Dominance genetic and maternal effects for genetic evaluation of egg production traits in dual-purpose chickens

• 1.?A study was conducted to study direct dominance genetic and maternal effects on genetic evaluation of production traits in dual-purpose chickens. The data set consisted of records of body weight and egg production of 49 749 Mazandaran fowls from 19 consecutive generations. Based on combinations of different random effects, including direct additive and dominance genetic and maternal additive genetic and environmental effects, 8 different models were compared.

• 2.?Inclusion of a maternal genetic effect in the models noticeably improved goodness of fit for all traits. Direct dominance genetic effect did not have noticeable effects on goodness of fit but simultaneous inclusion of both direct dominance and maternal additive genetic effects improved fitting criteria and accuracies of genetic parameter estimates for hatching body weight and egg production traits.

• 3.?Estimates of heritability (h²) for body weights at hatch, 8 weeks and 12 weeks of age (BW0, BW8 and BW12, respectively), age at sexual maturity (ASM), average egg weights at 28–32 weeks of laying period (AEW), egg number (EN) and egg production intensity (EI) were 0.08, 0.21, 0.22, 0.22, 0.21, 0.09 and 0.10, respectively. For BW0, BW8, BW12, ASM, AEW, EN and EI, proportion of dominance genetic to total phenotypic variance (d²) were 0.06, 0.08, 0.01, 0.06, 0.06, 0.08 and 0.07 and maternal heritability estimates (m²) were 0.05, 0.04, 0.03, 0.13, 0.21, 0.07 and 0.03, respectively. Negligible coefficients of maternal environmental effect (c²) from 0.01 to 0.08 were estimated for all traits, other than BW0, which had an estimate of 0.30.

• 4.?Breeding values (BVs) estimated for body weights at early ages (BW0 and BW8) were considerably affected by components of the models, but almost similar BVs were estimated by different models for higher age body weight (BW12) and egg production traits (ASM, AEW, EN and EI). Generally, it could be concluded that inclusion of maternal effects (both genetic and environmental) and, to a lesser extent, direct dominance genetic effect would improve the accuracy of genetic evaluation for early age body weights in dual-purpose chickens.

     

Estimation of genetic parameters for superovulatory response traits in Japanese Black cows

The aim of this study was to estimate genetic parameters for superovulatory response traits in order to explore the possibility of genetic improvement in Japanese Black cows. We analyzed 19 155 records of the total number of embryos and oocytes (TNE) and the number of good embryos (NGE) collected from 1532 donor cows between 2008 and 2018. A two-trait repeatability animal model analysis was performed for both. Because records of TNE and NGE did not follow a normal distribution, the records were analyzed following no, logarithmic, or Anscombe transformation. Without transformation, the heritability estimates were 0.26 for TNE and 0.17 for NGE. With logarithmic transformation, they were 0.22 for TNE and 0.18 for NGE. With Anscombe transformation, they were 0.26 for TNE and 0.18 for NGE. All analyses gave similar genetic correlations between TNE and NGE, ranging from 0.60 to 0.71. Spearman’s rank correlation coefficient between breeding values of cows with more than 10 records was ≥0.95 with both transformations. Thus, the genetic improvement of TNE and NGE of donor cows could be possible in Japanese Black cattle.     

猪配套系生长性状基因效应与杂种优势的分析

测定杜长大三元杂交体系和斯格配套系各杂交组合的生长性能,计算出生长性状的杂种优势率;选用5个与生长性状紧密连锁的微卫星标记对测定个体进行基因型检测,利用混合效应线性模型计算出生长性状各位点的基因效应。结果显示:斯格配套系父母代与商品代各时期的平均日增重的差异均达到极显著水平(P<0.01),杜长大杂交体系父母代与商品代各时期的平均日增重的差异均达到显著水平(P<0.05),斯格配套系父母代和商品代与杜长大杂交体系的父母代和商品代的差异达到极显著水平(P<0.01),前期的的杂优率处于较高水平,后期及全程的杂优率不高。基因效应分析显示早期日增重的基因效应既有加性效应又有显性效应,后期日增重和全程日增重的加性效应明显,因而加性效应是日增重杂种优势的主要遗传学基础。     

