Ismo Strandén

Ismo Strandén
Natural Resources Institute Finland (Luke) · Animal Genetics and Breeding

PhD

About

138
Publications
18,659
Reads
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2,392
Citations
Citations since 2016
30 Research Items
1226 Citations
2016201720182019202020212022050100150200
2016201720182019202020212022050100150200
2016201720182019202020212022050100150200
2016201720182019202020212022050100150200
Introduction
Ismo Strandén currently works at the Natural Resources Institute Finland (Luke), Applied Statistical Methods group. Ismo does research in Animal Science, particularly development of computational methods in use of genomic information in genetic evaluations.
Additional affiliations
November 2014 - December 2014
MTT Agrifood Research
Position
  • Professor (Full)
October 2009 - November 2014
MTT Agrifood Research
Position
  • Group Leader
January 1997 - September 2009
MTT Agrifood Research Finland
Position
  • Senior Researcher

Publications

Publications (138)
Article
Full-text available
Background Genomic estimated breeding values (GEBV) by single-step genomic BLUP (ssGBLUP) are affected by the centering of marker information used. The use of a fixed effect called J factor will lead to GEBV that are unaffected by the centering used. We extended the use of a single J factor to a group of J factors. Results J factor(s) are usually...
Article
Approximate multistep methods to calculate reliabilities for estimated breeding values in large genetic evaluations were developed for single-trait (ST-R²A) and multitrait (MT-R²A) single-step genomic BLUP (ssGBLUP) models. First, a traditional animal model was used to estimate the amount of nongenomic information for the genotyped animals. Second,...
Article
Full-text available
Genomic selection is widely used in dairy cattle breeding, but still, single-step models are rarely used in national dairy cattle evaluations. New computing methods have allowed the utilization of very large genomic data sets. However, an unsolved model problem is how to build genomic- (G) and pedigree- (A22) relationship matrices that satisfy the...
Article
Full-text available
Genetic groups are often used in genetic evaluations to account for selection that cannot be accounted for by kinship. The genetic groups can be fitted as random or fixed effects, both in traditional BLUP and in single-step genomic predictions (ssGBLUP). In this study, we investigate how inclusion of genetic groups affect the predictive ability and...
Article
Full-text available
Genomic data are widely used in predicting the breeding values of dairy cattle. The accuracy of genomic prediction depends on the size of the reference population and how related the candidate animals are to it. For populations with limited numbers of progeny-tested bulls, the reference populations must include cows and data from external populatio...
Article
The growing amount of genomic information in dairy cattle has increased computational and modeling challenges in the single-step evaluations. The computational challenges are due to the dense inverses of genomic (G) and pedigree (A22) relationship matrices of genotyped animals in the single-step mixed model equations. An equivalent mixed model equa...
Article
Full-text available
Calculation of individual animal reliability of estimated genomic breeding value by SNP-BLUP requires inversion of the mixed model equations (MME). When the SNP-BLUP model includes a residual polygenic (RPG) effect, the size of the MME will be at least the number of genotyped animals (n) plus the number of SNP markers (m). Inversion of the MME in S...
Article
Full-text available
Pigs are housed in groups during the test period. Social effects between pen mates may affect average daily gain (ADG), backfat thickness (BF), feed conversion rate (FCR), and the feeding behaviour traits of pigs sharing the same pen. The aim of our study was to estimate the genetic parameters of feeding behaviour and production traits with statist...
Article
Full-text available
The snp_blup_rel program computes model reliabilities for genomic breeding values. The program assumes a single trait SNP-BLUP model where the breeding value can include a residual polygenic (RPG) effect. The reliability calculation requires elements of the inverse of the mixed model equations (MME). The calculation has three steps: 1) MME calculat...
Article
Full-text available
Base population allele frequencies (AF) should be used in genomic evaluations. A program named Bpop was implemented to estimate base population AF using a generalized least squares (GLS) method when the base population individuals can be assigned to groups. The required dense matrix products involving (A22 )-1v were implemented efficiently using sp...
Article
Genomic selection has been adopted in many plant breeding programmes. In this paper, we cover some aspects of information necessary before starting genomic selection. Spring oat and barley breeding data sets from commercial breeding programmes were studied using single, multitrait and trait‐assisted models for predicting grain yield. Heritabilities...
