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The aim of our study was to estimate the genetic parameters of elk hunting traits in the Finnish Jamthund population. The phenotype data included 40 402 trial observations recorded in Finland between 2012 and 2020 and the pedigree data included information of 34 495 Jamthunds. The genetic parameters of the elk hunting traits were estimated using a repeatability animal model. Season, place, and type of the trial, weather during the trial, and dog sex and age were considered fixed effects in the models, and trial judge and dog litter were treated as random effects. Variance components were estimated with the AI-REML method using the DMU-software. Heritability estimates were generally low (0.01-0.04). The highest estimated heritability was 0.04 for searching. Repeatability estimates for elk hunting traits varied between 0.04 and 0.14. Genetic correlations varied from very weak to very strong (-0.21-1.00) and were particularly strong between the barking traits.

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 problem and has been successfully used on simulated and real multi-breed pig data. Advantages of the method are easily seen across breed evaluations, where pedigrees are traced to several pure breeds, which are thereafter used as MF. Application of the MF method to ruminants is complicated due to multi-breed pedigree structures and the inability to transmit existing unknown parent groups (UPG) to MF. In this study, we apply the MF approach for ssGBLUP evaluation of Finnish Red Dairy cattle treated as a single breed. Relationships among MF were accounted for by a (co)variance matrix (Γ) computed using estimated base population allele frequencies. The attained Γ was used to calculate a relationship matrix A 22 Γ for the genotyped animals. We tested the influence of SNP selection on the Γ matrix by applying a minor allele frequency (MAF) threshold (ΓMAF) where accepted markers had an MAF ≥0.05. Elements in the ΓMAF matrix were slightly lower than in the Γ matrix. Correlation between diagonal elements of the genomic and pedigree relationship matrices increased from 0.53 (A22) to 0.76 ( A 22 Γ and A 22 Γ MAF ). Average diagonal elements of A 22 Γ and A 22 Γ MAF matrices increased to the same level as in the G matrix. The ssGBLUP breeding values (GEBV) were solved using either the original 236 or redefined 8 UPG, or 8 MF computed with or without the MAF threshold. For bulls, the GEBV validation test results for the 8 UPG and 8 MF gave the same validation reliability (R2; 0.31) and over-dispersion (0.73, measured by regression coefficient b1). No significant R2 increase was observed in cows. Thus, the MF greatly influenced the pedigree relationship matrices but not the GEBV. Selection of SNP according to MAF had a notable effect on the Γ matrix and made the A22 and G matrices more similar.

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 populations. The aim of this study was to implement state-of-the-art single-step genomic evaluations for milk and fat yield in Holstein and Russian BlackWhite cattle in the Leningrad region (LR, Russia), using only a limited number of genotyped animals. We complemented internal information with external pseudo-phenotypic and genotypic data of bulls from the neighbouring Danish, Finnish and Swedish Holstein (DFS) population. Three data scenarios were used to perform single-step GBLUP predictions in the LR dairy cattle population. The first scenario was based on the original LR reference population, which constituted 1,080 genotyped cows and 427 genotyped bulls. In the second scenario, the genotypes of 414 bulls related to the LR from the DFS population were added to the reference population. In the third scenario, LR data were further augmented with pseudo-phenotypic data from the DFS population. The inclusion of foreign information increased the validation reliability of the milk yield by up to 30%. Suboptimal data recording practices hindered the improvement of fat yield. We confirmed that the single-step model is suitable for populations with a low number of genotyped animals, especially when external information is integrated into the evaluations. Genomic prediction in populations with a low number of progeny-tested bulls can be based on data from genotyped cows and on the inclusion of genotypes and pseudo-phenotypes from the external population. This approach increased the validation reliability of the implemented single-step model in the milk yield, but shortcomings in the LR data recording scheme prevented improvements in fat yield.

The Korat chicken (KR), developed in Thailand, is a slow-growing breed developed as an alternative breed for Thai chicken producers. The growing interest in slow-growing chicken meat, due to its unique taste, distinct texture, health benefits, and higher broiler welfare have led to higher market demand for KR. However, its low feed efficiency (FE) has a significant negative impact on farm profitability. Understanding the molecular mechanism regulating FE allows for designing a suitable selection program and contributing to breeding more efficient chicken for poultry production. Thus, the objective of our study was to investigate the proteome differences and possible pathways associated with FE in male KR using a label-free quantitative proteomic approach. Seventy-five KR males were individually evaluated for FE, and duodenum samples from 6 animals (3 high-FE and 3 low-FE chickens) were collected at 10 wk of age for differential abundant proteins (DAPs), protein networks, functional enrichment, and pathway analyses. In this study, we found 40 DAPs significantly associated with FE pathways, including glycolysis/gluconeogenesis, peroxisome, oxidative phosphorylation, tight junction, and cysteine and methionine metabolism. Thus, variations in observed DAPs or genes related to DAPs could be interesting biomarker candidates for selection for higher feed utilization efficiency in chicken.

