associated with age,body weight and growth rate

The objective of the present study was to determine the number of ovulations in culled Landrace × Yorkshire (LY) crossbred gilts in the tropics associated with age, body weight and growth rate. The genital organs from 316 gilts were examined for gross abnormalities, and those with normal cyclic ovaries (n=155, 307 ± 4.1 days of age, 148 ± 1.6 kg body weight) were included in the analyses. Number of ovulations was defined by a count of the corpora lutea (CL) from both ovaries. On average, the number of ovulations in LY gilts was 15.9 ± 0.3 (range 4 to 27). The number of ovulations correlated with the body weight (r=0.31, P<0.001) and growth rate (r=0.20, P=0.015) of the gilts, but not with their age (P>0.05). Gilts with a body weight of 141 to 150 kg (17.0 CL, n=31) ovulated more than those with a body weight ≤130 kg (14.1 CL, P=0.014, n=23). In conclusion, both the body weight and growth rate of the gilts were significantly correlated with the number of ovulations. The maximum number of ovulations was found in gilts at a body weight of above 141 kg.     

大白猪、长白猪和杜洛克猪催乳素受体基因多态性及其与繁殖性能的关系

本试验通过PCR-RFLP技术对大白猪、长白猪和杜洛克猪的催乳素受体(prolactin receptor,PRLR)基因第10外显子AluⅠ酶切位点进行多态性分析,并对各基因型母猪的第1至第3胎次产仔数、产活仔数、断奶仔猪数、初生窝重、21日龄窝重及断奶成活率进行测定,进而分析PRLR基因多态性与繁殖性能的关系。结果表明,PRLR基因在3个品种中均存在多态位点,且AA基因型都是其优势基因型。关联分析结果表明,大白猪AA基因型个体第1、2和3胎各繁殖性状均呈现出高于AB和BB基因型的趋势。在繁殖性能已经稳定的第3胎次AA基因型个体产仔数、产活仔数、断奶仔猪数、初生窝重及断奶成活率比BB基因型个体平均分别高出0.31头、0.63头、0.02头、0.65 kg和0.43%,但差异均不显著(P>0.05)。