Article
Single-step genomic BLUP (ssGBLUP) is a powerful approach for breeding value prediction in populations with a limited number of genotyped animals. However, conflicting genomic (G) and pedigree (A22) relationship matrices complicate the implementation of ssGBLUP into practice. The metafounder (MF) approach is a recently proposed solution for this pr...
Article
An SNP-BLUP model is computationally scalable even for large numbers of genotyped animals. When genetic variation cannot be completely captured by SNP markers, a more accurate model is obtained by fitting a residual polygenic effect (RPG) as well. However, inclusion of the RPG effect increases the size of the SNP-BLUP mixed model equations (MME) by...
Article
During the last decade, genomic selection has revolutionized dairy cattle breeding. For example, Nordic dairy cows (Denmark, Finland, and Sweden) born in 2018 were >90% sired by young genomically tested bulls. Thus, the average age of sires for Red Dairy Cattle cows born in 2018 was only 3.1 yr, whereas in 2011 it was 5.7 yr. Earlier the key driver...
Article
Monte Carlo (MC) methods have been found useful in estimation of variance parameters for large data and complex models with many variance components (VC), with respect to both computer memory and computing time. A disadvantage has been a fluctuation in round‐to‐round values of estimates that makes the estimation of convergence challenging. Furtherm...
Article
Livestock production both contributes to and is affected by global climate change, and substantial modifications will be required to increase its climate resilience. In this context, reliance on dominant commercial livestock breeds, featuring small effective population sizes, makes current production strategies vulnerable if their production is res...
Article
Full-text available
Background: For marker effect models and genomic animal models, computational requirements increase with the number of loci and the number of genotyped individuals, respectively. In the latter case, the inverse genomic relationship matrix (GRM) is typically needed, which is computationally demanding to compute for large datasets. Thus, there is a...
Article
We developed a multiple‐trait animal model for blue fox fertility evaluation and estimated genetic parameters simultaneously for seven traits: first three litter sizes (LS), pregnancy rate (PREG), whelping success (WHELP), grading size (gSI) and fur quality (gQU). Grading size and quality were included into the new multiple‐trait model as correlate...
Article
Joint Nordic (Denmark, Finland, Sweden) genetic evaluation of female fertility is currently based on the multiple trait multilactation animal model (BLUP). Here, single step genomic model (ssGBLUP) was applied for the Nordic Red dairy cattle fertility evaluation. The 11 traits comprised of nonreturn rate and days from first to last insemination in...
Article
Full-text available
Single-step genomic prediction models utilizing both genotyped and nongenotyped animals are likely to become the prevailing tool in genetic evaluations of livestock. Various single-step prediction models have been proposed, based either on estimation of individual marker effects or on direct prediction via a genomic relationship matrix. In this stu...
Article
Mixed linear models have been applied for predicting breeding values of dairy cattle in most of the developed countries since the 1980s. However, the Russian Federation is still using the old contemporary comparison method. The objective of our study was to develop a best linear unbiased prediction (BLUP) for an animal model of breeding values for...
Article
Full-text available
The number of genotyped animals has increased rapidly creating computational challenges for genomic evaluation. In animal model BLUP, candidate animals without progeny and phenotype do not contribute information to the evaluation and can be discarded. In theory, genotyped candidate animal without progeny can bring information into single-step BLUP...
Article
Full-text available
Background Single-step genomic best linear unbiased prediction (BLUP) evaluation combines relationship information from pedigree and genomic marker data. The inclusion of the genomic information into mixed model equations requires the inverse of the combined relationship matrix \({\mathbf{H}}\), which has a dense matrix block for genotyped animals....
Article
An equivalent computational approach called ssGTBLUP was formulated for the original single-step GBLUP (ssGBLUP). In ssGTBLUP, the genomic relationship matrix has the form = ' + , where the (centered and scaled) marker matrix has size x (numbers of genotypes and markers), and the matrix can be easily inverted. The inverse can be written as = - ' wh...
Article
Single-step genomic BLUP (ssGBLUP) requires a dense matrix of the size equal to the number of genotyped animals in the coefficient matrix of mixed model equations (MME). When the number of genotyped animals is high, solving time of MME will be dominated by this matrix. The matrix is the difference of two inverse relationship matrices: genomic (G) a...