A recessive sperm defect of Yorkshire boars was detected more than a decade ago. Affected boars produce ejaculates that contain spermatozoa with defective acrosomes, resulting in low fertility. The acrosome defect was mapped to porcine chromosome 15 but the causal mutation has not been identified. We re-analyzed microarray-derived genotypes of affected boars and confirmed that the acrosome defect maps to a 12.24 Mb segment of porcine chromosome 15. To detect the mutation causing defective acrosomes, we sequenced the genomes of two affected and three unaffected boars to an average coverage of 11-fold. Read depth analysis revealed a 55 kb deletion that is associated with the acrosome defect. The deletion encompasses the BOLL gene encoding the boule homolog, an RNA binding protein which is an evolutionarily conserved member of the DAZ (Deleted in AZoospermia) gene family. Lack of BOLL expression causes spermatogenic arrest and sperm maturation failure in many species. Boars that carry the deletion in the homozygous state produce sperm but their acrosomes are defective, suggesting that lack of porcine BOLL compromises acrosome formation. Our findings warrant further research to investigate the role of BOLL during spermatogenesis and sperm maturation in pigs.

SummaryA recessively inherited sperm defect of Finnish Yorkshire boars was detected more than a decade ago. Affected boars produce ejaculates that contain many spermatozoa with defective acrosomes resulting in low fertility and small litters. The acrosome defect was mapped to porcine chromosome 15 but the causal mutation has not been identified. We re-analyzed microarray-derived genotypes of affected boars and performed a haplotype-based association study. Our results confirmed that the acrosome defect maps to a 12.24 Mb segment of porcine chromosome 15 (P=3.38 × 10−14). In order to detect the mutation causing defective acrosomes, we sequenced the genomes of two affected and three unaffected boars to an average coverage of 11-fold. Read-depth analysis revealed a 55 kb deletion that segregates with the acrosome defect. The deletion encompasses the BOLL gene encoding the boule homolog, RNA binding protein which is an evolutionarily highly conserved member of the DAZ (deleted in azoospermia) gene family. Lack of BOLL expression causes spermatogenic arrest and sperm maturation failure in many species. Our study reveals that absence of BOLL is associated with a sperm defect also in pigs. The acrosomes of boars that carry the deletion in the homozygous state are defective suggesting that lack of porcine BOLL compromises acrosome formation. Our findings warrant further research to investigate the precise function of BOLL during spermatogenesis and sperm maturation in pigs.

Inbreeding gives rise to continuous lengths of homozygous genotypes called runs of homozygosity (ROH) that occur when identical haplotypes are inherited from both parents. ROHs are enriched for deleterious recessive alleles and can therefore be linked to inbreeding depression, defined as decreased phenotypic performance of the animals. However, not all ROHs within a region are expected to have harmful effects on the trait of interest. We aimed to identify ROHs that unfavourably affect female fertility and milk production traits in the Finnish Ayrshire population. The estimated effect of ROHs with the highest statistical significance varied between parities from 9 to 17 days longer intervals from calving to first insemination, from 13 to 38 days longer intervals from first to last insemination and from 0.3 to 1.0 more insemination per conception. Similarly, for milk production traits ROHs were associated with a reduction of 208 kg for milk yield, 7 kg for protein yield and 16 kg for fat yield. We also found regions where ROHs displayed unfavourable effects across multiple traits. Our findings can be exploited for more efficient control of inbreeding depression, for example by minimizing the occurrence of unfavourable haplotypes as homozygous state in breeding programmes.

A major proportion of the costs of pork production is related to feed. The feed conversion rate (FCR) or residual feed intake (RFI) is thus commonly included in breeding programmes. Feeding behaviour traits do not directly have economic value but, if correlated with production traits, can be used as auxiliary traits. The aim of this study was to estimate the heritability of feeding behaviour traits and their genetic correlations with production traits in the Finnish Yorkshire pig population. The data were available from 3,235 pigs. Feeding behaviour was measured as the number of visits per day (NVD), time spent in feeding per day (TPD), daily feed intake (DFI), time spent feeding per visit (TPV), feed intake per visit (FPV) and feed intake rate (FR). The test station phase was divided into five periods. Estimates of heritabilities of feeding behaviour traits varied from 0.17 to 0.47. Strong genetic correlations were obtained between behaviour traits in all periods. However, only DFI was strongly correlated with the production traits. Interestingly, a moderate positive genetic correlation was obtained between FR and backfat thickness (0.1?0.5) and between FR and average daily gain (0.3?0.4), depending on the period. Based on the results, there is no additional benefit from including feeding-related traits other than those commonly used (FCR and RFI) in the breeding programme. However, if correlated with animal welfare, the feeding behaviour traits could be valuable in the breeding programme.

