The effect of including genomic relationships in the estimation of genetic parameters of functional traits in pigs

The term functionality in animal breeding is used for traits that increase the efficiency of production by lowering the input cost, such as animal health and leg weakness related to longevity. The main objective of the study was to investigate the impact of genomic information, in a multivariate variance component analysis, on some of these traits. In addition, the effect of the inclusion was studied by testing the model's prediction ability based on best linear unbiased estimates for fixed and random effects. The material in this study consists of phenotypes from 76 683 animals, of which 4933 animals are genotyped. The heritabilities for front leg conformation, stayability, osteochondrosis and arched back, estimated using the traditional pedigree, were found to be between 0.12 and 0.29. When using the combined genomic and pedigree relationship matrix, the heritabilities were between 0.14 and 0.36. The results show that the combined relationship matrix can be used for the estimation of (co)variance components, and that the predictive ability of the model in this study marginally increases with the inclusion of genomic information.     

Genetic parameters for direct and maternal calving ease in Walloon dairy cattle based on linear and threshold models

Calving ease scores from Holstein dairy cattle in the Walloon Region of Belgium were analysed using univariate linear and threshold animal models. Variance components and derived genetic parameters were estimated from a data set including 33 155 calving records. Included in the models were season, herd and sex of calf × age of dam classes × group of calvings interaction as fixed effects, herd × year of calving, maternal permanent environment and animal direct and maternal additive genetic as random effects. Models were fitted with the genetic correlation between direct and maternal additive genetic effects either estimated or constrained to zero. Direct heritability for calving ease was approximately 8% with linear models and approximately 12% with threshold models. Maternal heritabilities were approximately 2 and 4%, respectively. Genetic correlation between direct and maternal additive effects was found to be not significantly different from zero. Models were compared in terms of goodness of fit and predictive ability. Criteria of comparison such as mean squared error, correlation between observed and predicted calving ease scores as well as between estimated breeding values were estimated from 85 118 calving records. The results provided few differences between linear and threshold models even though correlations between estimated breeding values from subsets of data for sires with progeny from linear model were 17 and 23% greater for direct and maternal genetic effects, respectively, than from threshold model. For the purpose of genetic evaluation for calving ease in Walloon Holstein dairy cattle, the linear animal model without covariance between direct and maternal additive effects was found to be the best choice.     

Genetic parameters for chronic progressive lymphedema in Belgian Draught Horses

Genetic parameters for chronic progressive lymphedema (CPL)‐associated traits in Belgian Draught Horses were estimated, using a multitrait animal model. Clinical scores of CPL in the four limbs/horse (CPL_clin), skinfold thickness and hair samples (hair diameter) were studied. Due to CPL_clin uncertainty in younger horses (progressive CPL character), a restricted data set (D_3+) was formed, excluding records from horses under 3 years from the complete data set (D_full). Age, gender, coat colour and limb hair pigmentation were included as fixed, permanent environment and date of recording as random effects. Higher CPL_clin certainty (D_3+) increased heritability coefficients of, and genetic correlations between traits, with CPL_clin heritabilities (SE) for the respective data sets: 0.11 (0.06) and 0.26 (0.05). A large proportion of the CPL_clin variance was attributed to the permanent environmental effect in D_full, but less in D_3+. Date of recording explained a proportion of variance from 0.09 ± 0.03 to 0.61 ± 0.08. Additive genetic correlations between CPL_clin and both skinfold thickness and hair diameter showed the latter two traits cannot be used as a direct diagnostic aid for CPL. Due to the relatively low heritability of CPL_clin, selection should focus on estimated breeding values (from repeated clinical examinations) to reduce CPL occurrence in the Belgian Draught Horse.     