Genetic parameters for linear type traits in the Rendena dual‐purpose breed

The aim of the study was to estimate the genetic parameters for five composite traits and 20 individual type traits on 10 735 first‐parity Rendena dual‐purpose cows. Fixed effects included in the linear animal mixed models were herd‐year‐classifier, days in milk and age at first calving; the additive genetic effect of the animal was included as a random effect. Heritability estimates varied from 0.12 (feet) to 0.52 (stature). Genetic correlations between the individual body size traits were all ≥0.69; similar strong genetic correlations existed between traits describing similar morphological characteristics (e.g. mammary system, fleshiness). Many of the body size traits were negatively genetically correlated with animal fleshiness. Genetic trends showed that genetic merit for body size increased consistently over the last 10 years, while genetic merit for fleshiness declined. These results suggest that the characteristics of the dual‐purpose Rendena cattle are becoming more like specialized milk‐producing animals. Nonetheless, sufficient genetic variation exists to halt or reverse the deterioration in fleshiness.     

Estimation of genetic parameters of conformation traits in Iranian Thoroughbred horses

The aim of this study was to estimate the genetic parameters of conformation traits in Iranian Thoroughbred race horses. The data set included the conformation records of 607 Thoroughbred horses. In this study, 10 conformation traits were recorded. The effect of sex was significant for length of back line (P < 0.05), withers height (P < 0.05), circumference of front cannon (P < 0.001), and circumference of hind cannon (P < 0.001). The effect of age was significant for all traits (P < 0.01). The genetic parameters were estimated by the restricted maximum likelihood (REML) method using DFREML program. The heritability estimates were for head length 0.39, length of back line 0.41, length of shoulder 0.24, heart girth 0.49, chest width 0.22, withers height 0.38, front cannon height 0.27, circumference of front cannon 0.30, hind cannon height 0.29 and circumference of hind cannon 0.34. The estimates of genetic correlation ranged from 0.18 to 0.96 and those of phenotypic correlation varied from 0.16 to 0.83.     

撒坝猪繁殖性状的表型和遗传参数分析

对 6个世代共 2 31头撒坝母猪的繁殖性能数据资料进行了分析。在建立混合线性模型的基础上 ,采用HARVEY程序估计了总产仔数、活产仔数、初生窝重、 2 0日龄窝重、 60日龄断奶仔数和断奶窝重等 6个繁殖性状的表型和遗传参数。结果表明 ,撒坝猪繁殖性能在选育过程中有一定程度的提高 ,但速度平缓 ;上述 6个性状的遗传力分别为 0 0 37,0 0 75,0 1 1 1 ,0 1 55 ,0 1 0 3和 0 31 0 ,多为低遗传力性状 ;各性状间的遗传相关介于 0 532～ 0 773之间 ,表型相关和环境相关分别在 0 30 3～ 0 946和 0 442～ 0 972之间     

Influence of imported sport horses on the genetic evaluation of Swedish Warmblood stallions

There is substantial international influence on the Swedish Warmblood (SWB) sport horse population. The SWB Association suspects that imported horses are pre-selected based on their anticipated performance level, which could lead to biased estimated breeding values (EBVs) for stallions. This study examined different strategies to handle records for imported horses in the genetic evaluation. The stallions were evaluated for 10 traits using 3 different EBV estimation methods that were compared based on ranking comparisons of stallions, accuracy, correlations and absolute differences between EBVs. The results showed that the stallions’ EBVs were affected by imported offspring which, as a group, had higher average scores than horses born in Sweden. Sire EBVs differed by up to 0.6 genetic standard deviation of the trait between methods for stallions with >50% imported offspring. Excluding imported offspring lowered the accuracies and caused larger re-ranking compared with including a fixed effect of origin in the model.     

Modelling genetic evaluation for dressage in Pura Raza Español horses with focus on the rider effect

The most popular use of the Pura Raza Español horse in sport is for dressage competitions. Tests on young sport horses were first established in 2004 in Spain to collect data for the genetic evaluation of this breed's suitability for dressage. The aim of this study was to compare eight different models to find out the most appropriate way to include the rider in the genetic evaluation of dressage. A progressive removal of systematic effects from model was also analysed. A total of 8867 performance records collected between 2004 and 2011 from 1234 horses aged between 4 and 6 years old were used. The final score in the dressage test was used as the performance trait. The pedigree matrix contained 8487 individuals. A BLUP animal model was applied using a Bayesian approach with TM software. The horse's age, gender, travelling time, training level, stud of birth and event were included as systematic effects in all the models. Apart from the animal and residual effects that were present in all models, different models were compared combining random effects such as the rider, match (i.e. rider–horse interaction) and permanent environmental effects. A cross‐validation approach was used to evaluate the models' prediction ability. The best model included the permanent environmental, rider and match random effects. As far as systematic effects are concerned, the event or the stud of birth was essential effects needed to fit the data.     