Inbreeding increases homozygosity, which in turn increases the frequency of harmful recessive alleles, resulting in inbreeding depression. Inbreeding depression on fertility reduces the profitability of dairy farming by decreasing the lifetime milk production of cows and by increasing insemination and veterinary costs. Continuous homozygous segments, called runs of homozygosity (ROH), are currently considered to provide an effective measure of genomic inbreeding. The aim of this study was to estimate the effect of increased intrachromosomal homozygosity for female fertility in the Finnish Ayrshire population using ROH and haplotype analysis. Genotypes were obtained from 13,712 females with the Illumina BovineLD v.2 BeadChip low-density panel (Illumina Inc., San Diego, CA) and imputed to 50K density. After quality control, 40,554 single nucleotide polymorphisms remained for the analysis. Phenotypic data consisted of records for nonreturn rate, intervals from first to last insemination (IFL), and intervals from calving to first insemination. The raw phenotypic values were preadjusted for systematic effects before statistical analyses. The ROH-based inbreeding coefficients (F-ROH) were used as covariats in the mixed model equation to estimate the association between inbreeding and inbreeding depression on female fertility. First, we estimated the effect of increased chromosomal F-ROH. We detected significant inbreeding depression on IFL. Based on our results, a 10% increase in F-ROH on chromosomes 2, 18, and 22 were associated with IFL of heifers lengthening by 1.6, 0.9, and 0.7 d, respectively. Similarly, a 10% increase in F-ROH on chromosome 15 was associated with IFL of second-parity cows increasing by 2.3 d. Next, we located the regions within the chromosomes showing inbreeding depression. Our analysis revealed regions near the beginning of chromosome 2 and toward the ends of chromosomes 15, 18, and 22 that were associated with inbreeding depression on IFL. Last, we performed a haplotype analysis for the detected regions. The most promising haplotypes of each region were associated with IFL of heifers increasing by 4.4, 3.2, and 4.1 d on chromosomes 2, 18, and 22, respectively. The haplotype on chromosome 15 associated with IFL of second-parity cows increasing by 7.6 d. Overall, the breeding program requires inbreeding control, as increased genomic inbreeding in our study was associated with reduced reproductive ability in Finnish Ayrshire cattle.

Pigs are housed in groups during the test period. Social effects between penmates 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 statisticalmodels that include social genetic effects (SGEs). The data contained 3075 Finnish Yorkshire, 3351 Finnish Landrace, and 968 F1-crossbred pigs. Feeding behaviour traits were measured as the number of visits per day (NVD), time spent in feeding per day (TPD), daily feed intake (DFI), time spent in feeding per visit (TPV), feed intake per visit (FPV), and feed intake rate (FR). The test period was divided into five periods of 20 days. The number of pigs per pen varied from 8 to 12. Two model approaches were tested, i.e. a fixed group size model and a variable group size model. For the fixed group size model, eight random pigs per pen were included in the analysis, while all pigs in a pen were included for the variable group size model. The linear mixed-effectsmodel included sex, breed, and herd*year*season as fixed effects and group (batch*pen), litter, the animal itself (direct genetic effect (DGE)), and penmates (SGEs) as random effects. For feeding behaviour traits, estimates of the total heritable variation (T-2 +/- SE) and classical heritability (h(2) +/- SE, values given in brackets) from the variable group size model (e.g. period 1) were 0.34 +/- 0.13 (0.30 +/- 0.04) for NVD, 0.41 +/- 0.10 (0.37 +/- 0.04) for TPD, 0.40 +/- 0.15 (0.14 +/- 0.03) for DFI, 0.53 +/- 0.15 (0.28 +/- 0.04) for TPV, 0.66 +/- 0.17 (0.28 +/- 0.04) for FPV, and 0.29 +/- 0.13 (0.22 +/- 0.03) for FR. The effect of social interaction was minimal for ADG (T-2 = 0.29 +/- 0.11 and h(2) = 0.29 +/- 0.04), BF (T-2 = 0.48 +/- 0.12 and h(2) = 0.38 +/- 0.07), and FCR (T-2 = 0.37 +/- 0.12 and h(2) = 0.29 +/- 0.04) using the variable group size model. In conclusion, the results indicate that social interactions have a considerable indirect genetic effect on the feeding behaviour and FCR of pigs but not on ADG and BF. (C) 2020 The Authors. Published by Elsevier Inc. on behalf of The Animal Consortium.