Article
The profit and production of an average Finnish blue fox farm was simulated using a deterministic bio-economic farm model. Risk was included using Arrow-Prat absolute risk aversion coefficient and profit variance. Risk-rated economic values were calculated for pregnancy rate, litter loss, litter size, pelt size, pelt quality, pelt colour clarity, f...
Article
Pohjoismaista lypsykarjan hedelmällisyysominaisuuksien jalostusarvostelua ollaan päivittämässä. Koska yhä useammasta eläimestä on genominen tieto, uutta mallia halutaan testata myös niin että genominen tieto on yhdistettynä arvosteluihin. Yleinen menetelmä genomisen ja perinteisen tiedon yhdistämiseen on ns. genominen eläinmalli eli single-step –me...
Article
Genotyypitettyjen eläinten lukumäärä on noussut nopeasti ja yhä enemmän genotyypitetään myös lehmiä. Tämä luo genomisille arvosteluille laskennallisia haasteita. Lähitulevaisuudessa on siirryttävä genomisen eläinmallin (ssGBLUP) käyttöön, jotta arvostelujen harhattomuus voidaan taata. Yksi kysymys genomiarvostelujen laskennassa on nuorten ja karsit...
Article
Full-text available
We studied the effect of including genomic data for cows in the reference population of single-step evaluations. Deregressed individual cow genetic evaluations (DRP) from milk production evaluations of Nordic Red Dairy cattle were used to estimate the single-step breeding values. Validation reliability and bias of the evaluations were calculated wi...
Article
The frequency of eye infections in the Finnish blue fox population has increased during the past decade. Eye infection may incur economic losses to producers due to reduced selection intensity, but ethical aspects need to be considered as well because eye infection can be quite painful and reduce animal well-being. The purpose of this study was to...
Article
Full-text available
The objectives of this study were to evaluate the feasibility of use of the test-day (TD) single-step genomic BLUP (ssGBLUP) using phenotypic records of Nordic Red Dairy cows. The critical point in ssGBLUP is how genomically derived relationships (G) are integrated with population-based pedigree relationships (A) into a combined relationship matrix...
Article
Full-text available
Three random regression models were developed for routine genetic evaluation of Danish, Finnish, and Swedish dairy cattle. Data included over 169 million test-day records with milk, protein, and fat yield observations from over 8.7 million dairy cows of all breeds. Variance component analyses showed significant differences in estimates between Hols...
Book
Full-text available
RelaX2 program has been written for studying relationships of animals in large pedigrees. The program needs a pedigree file which has columns for animal, its sire and dam identification codes. Main functions of the program are • pedigree checking (consistency with or without knowing birth date) • pedigree pruning (e.g., for estimation of variance c...
Article
Full-text available
Profitability of beef production can be increased by genetically improving carcass traits. To construct breeding value evaluations for carcass traits, breed-specific genetic parameters were estimated for carcass weight, carcass conformation and carcass fat in five beef cattle breeds in Finland (Hereford, Aberdeen Angus, Simmental, Charolais and Lim...
Conference Paper
Abstract Text: We studied the effect of including genotyped cows in the reference population of the Nordic Red Dairy Cattle on the validation accuracy of genomic breeding values. Deregressed individual cow EBVs (DRP) were used in single-step genomic evaluations. The accuracy of evaluations was calculated after including 0 or 3,111 or 5,593 genotype...
Conference Paper
Abstract Text: We studied the possibility to utilize the Monte Carlo algorithm in estimation of standard errors for MC EM REML variance component estimates. Approach is based on the principle that the expected information matrix at the maximum likelihood estimate is equal to the variance of score function. While score functions include EM updates,...
Conference Paper
Abstract Text: The frequency of eye infections in the Finnish blue fox population has increased during the past decade. Eye infection may incur economic losses to producers due to reduced selection intensity. Ethical aspects also need to be considered, since eye infection reduces animal wellbeing. The purpose of this study was to estimate genetic p...
Conference Paper
Abstract Text: We present an equivalent equation system for solving single-step genomic BLUP that does not require separate forming or inversion of the pedigree relationship matrix of genotyped animals. The equation system is contrasted with original single-step equations and two augmented equation systems. Comparison was based on a small data havi...
