Multivariate Restricted Maximum Likelihood Research Articles

Genetic and phenotypic parameters for productive traits in the first three lactations of Khuzestan buffaloes in Iran

Abstract. The objective of this study was to estimate genetic parameters for milk and fat yields in Khuzestan buffaloes of Iran. A total of 5 258 production records of the first three lactations of the Khuzestan buffaloes obtained from the Animal Breeding Centre of Iran between 1993 and 2009 were used for the analysis. Genetic parameters were estimated by the multivariate restricted maximum-likelihood (REML) procedure in the Wombat program. The averages of milk and fat production were 2 220.0 kg and 137.6 kg for first lactation; 2 236.8 kg and 137.9 kg for second lactation; and 2 303.6 kg and 143.3 kg for third lactation, respectively. Heritability estimates for milk and fat yields were 0.06 and 0.24 for the first; 0.06 and 0.28 for the second and 0.26 and 0.47 for the third lactation, respectively. Genetic correlation estimates between first and second, first and third, and second and third lactations were 0.77, 0.67 and 0.79 for milk and −0.61, −0.21 and −0.25 for fat yields. These estimates for milk yield are consistent with previous estimates obtained from animal models. Milk production of different lactations is essentially the same trait genetically and combining all lactation records as a single trait is appropriate. On the other hand, negative genetic correlations for fat yield in different lactations indicated that fat yields in all lactations were determined by different genes.

Genetic and environmental dispersion parameter estimation by test interval method in dairy sheep

Genetic and environmental parameters for 38 983 test-day records of daily milk yield (DMY), fat (FC) and protein (PC) content, collected between 1994 and 2002, were estimated on 3,068 dairy ewes of the three Slovenian breeds. A multivariate restricted maximum likelihood method was used for estimation, where every test-day record was treated as a different trait. Fixed part of the multitrait animal model for DMY, FC, and PC included breed and lambing season as classes, while stage of lactation, parity, and litter size were covariates. Random part of the model contained additive genetic effect and the effects of flock test month and permanent environment over lactations. Heritability estimates for individual test-days were between 0.10 and 0.23 for DMY, 0.09 and 0.18 for FC, and 0.19 and 0.28 for PC. The flock test month effect explained most of the phenotypic variance: 0.18 to 0.41 for DMY, 0.26 to 0.45 for FC, and 0.24 to 0.44 for PC. A lower variance ratio was explained by the permanent environment effect over lactations: 0.09 to 0.15 for DMY, 0.02 to 0.11 for FC, and 0.02 to 0.09 for PC. Additive genetic correlations between individual test-days were high in all three milk traits for adjacent months of lactation. They decreased when the interval between months of lactation increased. The structure of additive genetic correlations showed that the observed milk traits in the different stages of lactation were genetically not the same trait, since the correlations between distant months of lactation were lower than one.

Quantitative analysis of production traits in saltwater crocodiles (Crocodylus porosus): II. age at slaughter

Crocodile morphometric (head, snout-vent and total length) measurements were recorded at three stages during the production chain: hatching, inventory [average age (+/-SE) is 265.1 +/- 0.4 days] and slaughter (average age is 1037.8 +/- 0.4 days). Crocodile skins are used for the manufacture of exclusive leather products, with the most common-sized skin sold having 35-45 cm in belly width. One of the breeding objectives for inclusion into a multitrait genetic improvement programme for saltwater crocodiles is the time taken for a juvenile to reach this size or age at slaughter. A multivariate restricted maximum likelihood analysis provided (co)variance components for estimating the first published genetic parameter estimates for these traits. Heritability (+/-SE) estimates for the traits hatchling snout-vent length, inventory head length and age at slaughter were 0.60 (0.15), 0.59 (0.12) and 0.40 (0.10) respectively. There were strong negative genetic (-0.81 +/- 0.08) and phenotypic (-0.82 +/- 0.02) correlations between age at slaughter and inventory head length.

Prevalence of spondylosis deformans and estimates of genetic parameters for the degree of osteophytes development in Italian Boxer dogs.