Holstein bulls and semen have been imported to Russia from Western countries since the 1970s. The objective of our study was to examine the effect of this introgression on genetic diversity between various commercial Holstein herds in the Leningrad region. A total of 803 Holstein cows from 13 herds were genotyped using the Illumina BovineSNP50 v.2 array. The pairwise Hudson’s estimator of Fst values between 13 herds varied from 0.002 to 0.015, which is less than values usually obtained between dairy cattle breeds (> 0.1). The mean of these pairwise Fst values revealed differences between herds depending, mainly, on the proportion of common sires shared between the herds. In addition, we investigated the cause of negative Fst values. Based on our results, these negative values could be interpreted as an excess of within-herd genetic diversity over the between-herds genetic diversity. Our results show that introgressions of Holstein genes into Russian Black and White cattle of the Leningrad region have created genetic separation between herds similar with those for Jersey cows in USA, Australia and New Zealand.

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 the Leningrad region. We tested both a first-lactation model (FLM) and a multi-lactation repeatability model (MLM). The data included milk records of 206 114 cows from 49 herds. Estimated heritabilities from FLM were 0.24, 0.20, and 0.20 for milk, protein, and fat yields, respectively, and 0.18, 0.19, and 0.20 from MLM. Repeatabilities were 0.34 for milk yield and 0.31 for both fat and protein yields. Genetic trends were similar for both models (FLM vs MLM): 59 vs 56 kg year(-1) for milk, 1.90 vs 1.84 kg year(-1) for fat, and 1.67 vs 1.62 kg year(-1) for protein yield during 2000-2016. Based on the difference between the genetic trends in FLM and MLM, the applied BLUP method passed the validation method I by Interbull.

[Background]: Pigs were domesticated independently in Eastern and Western Eurasia early during the agricultural revolution, and have since been transported and traded across the globe. Here, we present a worldwide survey on 60K genome-wide single nucleotide polymorphism (SNP) data for 2093 pigs, including 1839 domestic pigs representing 122 local and commercial breeds, 215 wild boars, and 39 out-group suids, from Asia, Europe, America, Oceania and Africa. The aim of this study was to infer global patterns in pig domestication and diversity related to demography, migration, and selection., [Results]: A deep phylogeographic division reflects the dichotomy between early domestication centers. In the core Eastern and Western domestication regions, Chinese pigs show differentiation between breeds due to geographic isolation, whereas this is less pronounced in European pigs. The inferred European origin of pigs in the Americas, Africa, and Australia reflects European expansion during the sixteenth to nineteenth centuries. Human-mediated introgression, which is due, in particular, to importing Chinese pigs into the UK during the eighteenth and nineteenth centuries, played an important role in the formation of modern pig breeds. Inbreeding levels vary markedly between populations, from almost no runs of homozygosity (ROH) in a number of Asian wild boar populations, to up to 20% of the genome covered by ROH in a number of Southern European breeds. Commercial populations show moderate ROH statistics. For domesticated pigs and wild boars in Asia and Europe, we identified highly differentiated loci that include candidate genes related to muscle and body development, central nervous system, reproduction, and energy balance, which are putatively under artificial selection., [Conclusions]: Key events related to domestication, dispersal, and mixing of pigs from different regions are reflected in the 60K SNP data, including the globalization that has recently become full circle since Chinese pig breeders in the past decades started selecting Western breeds to improve local Chinese pigs. Furthermore, signatures of ongoing and past selection, acting at different times and on different genetic backgrounds, enhance our insight in the mechanism of domestication and selection. The global diversity statistics presented here highlight concerns for maintaining agrodiversity, but also provide a necessary framework for directing genetic conservation., This study is supported by National Production Technology System for the Pig Industry in China (nycytx-008) and Outstanding Talents and Innovation Team of Agricultural Science (2011-81) to LH, AGL2010-14822 and AGL2013-41834-R (Ministry of Economy and Science, Spain) to MPE. LI received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No. 656697. HJM received funding from the IMAGE project (Horizon 2020, No. 677353).

Single nucleotide polymorphism (SNP) data enable the estimation of inbreeding at the genome level. In this study, we estimated inbreeding levels for 19,075 Finnish Ayrshire cows genotyped with a low-density SNP panel (8K). The genotypes were imputed to 50K density, and after quality control, 39,144 SNPs remained for the analysis. Inbreeding coefficients were estimated for each animal based on the percentage of homozygous SNPs (F-PH), runs of homozygosity (F-ROH) and pedigree (F-PED). Phenotypic records were available for 13,712 animals including non-return rate (NRR), number of inseminations (AIS) and interval from first to last insemination (IFL) for heifers and up to three parities for cows, as well as interval from calving to first insemination (ICF) for cows. Average F-PED was 0.02, F-ROH 0.06 and F-PH 0.63. A correlation of 0.71 was found between F-PED and F-ROH, 0.66 between F-PED and F-PH and 0.94 between F-ROH and F-PH. Pedigree-based inbreeding coefficients did not show inbreeding depression in any of the traits. However, when F-ROH or F-PH was used as a covariate, significant inbreeding depression was observed; a 10% increase in F-ROH was associated with 5days longer IFL0 and IFL1, 2weeks longer IFL3 and 3days longer ICF2 compared to non-inbred cows.