Development of genetic evaluation for milk production traits of Holsteins in Japan

The procedure used for the genetic evaluation of dairy cattle in Japan has developed from a lactation sire–MGS model to a multiple‐lactation random regression test‐day animal model. Genetic evaluation of Holstein bulls in Japan began in 1989 with the use of field‐style progeny testing; dairy herd improvement program data from all over Japan were used, along with a sire and maternal grandsire model. In 1993, an animal model was introduced to estimate breeding values for yield and type traits. A random regression test‐day model was first applied in 2010. In the business of breeding dairy cattle, it is very important to users that estimated breeding values are reliable and stable among subsequent routine evaluations. With experience in the genetic evaluation of dairy cattle in Japan, Japanese researchers have found ways to improve the stability of estimated breeding values. These modifications involve changes in data editing, development of evaluation models, changes to the structures of unknown‐parent groups, awareness of the problems of predicting lactation yield from partial test‐day records, and adjustment for heterogeneity within herd variances. Here, I introduce developments in, and our experiences with, the genetic evaluation of yield traits of Holstein cattle in Japan.     

Multiple trait genetic evaluation of ewe traits in Icelandic sheep

The prolificacy of the ewes was measured as the number of lambs born per ewe mated (NLB) when the ewes were 1–4 years of age. The ewe productivity related to the same age interval was measured by special ewe production indices (EPI). The genetic parameters for these traits were estimated by a series of bivariate REML analyses using animal models. The material used for the genetic analysis contained records on 193 213 ewes. The heritability estimates for NLB were h² = 0.17, 0.13, 0.11, 0.10 for the four respective age classes. Corresponding estimates for EPI were h² = 0.16, 0.17, 0.17, 0.15. The genetic correlations among NLB at different ages ranged from 0.63 to 0.98 and among EPI from 0.82 to 0.99. The genetic correlations between NLB and EPI were generally low. The material used for estimating the breeding values by the MT‐BLUP Animal Model consisted of 1.5 million individuals in the pedigree file. In total 815 782 ewes had records for the NLB and 763 491 ewes had production index (at least 1 year). The records were registered in the years 1990–2006. All possible missing patterns were present in the data. In the iteration process expected values for missing traits were generated and solutions were obtained on canonical transformed scale. The genetic evaluations were run independently for NLB and EPI for computational convenience given the correlations between these traits were negligible.     

Improvement in the national genetic evaluation of warmblood riding horses by including information from related studbooks

Abstract

Young horse performance test data from two warmblood riding horse populations, Norwegian warmblood (NWB) and Swedish warmblood (SWB), were analysed to examine whether including information from a related studbook would increase the accuracy of the genetic evaluations within a population. Ten conformation and performance traits from 31,588 horses, 774 NWB and 30,814 SWB were analysed separately and jointly using single trait animal models. Heritabilities were moderate to high, and varied from 0.15 (conformation, joint data) to 0.74 (jumping technique, NWB data). The genetic similarity (GS) between populations was 31%, with the SWB, as expected given the size of the populations, contributing most to the GS (98%). Genetic correlations between the same traits in the two populations were 0.43–0.90 but with large standard errors (0.2–0.3). Including information from the other population increased the average accuracy of estimated breeding values for common stallions, on average 4% for SWB and 110% for NWB.     