The aim of this study was to assess the prevalence of spondylosis deformans and to investigate genetic aspects of the degree of osteophytes development (DOD) in the Italian Boxer dog population. A total of 849 Boxer dogs was radiographed on the thoracic, lumbar, and sacral regions of the spine and scored for DOD. Grading of DOD was performed for all 20 intervertebral sites comprised within the first thoracic site (site T1-T2) and the site between the seventh lumbar and the first sacral vertebra (site L7-S1). Scores for DOD ranged from 0 (no osteophytes development) to 3 (presence of a bony spur formed by osteophytes on adjoining vertebrae). The first five thoracic sites exhibited no variation for DOD and were not considered in the analysis. The prevalence of spondylosis deformans was 84%, and frequency of dogs showing at least one intervertebral site that scored 3 for DOD was 50%. Scores for DOD at different sites were analyzed as different traits. Nongenetic effects influencing DOD scores were sex, age at screening, and the kennel. Posterior densities of heritability (h2) were estimated using a univariate Bayesian analysis. Eight sites exhibited a posterior probability greater than 0.8 for h2 > 10% and were considered in a multivariate restricted maximum likelihood analysis. Estimated h2 from multivariate analysis ranged from 25 to 48% (SE from 5 to 7%). Three sites exhibited h2 estimates greater than 40%. Genetic correlations for DOD scored at different sites ranged from 0.07 to 0.96. All thoracic sites had estimated correlations larger than 0.85 with other thoracic sites. Genetic correlation between the first and the second lumbar site was 0.91. Correlations between thoracic sites and the first two lumbar sites ranged from 0.5 to 0.9. Sites L6-L7 and L7-S1 also exhibited weak relationships with all remaining sites. Breeding values of dogs for DOD at the eight sites were predicted using estimated covariance matrices. A selection index for DOD was computed from predicted breeding values and a set of relative weighting factors produced by a panel of veterinarians. The index was the most important effect influencing phenotypic differences between dogs for average DOD score, number of affected sites, and number of sites with a DOD score > 1 (P < 0.001). The degree of osteophytes development is a trait showing exploitable additive genetic variance, and breeding programs for decreasing prevalence and severity of spondylosis deformans might focus on this trait.

Genetic variation in wood properties of interior spruce. I. Growth, latewood percentage, and wood density

Quantitative genetic variation in growth, latewood percentage, and wood density was investigated for British Columbia's interior spruce (the common name for white spruce, Picea glauca (Moench) Voss; Engelmann spruce, Picea engelmanni Parry ex Engelm.; and their hybrids). The study included 160 half-sib families from the East Kootenay and Prince George regions. At the time of sampling, progeny tests for those two regions were 20 and 22 years old, respectively. Univariate and multivariate restricted maximum likelihood (REML) estimates of genetic parameters were obtained. Estimates of genetic variances and heritabilities differed greatly across planting sites for the examined traits, especially after transplantation between the regions. Significant negative genetic correlation between overall growth and wood density was found for the East Kootenay progenies, while negative but nonsignificant genetic correlation between these traits was found for the Prince George progenies. Generally, there was no significant decrease in heritability for ring width and latewood percentage in successive growth rings. A general age trend for genetic correlation between those traits was not apparent, except that the correlation remained negative during the observed period. Our results show that it is not possible to select certain families as superior based on 1-year results because of the family by growing season interactions. Nevertheless, genetic age–age correlations for cumulative increments were high, having a decreasing trend with increasing difference in age.

Genetic correlation estimations between artificial insemination sire performances and their progeny beef traits both measured in test stations

In France, beef traits of artificial insemination (AI) beef bulls are improved through the sequential selection for their own performances and for their male progeny performances, both being recorded in test stations. The efficiency of such programmes mainly depends on the genetic correlations between sire performances and progeny beef traits. Such correlations were independently estimated, using the multivariate REML (restricted maximum likelihood) method in a Limousin and a Charolais programme. In both breeds, high genetic correlations were observed between sires and progeny analogous morphology scores (from 0.64 to 0.82). Genetic correlations estimated between sires and progeny growth (from 0.41 to 0.70) were lower probably due to the difference of diet in central and progeny stations. Correlations between sire muscling scores and progeny skeletal frames (and vice-versa) were negative (from -0.05 to -0.58). The genetic correlations of sire traits with progeny dressing percentage (DPp) and carcass fatness score (CFp) were only low to moderate. These results show that the selection of bulls at the end of performance testing in test stations may be efficient in improving progeny growth and morphology. However, such a selection is insufficient in improving their dressing percentage and carcass composition.