Meat quality is important both to consumers and to the meat processing industry. Commonly used measures of porcine meat quality are the pH and color of the meat. The purpose of this study was to identify SNP associated with these meat quality traits in Finnish Yorkshire using the Illumina PorcineSNP60 BeadChip. The association of each SNP with the quality traits was tested with a weighted linear model. The relatedness of samples was accounted for by a random polygenic genetic effect with the accompanying full relationship matrix. The original EBV from single-trait evaluations were deregressed before analysis. The statistical significance of SNP was established using the Bonferroni correction to adjust for multiple testing. Three genomic regions were significant for the meat quality traits. The PRKAG3 region on chromosome 15 was significant for pH measured from loin and ham and for a* (redness) measured from loin. The smallest P-value in the region was obtained for pH measured from loin (ASGA0070634, P-value = 3.8 × 10(-13)). The allele substitution effect (-0.047) of the unfavorable allele A corresponds to 1 SD of the polygenic effect. The second significant region, on chromosome 2 at around 31 megabases (Mb), was associated with pH and L* (lightness) measured from loin. The most significant SNP (ASGA0009814, P-value = 3.89 × 10(-10)) had an allele substitution effect of 0.86, corresponding to 0.7 SD of the polygenic effect of L*. The third region, located on chromosome 6 at around 83 Mb, was significant for a* measured from ham. The P-value of the best SNP (ALGA0035896) was 8.71 × 10(-7) and the allele substitution effect -0.38, corresponding to 0.5 SD of the polygenic effect of a*. The significant association of PRKAG3 with pH was not due to the known AA substitutions. The candidate gene on chromosome 2 associated with color L* is RCN1, which has a high affinity Ca(2+)-binding motif, the EF hand. The significant region on chromosome 6 for color a* contains several genes, so more data are needed to identify the causative gene. Our results indicate that instead of the known AA substitutions of PRKAG3, some yet-unknown AA substitutions are causative for the pH variation in Finnish Yorkshire. Also, a new major QLT for L* was found on chromosome 2. The significant SNP identified in this study can be used in marker-assisted selection.

Harmful recessive haplotypes for reproductive and fertility traits have previously been detected in cattle, but so far, no studies have been published for pigs. The aim of this study was to locate chromosomal regions with putative lethal haplotypes and estimate the effects of the identified haplotypes on reproductive traits in the Finnish Yorkshire pig breed. We used marker genotypes of 871 Finnish Yorkshire AI boars, genotyped with Illumina's PorcineSNP60 BeadChip. The analysed traits were number of stillborn piglets in first (NSB1) and later (NSB2) parities, total number of piglets born in first and later parities and piglet mortality between birth and weaning in first and later parities. A haplotype was claimed as a putative lethal if it was common in the population, but no homozygous animals were found. We detected altogether 26 putative lethal haplotypes, but only one haplotype on chromosome 8 (position 107.0-113.3 Mb) was significantly associated with traits NSB1 and NSB2. Three possible candidate genes were found in this chromosomal region: MAD2LI, FGF2 and ANXA5. Further analysis is needed to confirm the role of these genes on pig reproductive performance.

Background: The Hovawart is a working and companion dog breed of German origin. A few hundred Hovawart dogs are registered annually in Finland. The most common disease with a proposed genetic background in Hovawarts is hypothyroidism. The disease is usually caused by lymphocytic thyroiditis, an autoimmune disorder which destroys the thyroid gland. Hypothyroidism can be treated medically with hormone replacement. Its overall incidence could also be reduced through selection, provided that the trait shows an adequate genetic basis. The aim of this study was to estimate the heritability of hypothyroidism in the Finnish Hovawart population. Results: The pedigree data for the study were provided by the Finnish Kennel Club and the hypothyroidism data by the Finnish Hovawart Club. The data included 4953 dogs born between 1990 and 2010, of which 107 had hypothyroidism and 4846 were unaffected. Prior to the estimation of heritability, we studied the effects of gender, birth year, birth month, and inbreeding on susceptibility to hypothyroidism. Heritability was estimated with the probit model both via restricted maximum likelihood (REML) and Gibbs sampling, using litter and sire of the dog as random effects. None of the studied systematic effects or level of inbreeding had a significant effect on susceptibility to hypothyroidism. The estimated heritability of hypothyroidism varied from 0.47 (SE=0.18) using REML to 0.62 (SD=0.21) using Gibbs sampling. Conclusions: Based on our analysis, the heritability of hypothyroidism is moderate to high, suggesting that its prevalence could be decreased through selection. Thus, breeders should notify the breed association of any affected dogs, and their use for breeding should be avoided.