云瑞系列甘蔗亲本的遗传力和配合力分析

[目的]对云瑞系列甘蔗亲本及组合的优劣进行评价,为加速云南甘蔗野生资源利用,提高种质创新水平,合理利用云瑞系列亲本选配杂交组合和甘蔗新品种提供参考.[方法]用28个云瑞系列亲本与36个国内外引进亲本进行杂交,获得65个杂交组合,采用家系试验评价方法,分析杂交后代主要性状的遗传力和配合力.[结果]母本、父本及组合对杂交后代株高、茎径、有效茎数和产量等性状的影响均达显著以上水平.母本、父本和组合对后代的遗传力贡献表现为组合（66.39％）＞母本（59.89％）＞父本（51.59％）,后代主要性状的遗传力大小顺序为有效茎数＞茎径＞锤度＞株高;母本对F1代的株高、茎径、有效茎数、锤度等性状的遗传力贡献分别为51.28％、65.63％、68.95％、53.71％,父本的贡献分别为19.72％、66.42％ 、78.13％、42.07％.云瑞系列亲本用作父本时产量和锤度的一般配合力高于用作母本的一般配合力.根据特殊配合力的大小和作用方向,可将28个云瑞系列亲本及衍生的65个组合分为高产高糖类、高产类、高糖类及表现较差不适宜用作品种选育等4种类型.[结论]云瑞系列亲本与其他系列亲本杂交时适合用作父本,而不适合用作母本;筛选出的高产高糖类、高产类、高糖类云瑞系列优良亲本及组合具有一定的育种潜力.     

Heritability of juvenile growth traits in red drum (Sciaenops ocellatus L.)

Heritability of juvenile growth rate was estimated for red drum (Sciaenops ocellatus), an economically important sciaenid fish in the southern USA. Thirty‐eight families were generated via ‘natural’ spawning of multiple sets of five breeders (three dams × two sires) in individual brood tanks. Offspring were individually tagged with Passive Integrated Transponder (PIT) tags and mixed for grow‐out in replicate ‘common‐garden’ tanks. Juvenile growth was followed from 166.4±18.6 to 254.0±27.0 mm (total length). Offspring were assigned a posteriori to individual brood fish (dam and sire) based on genotypes at nuclear‐encoded microsatellites. Heritability (h²) of a thermal growth coefficient was estimated using an animal‐additive model and a restricted maximum‐likelihood algorithm. Estimates of h² were 0.33±0.08 and 0.31±0.08 for thermal growth coefficient based on length and weight respectively. These results indicate a significant genetic component in juvenile growth rate in red drum. Estimates of h² for condition coefficient (K) at various measurement dates averaged 0.38, suggesting a genetic component to shape in juvenile red drum.     

Quantitative genetic parameter estimates for size and growth rate traits in Pacific white shrimp, Penaeus vannamei (Boone 1931) when reared indoors

Heritabilities of size traits and growth rate traits, as well as genetic, phenotypic and environmental correlations were estimated at three ages for a captive population of Pacific white shrimp (Penaeus vannamei) grown indoors. A covariate, mean size or mean growth rate during early growth in individual tanks before tagging and mixing, was introduced in the analyses to reduce the error caused by unique previous growth conditions on variance components. Heritabilities of size traits increased with age, with the h² for TL, AL, TWt and Wi1AS being 0.15, 0.20, 0.20 and 0.22, respectively, at 17 weeks, increasing to 0.28, 0.33, 0.34 and 0.35 at 29 weeks of age. Heritabilities of growth rate traits estimated between consecutive growth periods decreased from the first (h² for ΔTL 0.65, ΔAL 0.71, ΔTWt 0.63 and ΔWi1AS 0.84) to the second period (h² for ΔTL 0.34, ΔAL 0.50, ΔTWt 0.54 and ΔWi1AS 0.52). Phenotypic correlations were always larger than genetic correlations for both, size and growth rate traits. Genetic correlations between size traits within age were high (r_G >0.95), but those between the same size trait at different ages decreased as the age difference increased in spite of a consistently high environmental correlation (r_E 0.80–0.85) between the same trait at different ages. Phenotypic and genetic correlation's between the same growth rate trait at the two different growth periods evaluated were negative or zero (r_G TL –0.26, AL –0.24, Wi1AS 0.00) with the exception of total weight (r_G TW 0.35) and the environmental correlations between growth periods were also low (r_E 0.13–0.32).     