Estimativas de parâmetros genéticos e de tendências fenotípica , genética e de ambiente de algumas características produtivas da raça Gir Leiteiro

Os objetivos do estudo foram estimar os parâmetros genéticos e as tendências fenotípica, genética e de ambiente para produção de leite (PL), duração da lactação (DL), produção de gordura (PG) e porcentagem de gordura (CG) no leite, na raça Gir, utilizando análises uni e bivariadas sob o método da máxima verossimilhança restrita, por meio de algorítmo livre de derivadas (MTDFREML), ajustando modelos-animal. O modelo matemático adotado para as quatro características produtivas incluiu os efeitos fixos de rebanho-ano de parto, época de parto e idade ao parto como covariável (linear e quadrática) e, além do resíduo, os efeitos aleatórios de animal e ambiente permanente. Por meio de análises bivariadas, as estimativas de herdabilidade foram, respectivamente: PL e DL, 0,21 e 0,11; PL e PG, 0,22 e 0,21; PL e CG, 0,19 e 0,12. As estimativas de repetibilidade foram PL, 0,51; DL, 0,32; PG, 0,47; e CG, 0,13. As correlações fenotípicas, genéticas e de ambiente foram, respectivamente: para PL e DL, 0,62, 0,76 e 0,57; para PL e PG, 0,93, 0,97 e 0,91; para PL e CG, -0,02, -0,11 e -0,01. As estimativas das mudanças anuais fenotípica, genética e de ambiente para as características produtivas estudadas foram, respectivamente: para PL, 66,93± 7,06 (P&lt;0,01), 10,46± 1,08 (P&lt;0,01) e 56,47 kg/ano na população de vacas, e 29,63± 14,34 (P&lt;0,05), 19,29± 5,27 (P&lt;0,01) e 10,34 kg/ano na população de touros; para DL, -0,16± 0,31 (P&gt;0,05), 0,21± 0,09 (P&lt;0,05) e -0,37 dias/ano na população de vacas, e -0,69± 0,44 (P&gt;0,05), -0,10± 0,28 (P&gt;0,05) e -0,59 dias/ano na população de touros; para PG, 3,53± 0,58 (P&lt;0,01), 0,40± 0,09 (P&lt;0,01) e 3,13 kg/ano na população de vacas, e 1,37± 0,95 (P&gt;0,05), 0,47± 0,29 (P&gt;0,05) e 0,90 kg/ano na população de touros; para CG no leite, 0,039± 0,014 (P&lt;0,05), 0,001± 0,001 (P&gt;0,05) e 0,038 %/ano na população de vacas, e 0,010± 0,011 (P&gt;0,05), 0,000± 0,003 (P&gt;0,05) e 0,010 %/ano na população de touros.

Genetic correlation estimations between artificial insemination sire performances and their progeny beef traits both measured in test stations.

In France, beef traits of artificial insemination (AI) beef bulls are improved through the sequential selection for their own performances and for their male progeny performances, both being recorded in test stations. The efficiency of such programmes mainly depends on the genetic correlations between sire performances and progeny beef traits. Such correlations were independently estimated, using the multivariate REML (restricted maximum likelihood) method in a Limousin and a Charolais programme. In both breeds, high genetic correlations were observed between sires and progeny analogous morphology scores (from 0.64 to 0.82). Genetic correlations estimated between sires and progeny growth (from 0.41 to 0.70) were lower probably due to the difference of diet in central and progeny stations. Correlations between sire muscling scores and progeny skeletal frames (and vice-versa) were negative (from -0.05 to -0.58). The genetic correlations of sire traits with progeny dressing percentage (DPp) and carcass fatness score (CFp) were only low to moderate. These results show that the selection of bulls at the end of performance testing in test stations may be efficient in improving progeny growth and morphology. However, such a selection is insufficient in improving their dressing percentage and carcass composition.

Estimativas de parâmetros genéticos e de tendência fenotípica, genética e de ambiente de algumas características reprodutivas na raça Gir