Sianlihan laadulla on tärkeä merkitys teollisten lihatuotteiden eri prosessointivaiheissa ja kuluttajien käyttäessä tuorelihaa ruuan valmistukseen. Sianlihasta valmistetun ruuan tulee olla sekä maukasta, terveellistä että rakenteeltaan hyvää. Lihan laatuun vaikuttavat ominaisuudet mm. lihan pH ja väripisteet ovat olleet kansallisesti jalostettavia ominaisuuksista jo noin 20 vuoden ajan. Nykyinen lihan laatuominaisuuksien jalostaminen perustuu koeasemalla kasvatettujen eläinten ruhoista mitattuihin sisäpaistin ja kyljyksen pH-arvoon (noin 20h teurastuksesta), lihan vaaleuteen (L*) ja lihan punaisuuteen (a*). Lihan laatuominaisuuksiin vaikuttaa oletettavasti suuri joukko eri geenejä, tosin joitain suurivaikutteisia geenimuotoja esim. halotaanigeenissä ja RN-geenissä on myös olemassa eri osuuksilla eri roduissa. Tämän tutkimuksen tarkoituksena oli löytää kromosomialueita ja geenejä, jotka vaikuttavat lihan laatuominaisuuksiin. Tutkimuksessa määritettiin 328 Suomalaisen maatiaisrotuisen keinosiemennyskarjun ja 295 yorkshire-rotuisen keinosiemennyskarjun genotyypit noin 50 000 SNP (single nucleotide polymorhism) suhteen käyttämällä kaupallista Illumina PorcineSNP60 sirua. Tutkittavina muuttujina käytettiin kansallisesta jalostusarvostelusta saatuja jalostusarvon ennusteita eri lihanlaatuominaisuuksien suhteen. SNP assosiaatio lihanlaatuominaisuuksien suhteen testattiin painotetun lineaarisen mallin avulla, joka sisälsi SNP-vaikutuksen lisäksi eläinten sukulaisuudet huomioivan polygeenisen tekijän. Mallin painokerroin perustui jalostusarvojen ennusteiden luotettavuudelle. Tilastollisesti merkitseviksi SNP:ksi katsottiin SNP, jonka P-arvo oli alle 2,0E-06 (merkitsevyysraja määritetty Bonferroni-korjauksen avulla). Maatiaisrodulla kaksi SNP kromosomissa 7 (ASGA0037025, 130470366bp, P-arvo=8,6E-07 ja MARC0045334, 133942365bp, P-arvo=1,8E-06) olivat merkitseviä kyljyslihan a*-värin suhteen ja yksi SNP kromosomissa 15 (INRA0050276, 114169040 bp, P-arvo=7,1E-07) oli tilastollisesti merkitsevä sisäpaistin pH-arvon suhteen. Sama kromosomin 15 alue oli myös tilastollisesti merkitsevä yorkshirerodulla (15 eri SNP:ä, joista paras SNP. ALGA0087116, 113451557bp, P-arvo 4,7E-09) sekä kyljyksestä että sisäpaistista mitatun pH:n suhteen. Tilastollisesti merkitsevä alue on 2Mb pitkä ja se sisältää mm. tunnetun RN-geenin (PRKAG3-geeni). Yorkshirerodulla oli myös tilastollisesti merkitsevä SNP kromosomissa 6 (M1GA0008574, 46347641pb, P-arvo= 7,5E-07) kyljyksen a*-värin sekä kuuden SNP määrittämä alue kromosomissa 2 (paras SNP, MARC0005485, 26930095bp, P-arvo= 7,0E-08) kyljyksen L*-värin suhteen. Tulokset osoittavat, että kummassakin kotimaisessa sikarodussa on mahdollista muuttaa lihan laatuominaisuuksia haluttuun suuntaan myös SNP-markkeritiedon avulla.