Effects of correcting missing daily feed intake values on the genetic parameters and estimated breeding values for feeding traits in pigs

Daily feed intake (DFI) is an important consideration for improving feed efficiency, but measurements using electronic feeder systems contain many missing and incorrect values. Therefore, we evaluated three methods for correcting missing DFI data (quadratic, orthogonal polynomial, and locally weighted (Loess) regression equations) and assessed the effects of these missing values on the genetic parameters and the estimated breeding values (EBV) for feeding traits. DFI records were obtained from 1622 Duroc pigs, comprising 902 individuals without missing DFI and 720 individuals with missing DFI. The Loess equation was the most suitable method for correcting the missing DFI values in 5–50% randomly deleted datasets among the three equations. Both variance components and heritability for the average DFI (ADFI) did not change because of the missing DFI proportion and Loess correction. In terms of rank correlation and information criteria, Loess correction improved the accuracy of EBV for ADFI compared to randomly deleted cases. These findings indicate that the Loess equation is useful for correcting missing DFI values for individual pigs and that the correction of missing DFI values could be effective for the estimation of breeding values and genetic improvement using EBV for feeding traits.     

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.     

Genetic parameter estimation and gene association analyses for meat quality traits in open-air free-range Iberian pigs

Meat quality of Iberian pigs is defined by the combination of their genetic characteristics and the particular production system. To carry out a genetic analysis of the main meat quality traits, we estimated their heritabilities, genetic correlations and the association effects of 32 selected SNPs of 12 candidate genes. A total of ten traits were measured in longissimus dorsi samples from 1,199 Iberian pigs fattened in the traditional free-range system: water holding capacity (thawing, cooking and centrifuge force water losses), instrumental colour (lightness L*, redness a* and yellowness b*), myoglobin content, shear force on cooked meat, and shear force and maximum compression force on dry-cured loin. Estimated heritability values were low to moderate (0.01 to 0.43) being the lowest for L* and the highest for cooking loss. Strong genetic correlations between water holding capacity traits (0.93 to 0.96) and between myoglobin content and a* (0.94) were observed. The association analyses revealed 19 SNPs significantly associated with different traits. Consistent and strong effects were observed between PRKAG3 SNPs (rs319678464G > C and rs330427832C > T), MYH3_rs81437544T > C, CASP3_rs319658214G > T and CTSL_rs332171512A > G and water losses. Also for CAPN1_rs81358667G > A and CASP3_rs319658214G > T and shear force. The SNPs mapping on PRKAG3 showed the highest effects on Minolta colour traits. Genotyping of these SNPs could be useful for the selection of Iberian young boars with similar estimated breeding values for productive traits.     

Comparison of models for genetic evaluation of survival traits in dairy cattle: a simulation study.

Three models for the analysis of functional survival data in dairy cattle were compared using stochastic simulation. The simulated phenotype for survival was defined as a month after the first calving (from 1 to 100) in which a cow was involuntarily removed from the herd. Parameters for simulation were based on survival data of the Canadian Jersey population. Three different levels of heritability of survival (0.100, 0.050 and 0.025) and two levels of numbers of females per generation (2000 or 4000) were considered in the simulation. Twenty generations of random mating and selection (on a second trait, uncorrelated with survival) with 20 replicates were simulated for each scenario. Sires were evaluated for survival of their daughters by three models: proportional hazard (PH), linear multiple-trait (MT), and random regression (RR) animal models. Different models gave different ranking of sires with respect to survival of their daughters. Correlations between true and estimated breeding values for survival to five different points in a cow's lifetime after the first calving (120 and 240 days in milk after first, second, third and fourth calving) favoured the PH model, followed by the RR model evaluations. Rankings of models were independent of the heritability level, female population size and sire progeny group size (20 or 100). The RR model, however, showed a slight superiority over MT and PH models in predicting the proportion of sire's daughters that survived to the five different end-points after the first calving.     

Plasticity effect of rider–horse interaction on genetic evaluations for Show Jumping discipline in sport horses

To obtain a sport horse that excels in the highest levels of competition, breeders must take into account certain genetic and environmental factors that could influence the sport horse's performance, such as the rider–horse interaction (RHI). The main aim of this study was to describe this interaction in a genetic model by modelling it in relation to the horse's age. A total of 31,129 sport results from Spanish Sport Horses were used from a total of 1,101 animals evaluated, and these were grouped in three age levels and had been ridden by 606 different riders. Only riders who had ridden more than one horse (and vice‐versa) were considered for the analyses. Five linear models with different random effects were analysed according to the covariates, the homogeneity/heterogeneity of the RHI and the relevant residual random effects. The model of best fit was then selected for the genetic evaluation of the animal. In general, models including the RHI effect (M2, M4 and M5) fitted better than the other models, and the best fit was obtained for M4 (with heterogeneous residual variance). The genetic variance increased constantly with age, whereas heritability showed a response on three intervals. This study revealed the varied evolution of the RHI with age, showing the different “plastic abilities” of this relationship.     