Phenotypic estimates and heritability values of Artemia franciscana

Artemia, in all stages of its life cycle, is suitable food for most diversified groups of aquatic animals. Although its size at different stages restricts its use as a food for some groups of fish, this problem can be overcome using selective breeding techniques. The formulation of any selective breeding programme calls for a proper understanding of the genetic architecture of the economically important traits of the population under study. Thus, heritability for certain important life history and reproductive traits was estimated in Artemia franciscana from the Great Salt Lake, Utah. In the present study, the sexwise heritability values for growth and reproduction traits were estimated using parent–offspring regression. The phenotypic parameters for the same traits are also recorded. The naupliar length was 487.0±2.0 and 490.6±1.8 μm for males and females, respectively, whereas the heritability values for naupliar length were 0.5851±0.2153 and 0.3766±0.1899 respectively. The length at 3 and 6 days of age were 1.87±0.03 and 4.10±0.08 mm, respectively, for males whereas 1.87±0.03 and 4.30±0.08 mm, respectively, for females. The heritability values for length at 3 and 6 days of age for males were 0.3272±0.3651 and 0.4965±0.2466, respectively, whereas the respective values for the females were 0.1167±0.3841 and 0.0222±0.2971. The estimates of length at first brood, pre‐reproductive period and number of offspring in first brood were 10.09±0.23 mm, 16.00±0.23 days and 53.57±1.37 days, respectively, whereas the heritability values for respective traits were 0.0403±0.1078, 0.3234±0.2874 and 0.3404±0.2202.     

水稻长穗大粒种质资源产量性状配合力及遗传力分析

选用5份籼稻恢复系和6份长穗大粒种质资源,按照NCII交配设计,对7个产量性状进行配合力和遗传力分析。结果表明,所考查的7个产量性状的遗传受亲本基因加性效应和显性效应的影响,基因加性效应起主要作用。除了株高、结实率、丛有效穗、单株产量外,其他性状的遗传表达受长穗大粒种质资源的影响较大。丛有效穗、单株产量除了受亲本特殊配合力的影响外,恢复系的一般配合力起着决定性的作用。株高、千粒重的狭义遗传力较高,可早代严格选择;主穗长度、每穗总粒数、结实率、丛有效穗、单株产量狭义遗传力较低,早代选择效果不佳。CD-1在多个性状上一般配合力最好;CD-4、CD-5可作为大粒型育种的农艺亲本。R527× CD-3作为选育大穗或重穗型亲本的优异组合;多系一号× CD-4作为选育多穗型亲本的组合;R527× CD-1作为选育大粒型亲本的组合。     

籼型杂交稻叶绿素荧光参数的配合力分析

参考籼型杂交稻叶绿素荧光参数的配合力及遗传特性,以6个籼型杂交稻不育系和5个恢复系按NC(II)交配设计的30个杂交稻组合及其亲本品种为材料,对其功能叶片的叶绿素荧光参数进行测定和分析。结果表明:1杂交稻组合的叶绿素荧光参数存在极显著的组合间遗传差异,杂交稻叶绿素荧光参数的最大荧光(Fm)、实际光能利用率ΦPSII、调节性能量耗散的量子产量ΦNPQ同时受基因的加性效应和非加性效应的影响,杂交稻其他叶绿素荧光参数主要受非加性效应的影响。2杂交稻不育系ΦPSII和ΦNPQ的一般配合力(GCA)方差大于杂交稻恢复系ΦPSII和ΦNPQ的GCA方差,表明这些叶绿素荧光参数受其不育系的影响大于受其恢复系的影响。3杂交稻叶绿素荧光参数的广义遗传力均大于其狭义遗传力,其中,Fm、ΦPSII、ΦNPQ、非光化学淬灭NPQ等叶绿素荧光参数的狭义遗传力为20%~50%,具有中等遗传力;Fo、原初光能利用率(Fv/Fm)、非调节性能量耗散的量子产量(ΦNO)、化学淬灭(qL)、叶绿素荧光参数的狭义遗传力在20%以下,遗传力较弱。4杂交稻ΦPSII的竞争优势与其母本GCA呈极显著水平的正相关,且具有较高的决定系数,表明杂交稻ΦPSII的母本GCA效应值较高,其杂交稻组合的竞争优势也强。在选配高光能利用效率的强优势杂交稻组合时,关键应优先选择ΦPSII的配合力和表型均优良的杂交稻不育系配组。