Immotile, short-tail sperm defect (ISTS) expanded in the Finnish Yorkshire population in the end of 1990s. The causal mutation for this defect is a recent L1 insertion within the SPEF2 gene in chromosome 16. Even though all homozygous boars are eliminated from the population because of infertility, the amount of affected boars increased rapidly until marker-assisted selection against the defect was established. To elucidate the associated effects of the ISTS defect on production traits, we have investigated the association of the L1 insertion and PRLR haplotype with reproduction traits in the Finnish Yorkshire population. Two data sets including 357 sows and 491 AI-boars were genotyped for the presence of the L1 insertion and analysed for association with reproduction traits. A Proc Mixed procedure (SAS Inc) and a software package for analysing multivariate mixed models (DMU) were used to study the effect of polymorphisms on reproduction traits. The L1-insertion within SPEF2 gene was associated with litter size in the first parity. The SPEF2 gene is located adjacent to a candidate gene for litter size in the pig, PRLR. Haplotypes within PRLR exon 10 were analysed in data set of 93 AI-boars for the association with reproduction traits. However, no associations were detected within the analysed data set indicating that PRLR sequence variants are not the causal cause for the identified effect on litter size.

The extent of linkage disequilibrium (LD) and effective population size in Finnish Landrace and Finnish Yorkshire pig populations were studied using a whole genome SNP panel (Illumina PorcineSNP60 BeadChip) and pedigree data. Genotypic data included 86 Finnish Landrace and 32 Finnish Yorkshire boars. Pedigree data included 608,138 Finnish Landrace 554,237 and Finnish Yorkshire pigs, and on average 15 ancestral generations were known for the reference animals, born in 2005 to 2009. The breeding animals of the 2 populations have been kept separate in the breeding programs. Based on the pedigree data, the current effective population size for Finnish Landrace is 91 and for Finnish Yorkshire 61. Linkage disequilibrium measures (D' and r(2)) were estimated for over 1.5 million pairs of SNP. Average r(2) for SNP 30 kb apart was 0.47 and 0.49 and for SNP 5 Mb apart 0.09 and 0.12 for Finnish Landrace and Finnish Yorkshire, respectively. Average LD (r(2)) between adjacent SNP in the Illumina PorcineSNP60 BeadChip was 0.43 (57% of the adjacent SNP pairs had r(2) > 0.2) for Finnish Landrace and 0.46 (60% of the adjacent SNP pairs had r(2) > 0.2) for Finnish Yorkshire, and average r(2) > 0.2 extended to 1.0 and 1.5 Mb for Finnish Landrace and Finnish Yorkshire, respectively. Effective population size estimates based on the decay of r(2) with distance were similar to those based on the pedigree data: 80 and 55 for Finnish Landrace and Finnish Yorkshire, respectively. Thus, the results indicate that the effective population size of Finnish Yorkshire is smaller than of Finnish Landrace and has a clear effect on the extent of LD. The current effective population size of both breeds is above the recommended minimum of 50 but may get smaller than that in the near future, if no action is taken to balance the inbreeding rate and selection response. Because a moderate level of LD extends over a long distance, selection based on whole genome SNP markers (genomic selection) is expected to be efficient for both breeds.

Reproduction traits play an important role in economically viable piglet production and are closely related to the quality and length of the produc- tive life of the sow. A increased removal rate of young sows is undesirable not only because of the associ- ated financial penalties incurred, but also because of ethical concerns. Candidate genes and gene pathways have been identified for fertility in model species, and recent studies have provided evidence that polymor- phisms within these genes are associated with repro- duction traits in American Yorkshire/Large White and Landrace populations. In this study we evaluated the impact of single polymorphisms (n = 7) in 7 candi- date genes on reproductive efficiency in Finnish York- shire (n = 280) and Landrace (n = 271) populations: IGFBP1, IGFBP2, IGFBP3, IGFBP5, CPTIA (carni- tine O-palmitoyltransferase I), COX2 (PG-endoperox- ide synthase 2, also known as cyclooxgenase-2), and SLC22A5 (organic cation/carnitine transporter 2 (sol- ute carrier family member I), OCTN2). In the Finnish Yorkshire population, only 4 of the analyzed markers were polymorphic. Significant effects on farrowing time were detected from the Yorkshire data, with polymor- phisms within the genes CPT1A (a (allele substitution effect of allele A) = 2.97 d for age at first farrowing)), IGFBP3 (a = 0.54 d for farrowing interval of parities >1), and IGFBP5 (a = 3.22, 1.27, and 0.85 d for age at first farrowing and farrowing interval in the first and later parities, respectively). For the Landrace popula- tion, 6 markers were polymorphic, and significant ef- fects were detected for traits affecting litter size. The polymorphism within the COX2 gene had an additive effect of 0.3 piglets for litter size in parities >1, and the IGFBP1 gene had an additive effect of 0.21, 0.26, and 0.11 piglets for litter size in the first parity, pari- ties >1, and stillborn in parities >1, respectively. The additive effect of the SNP within the IGFBP2 gene was 0.16, 0.09, and 0.09 piglets for litter size in parities >1 and stillborn in the first and later parities, respec- tively. Finally, the IGFBP5 gene had an additive effect of 0.18, 0.07, and 0.07 piglets for litter size in the first parity, stillborn in parities >1, and mortality between farrowing and weaning in the first parity, respectively. These results support the suitability of the candidate gene approach for identification of markers to improve the reproductive performance of sows and to provide potential markers for marker-assisted selection.