Evaluation of genetic trends and determination of the optimal number of cumulative records of parity required in reproductive traits in a Large White pig population

Genetic improvement of the reproductive performance of pigs is important for pig breeding despite their low heritabilities. The objectives of this study were to investigate the effectiveness of selection concerning reproductive traits and to determine the optimal number of parity records required for accurate estimation of breeding values (BVs) in the open population of a commercial pig breeding company. The study used records of 2220 purebred Large White pigs (9845 litters) farrowed between 1998 and 2009 in the two herds of the Pacific Ocean Breeding Co. Ltd. The traits studied included farrowing interval (FI), total number of piglets at birth (TNB), average weaning weight per litter (AWW), and raising rate (RR). A statistical model was applied to the 4‐trait repeatability animal model. The heritabilities of FI, TNB, AWW and RR were low. The genetic trends in TNB (h² = 0.09) showed approximately 1.0 increase in 6 years from 2003 to 2008. The predicted error variances indicated that up to fourth parity records are necessary for accurate genetic evaluation. The present study results indicated that even reproductive traits with low heritability can be improved.     

Quantitative genetic changes in reproductive performance of giant freshwater prawn after 10 years of selection for increased growth rate

Effect of long‐term selection for improved growth on reproductive performance of giant freshwater prawn (GFP) Macrobrachium rosenbergii has not been reported in the literature. The present study aimed to measure correlated responses in reproductive traits and to estimate genetic parameters for these characters in a GFP population selected for high growth over ten generations from 2007 to 2016. A total of 959 breeding females (offspring of 515 sires and 810 dams) had measurements for seven reproductive traits (weight before spawn WBS; weight after spawn WAS; Fecundity FEC or number of larvae per female at hatching; first age to reach post‐larvae PLAGE; zoea (e) weight ZOEAWT; larval survival during hatchery phase SURV1 and survival from PL to tagging SURV2. The restricted maximum likelihood (REML) and mixed model analysis were used to estimate genetic parameters and evaluate selection responses for the seven traits studied. Our REML analysis showed that heritability for these traits ranged from 0.04 to 0.42 (SE: 0.19–0.28). Female body weight either before or after spawning had strong positive phenotypic correlations with fecundity (0.52–0.98). By contrast, the phenotypic correlations of WBS/WAS with larval and fry survivals were not significant (?0.08–0.05). Genetic correlations among fecundity‐related traits studied were not different from zero due to their high standard errors. Correlated responses in reproductive traits were measured by comparing least squares means of the selection line and control group. Females of the selected line for high growth had significantly greater weight before or after spawning than that of the control group. There were, however, no statistical differences between the two lines in the other traits. It is concluded that selection for high growth did not have detrimental impact on reproductive performance of breeding females in the present population of GFP.     

偃麦草属种质资源在普通小麦育种中的应用现状简介

小麦作为我国最主要的粮食作物之一,其品质和产量的稳步提高对国家粮食安全起着极其重要的作用。偃麦草属作为小麦属的近缘属,具有很多普通小麦本身所不具备的遗传特性。控制这些特性的基因对改良普通小麦的抗性和品质等方面具有重要作用。本研究就偃麦草属种质资源在普通小麦远缘杂交育种中的应用现状进行了总结,涉及利用偃麦草属创制育种材料的研究和偃麦草属在改良小麦特性育种方面的应用。在后者中,分别从偃麦草属中的一些物种在小麦抗病、提高小麦抗逆境性能和改良小麦谷蛋白品质育种等方面进行了简介。结果表明,引入偃麦草属中的一些种的新的抗病基因,如抗条锈病的基因,抗黄矮病的基因以及抗赤霉病的基因等,发现其后代出现有优良的抗相关病的突变体,而且通过偃麦草与普通小麦的杂交及回交转育工作,获得了抗旱和耐胁迫的品质比较优良的小麦品种,偃麦草属在改良小麦谷蛋白品质方面有一初步介绍。