Conference Paper
Abstract Text: In admixed populations originating from different base breeds, such as Nordic Red dairy cattle, haplotypes of chromosomal segments instead of single SNP are expected to improve prediction accuracy in genomic evaluations, because linkage disequilibrium with QTL is likely to be more consistent for haplotypes than for SNP. The suggest...
Conference Paper
Full-text available
Abstract Text: Breeding values in genetic evaluation are compared between conventional animal model BLUP, single-step BLUP, and revised bivariate blending after genomic BLUP. The data are extracted from the production trait evaluation of Nordic Red dairy cattle. Genotyped bulls with daughters are used as training animals, and younger genotyped bu...
Article
Full-text available
Background Although the X chromosome is the second largest bovine chromosome, markers on the X chromosome are not used for genomic prediction in some countries and populations. In this study, we presented a method for computing genomic relationships using X chromosome markers, investigated the accuracy of imputation from a low density (7K) to the 5...
Article
Full-text available
Two heterogeneous variance adjustment methods and two variance models were compared in a simulation study. The method used for heterogeneous variance adjustment in the Nordic test-day model, which is a multiplicative method based on Meuwissen (J. Dairy Sci., 79, 1996, 310), was compared with a restricted multiplicative method where the fixed effect...
Article
Siniketun tärkeimmät jalostustavoitteet ovat pentue- ja nahkakoko sekä nahan laatu (värin puhtaus, tummuus ja yleislaatu). Merkittävin nahasta maksettavaan hintaa vaikuttava tekijä on koko. Rehu on puolestaan tuotantosuunnan suurin kustannustekijä ja rehukustannusten oletetaan nousevan edelleen. Tämän vuoksi siniketun parempi rehuhyötysuhde on nous...
Article
In admixed populations originating from different base breeds, such as the Nordic Red Dairy Cattle, identity by state of haplotypes instead of single nucleotide polymorphisms (SNP) is a better surrogate for identity by descent. Therefore, haplotypes are expected to be more useful in recovering genetic relationships among animals and linkage disequi...
Article
Full-text available
The observed low accuracy of genomic selection in multibreed and admixed populations results from insufficient linkage disequilibrium between markers and trait loci. Failure to remove variation due to the population structure may also hamper the prediction accuracy. We verified if accounting for breed origin of alleles in the calculation of genomic...
Article
Full-text available
Estimation of variance components by Monte Carlo (MC) expectation maximization (EM) restricted maximum likelihood (REML) is computationally efficient for large data sets and complex linear mixed effects models. However, efficiency may be lost due to the need for a large number of iterations of the EM algorithm. To decrease the computing time we exp...
Article
Pelt character traits (size, quality, colour clarity, darkness) are important economic traits in blue fox breeding. Better feed efficiency (FE) is another economically important and new breeding goal for fur animals. The purpose of this study was to determine the correlations between pelt character traits, FE and size traits and to estimate genetic...
Article
Full-text available
Different approaches of calculating genomic measures of relationship were explored and compared with pedigree relationships (A) within and across base breeds in a crossbreed population, using genotypes for 38,194 loci of 4,106 Nordic Red dairy cattle. Four genomic relationship matrices (G) were calculated using either observed allele frequencies (A...
Article
A bio-economic model was created to simulate production of an average Finnish blue fox farm. The studied traits were pelt quality, pelt size, pelt color clarity, litter size, pregnancy (barren or non-barren), and felicity (includes both aborting and females losing all pups before pups are 3 weeks). Marginal economic values of traits were estimated...
Article
A random regression model is presented as an approximation for multibreed variance model. The approximation is derived using the splitted multibreed model where the single breeding value is split to the breed specific and their segregation terms. The random regression model allows extending the multibreed information easily to genomic data models....
Article
The current study evaluates reliability of genomic predictions in selection candidates using multi-trait random regression model, which accounts for interactions between marker effects and breed of origin in the Nordic Red dairy cattle (RDC). The population structure of the RDC is admixed. Data consisted of individual animal breed proportions calcu...
Article
Interest is growing in finding indicator traits for the evaluation of nutritional or tissue energy status of animals directly at the individual animal level. The development and subsequent use of such traits in practice demands a clear understanding of the genetic and phenotypic associations with the various production and functional traits. In thi...