O objetivo do estudo foi estimar os parâmetros e as tendências fenotípica, genética e ambiental para idade ao primeiro parto (IPP) e intervalo de partos (IDP) na raça Gir, com o emprego de análises uni e bivariadas sob o método da máxima verossimilhança restrita, por meio de algoritmo livre de derivadas (MTDFREML), que ajusta o modelo animal. O modelo matemático adotado para estudo do IDP incluiu os efeitos fixos rebanho-ano de parto, época de parto e idade da vaca ao parto como covariável e os efeitos aleatórios de animal e ambiente permanente. Para a IPP, o modelo incluiu os efeitos fixos rebanho-ano de nascimento e época de nascimento e efeito de animal como aleatório. Por meio de análises bivariadas, as estimativas de herdabilidade foram 0,17 para IPP e 0,06 para IDP. A estimativa de repetibilidade para IDP foi 0,17. As correlações fenotípica, genética e de ambiente entre IPP e IDP foram, respectivamente, 0,06, 0,37 e 0,03. As mudanças anuais fenotípica, genética e de ambiente para IPP foram, respectivamente, -0,446±0,077 (P&lt;0,01), 0,008±0,013 e -0,454 meses, com base no valor genético das vacas, e -0,185± 0,083 (P&lt;0,05), 0,051± 0,059 e -0,236 meses com base no valor genético dos touros. As mudanças anuais fenotípica, genética e de ambiente para IDP foram, respectivamente, -1,25±0,95, -0,98±0,19 (P&lt;0,01) e -0,27 dias com base no valor genético das vacas e -0,88±1,07, -1,62±0,40 (P&lt;0,01) e 0,74 dias, com base no valor genético dos touros.

Use of Individual Tree Mixed Models to Account for Mortality and Selective Thinning When Estimating Base Population Genetic Parameters

Abstract The ability of individual tree mixed models to estimate unbiased genetic parameters was investigated for growth, Pilodyn penetration, and bark thickness, in an Eucalyptus urophylla progeny trial where the smaller trees have been previously thinned. A multivariate Restricted Maximum Likelihood (REML) analysis including the growth measurements of all trees prior to thinning, and later measurements of only those that remained, resulted in almost unbiased estimates of heritabilities and age-age genetic correlations for growth traits at all ages. Analysis based only on trees remaining after thinning resulted in considerably lower estimates of heritabilities and age-age genetic correlations. On the other hand, genetic parameters for Pilodyn penetration or bark thickness were not affected by the thinning. This was due to the low correlations between the thinning criteria (tree size) and the wood and bark traits. For. Sci. 44(2):246-253.

Animal x testing environment interaction on postweaning liveweight gains of young bulls

Postweaning liveweight gain records of 1610 young bulls obtained both in feedlot and under pasture were used to estimate (co)variance components using a multivariate restricted maximum likelihood analysis. The pedigree file included 3477 animals. Heritability estimates for liveweights and gain in both environments correspond to most previously reported estimates. The genetic correlation of gain between the 2 environments was -0·12, suggesting a large genotype testing environment interaction and re-ranking of animal breeding values across environments. Results of this analysis suggest the need for environment-specific breeding values for postweaning gain.

Missing Data Due to Culling of Pigs Before Testing and the Effects on the Estimation of (Co)Variance Components

Abstract A stochastic simulation of a pig breeding unit with 100 sows and 15 boars was used to examine the effects of culling before testing on the estimates of (co)variance components and parameters. The traits were age at test (AGE) and sidefat thickness (FAT) measured on farm. Data were simulated over 10 years and missing data were generated by deletion of records based on the phenotypic value of AGE. A situation with no culling (C-NO) was compared with culling at random (C-RAND), within litters (C-W/IN) and over litters (C-OVER). A multivariate restricted maximum likelihood procedure was applied to estimate (co)variance components, using the same model as that for the simulation of records. The heritabilities of AGE were over estimated in C-W/IN and C-OVER, and genetic, residual and phenotypic correlations became weaker. The litter variance ratio of AGE was seriously overestimated in C-W/IN and underestimated in C-OVER. A reduced model, without the litter effect included, resulted in even larger diffe...

Multivariate restricted maximum likelihood estimation of genetic parameters for production traits in three selected turkey strains

Multivariate restricted maximum likelihood estimation of genetic parameters for production traits in three selected turkey strains

Multivariate restricted maximum likelihood estimation of genetic parameters for production traits in three selected turkey strains

Multivariate restricted maximum likelihood estimation of genetic parameters for production traits in three selected turkey strains

Multivariate restricted maximum likelihood estimation of genetic parameters for production traits in three selected turkey strains*

Multivariate restricted maximum likelihood estimation of genetic parameters for production traits in three selected turkey strains*

Genetic correlations of clinical mastitis and feet and legs problems with milk yield type traits in Dutch Black and White dairy cattle