Article
Multiple-trait and random regression models have multiplied the number of equations needed for the estimation of variance components. To avoid inversion or decomposition of a large coefficient matrix, we propose estimation of variance components by Monte Carlo expectation maximization restricted maximum likelihood (MC EM REML) for multiple-trait li...
Article
This study evaluated random regression threshold models using linear splines (RRLS) versus Legendre polynomials (RRLP) as basis functions for the genetic analysis of clinical mastitis (CM) in first-lactation Finnish Ayrshire cows. Estimates of genetic parameters from RRLS models with 4 and 6-knots were compared to estimates from RRLP model fitting...
Article
Using a combined multi-breed reference population, this study explored the influence of model specification and the effect of including a polygenic effect on the reliability of genomic breeding values (DGV and GEBV). The combined reference population consisted of 2986 Swedish Red Breed (SRB) and Finnish Ayrshire (FAY) dairy cattle. Bayesian methodo...
Article
Full-text available
Several strategies to use genomic data in predictions have been proposed. The aim of this study was to compare different genomic prediction methods. The response variables used in the genomic predictions were deregressed proofs, which were derived from 2 estimated breeding value (EBV) data sets. The full EBV data set from March 2010 included the EB...
Article
The success of genomic selection (GS) in small breeds which are likely to have admixed structures has been minimal. This is because accuracy of GS depends on the extent of linkage disequilibrium (LD) between markers and quantitative trait loci (QTL) and LD depends on the genetic structure of the population and marker density. In the current study,...
Article
Genominen valinta tarkoittaa eläimen (ja kasvien) jalostusarvon ennustamista ja valintapäätöksen tekemistä yksilön DNA:n eli SNP- markkeritietojen perusteella. Viime vuosina genomisten jalostusarvojen laskentaan on kehitelty useita malleja. Yksinkertaisessa DNA markkeri eli SNP-BLUP menetelmään perustuvassa mallissa SNP-markkerivaikutuksia käsitell...
Article
Full-text available
Most genomic evaluations are currently based on multi step -approach that requires 1) traditional evaluation with an animal model, 2) extraction of pseudo-observations, and 3) the genomic model to predict direct genomic values (DGV) of candidate animals without own records. In the single step analysis the phenotypic records are combined directly wi...
Chapter
The frequency of eye infections in the Finnish blue fox population has increased during the past decade. Eye infection may incur economic losses to producers due to reduced selection intensity. Ethical aspects also need to be considered, since eye infection reduces animal wellbeing. The purpose of this study was to estimate genetic parameters for e...
Data
Results of relationship inference based on pairwise kinship coefficient ( Φ ) and probability of zero IBD-sharing ( π 0) as estimated by genomic or pedigree data. (DOC)
Article
Full-text available
Genome-wide SNP data provide a powerful tool to estimate pairwise relatedness among individuals and individual inbreeding coefficient. The aim of this study was to compare methods for estimating the two parameters in a Finnsheep population based on genome-wide SNPs and genealogies, separately. This study included ninety-nine Finnsheep in Finland th...
Article
Full-text available
This study investigated the possibility of increasing the reliability of direct genomic values (DGV) by combining reference populations. The data were from 3,735 bulls from Danish, Swedish, and Finnish Red dairy cattle populations. Single nucleotide polymorphism markers were fitted as random variables in a Bayesian model, using published estimated...
Article
Marker-assisted breeding value estimation is expected to increase the accuracy of estimated breeding values, especially for traits with low heritability. Several quantitative trait loci (QTL) have been found for somatic cell score and clinical mastitis. The objective of this study was to demonstrate marker-assisted breeding value estimation, combin...
Article
Full-text available
Genomic data are used in animal breeding to assist genetic evaluation. Several models to estimate genomic breeding values have been studied. In general, two approaches have been used. One approach estimates the marker effects first and then, genomic breeding values are obtained by summing marker effects. In the second approach, genomic breeding val...
Article
Full-text available
Litter size (LS) has been included in the Finnish mink breeding goal for several generations. Still, the phenotypic trend in the average number of pups per mated female has slightly decreased while animal size (AS) has increased. The aim of this study was to estimate genetic parameters for pregnancy rate (PREG) and felicity (FEL), and their genetic...