Direct selection for decreased disease incidence is difficult given low hsuperscript 2s and the absence of disease recording. Genetic correlations between diseases and type traits indicate possibilities for indirect selection; however, correlations often include experimentally instead of routinely scored type traits. The aim of this study was to estimate genetic correlations of clinical mastitis and feet and legs problems with milk yield and routinely scored type traits in Dutch Black and White [DBW; Dutch Black Pied] cows. From 1983 to 1991, the incidence of diseases was recorded at 44 farms with DBW dairy cattle. Records on 3617 cows sired by 224 bulls were analysed. Heritabilities for milk yield, type traits and diseases were obtained using an equal design multivariate Restricted Maximum Likelihood procedure considering all observations on a continuous scale. A bivariate threshold procedure was used to estimate hsuperscript 2s of diseases and genetic correlations of diseases with milk yield and type traits. Genetic correlations of clinical mastitis and feet and legs problems with milk yield were 0.16 and 0.26 respectively, and hsuperscript 2s for diseases were low 0.01-0.11. Unexpected positive relations between udder type traits and clinical mastitis were found (0.09-0.26), and possible reasons are discussed. Genetic correlations between type traits for feet and legs and problems of the feet and legs were negative -0.01 and -0.24 respectively. Final score for feet and legs could be used as a selection criterion to select to reduce the incidence of feet and legs problems.

Genetic and phenotypic correlations between linear type traits and production traits in Holstein-Friesian dairy cattle

AbstractFirst lactation production and linear type records of 72 559Holstein-Friesian cows, calving from 1982 to 1989, were analysed by multivariate restricted maximum likelihood, using a sire model. The data comprised offspring of 1066 randomly used sires, and 91 proven i.e. widely used bulls. All phenotypic correlations between the type traits and the yield traits were small, but moderate genetic correlations were obtained between milk, fat and protein yield and angularity (~—0·43) and between the yield traits and udder depth (~0·44), indicating that higher yielding heifers are more angular and have deeper udders. The heritabilities of the type traits were in line with previous analyses, but those for milk, fat and protein yield were rather high at 0·47, 0·52 and 0·45 respectively

Genetic and phenotypic relationships between conformation and production traits in Ayrshire heifers

AbstractFirst lactation records for production traits (milk, fat and protein yields) and 17 linear type traits for 7169 Ayrshire heifers were analysed to estimate genetic parameters for type traits and to examine the relationship between type and production traits. A multivariate restricted maximum likelihood procedure fitting a sire model with sire relationships included was used for all analyses.Heritabilities for production traits were approximately 0·3 and genetic correlations among them were high (&gt;0·84). The estimates of heritabilities for type traits were mainly low to moderate ranging from 0·04 to 0·42. Angularity (0·80), beef shape (0·49), foot angle (0·53) and stature (0·46) had higher heritabilities. Generally phenotypic correlations among type traits were lower than the genetic correlations. The highest negative genetic correlation was between rear legs side and rear legs rear (-0·95) and the highest positive correlation between chest width and beef shape (0·93).Genetic correlations between type and production were low to moderate and were similar for milk, fat and protein yields. The genetic correlations between the production traits and chest width, udder depth and beef shape were negative but were positive between production and angularity, rear udder width and teat placement side.

Selection for predicted carcass lean content in Scottish Blackface sheep

AbstractScottish Blackface sheep have been selected for either increased or decreased predicted carcass lean content at 20 weeks of age, using an index combining ultrasonic backfat depth and body weight. The index was designed to alter carcass lean content without changing body weight. After 4 years there have been large responses in the index and fat depth, the proportional difference between the divergent lines in fat depth is 0·28, but body weight and ultrasonic muscle depth have not changed between the lines. The realized heritability for the index is 0·45. Heritabilities for the index, ultrasonic fat depth, body weight and ultrasonic muscle depth, calculated using multivariate restricted maximum likelihood, are 0·47 (s.e. = 0·14), 0·39 (s.e. 0·13), 0·23 (s.e. 0·12) and 0·36 (s.e. 0·14), respectively. The selected lines will be used to investigate relationships between carcass lean content, viability and maternal performance under the harsh environmental conditions encountered in the Scottish hill environment.

Multivariate restricted maximum likelihood estimation of genetic parameters for growth, carcass and meat quality traits in French Large White and French Landrace pigs

Multivariate restricted maximum likelihood estimation of genetic parameters for growth, carcass and meat quality traits in French Large White and French Landrace pigs