Association between pre-eclampsia (PEE1) and the dimethylarginine dimethylaminohydrolase (DDAH) 1 and 2 genes, which play a role in the regulation of nitric oxide synthesis and release, was studied. In a case –control study design single nucleotide polymorphisms (SNPs) were determined at eight sites in the DDAH1 gene and at one site (Pro231Pro) in the DDAH2 gene from 132 women with pre-eclampsia and 112 healthy controls. Three SNPs in the DDAH1 gene were associated with preeclampsia, showing complete linkage disequilibrium with each other, but none of the associations in the allele or genotype data reached statistical significance in either of the genes after the correction for multiple testing. Haplotype frequencies were estimated using a population based on a maximum likelihood method (EM algorithm). Four common DDAH1 haplotypes were present and a significant association of haplotypes H2 and H3 with pre-eclampsia (P 5 0.03) was found. The risk of pre-eclampsia was greatest in individuals (odds ratio: 3.93; 95% confidence interval: 1.54 –9.99) who had two copies of the high-risk haplotypes (H2 or H3). The observed haplotypic association provides the first evidence of the importance of DDAH1 polymorphisms in pre-eclampsia susceptibility.

Background: Human serum paraoxonase eliminates carcinogenic lipid-soluble radicals. Because expression of the main human paraoxonase gene PON1 varies widely in humans, certain PON1 polymorphisms might be associated with increased risks of cancer. We sought new functional mutations in PON1 and determined whether known or new PON1 mutations were associated with the risk for prostate cancer in a prospective, random, population-based sample of Finnish men and in a case–control study. Methods: Serum paraoxonase activity was measured in 835 healthy men in the Kuopio Ischaemic Heart Disease Risk Factor Study. PON1 mutations were identified by hierarchical phenotype-targeted sequencing in DNAs from the 100 men with the lowest paraoxonase activity in this cohort, and 1595 men in the cohort were genotyped for PON1 mutations by restriction fragment length polymorphism. Multivariable analysis was used to investigate the association of known and new PON1 mutations with incident prostate cancer in 1569 cancer-free men in the cohort followed for 9–14 years. In a case–control study of Finnish men, the association of prostate cancer with the PON1 mutation identified in the cohort study was investigated in 69 case patients with familial prostate cancer and 69 unmatched healthy control subjects. Results: We identified a new single-nucleotide PON1 polymorphism associated with decreased serum paraoxonase activity that caused an isoleucine→valine change at codon 102 in exon 4 (I102V). Of the 1569 men cancer-free at baseline, 56 (3.6%) were carriers of the I102V mutation. After adjusting for age and cholesterol-lowering medications, the relative risk for developing prostate cancer during follow-up was 6.3 (95% confidence interval [CI] = 2.1 to 19.2) among 102V allele carriers compared with noncarriers. Other PON1 alleles were not statistically significantly associated with prostate cancer. In the case–control study, patients with familial prostate cancer were more likely to be carriers of the PON1 I102V mutation than control subjects (odds ratio = 4.3, 95% CI = 0.9 to 21.5). Conclusion: The PON1 102V allele appears to be associated with an increased risk for prostate cancer. [J Natl Cancer Inst 2003;95:812–8]

Several studies have previously provided some albeit weak evidence for linkage or association between chromosome 19q13 and multiple sclerosis (MS) susceptibility. We performed a two-stage association analysis with 19 markers spanning 7 Mb/5.5 cM of 19q13. In stage 1 analysis (135 MS families) allelic and haplotypic associations were found with markers within or close to the ApoE-ApoC subregion. These observations were taken as a hypothesis, which was tested in stage 2 in 125 families. However, none of the initial associations were replicated suggesting that they were most likely due to chance. Linkage analysis was performed in 27 Finnish multiplex families using 10 microsatellites spanning 23 Mb/24 cM of 19q13. DNA was available from 72 MS patients and 150 unaffected relatives. Parametric and non-parametric linkage analyses did not provide evidence for linkage when all families were tested. After stratifying the families according to HLA-DR15 there was weak evidence for linkage to the 19q13.1 subregion in DR15 negative families (LOD(max)=1.8). Taken together these results do not support a major role of chromosome 19q13.2-q13.3 in MS susceptibility among Finnish MS patients, whereas conclusions on the 19q13.1 subregion are less clear and this region requires further study.

QTL mapping experiments in plant breeding may involve multiple populations or pedigrees that are related through their ancestors. These known relationships have often been ignored for the sake of statistical analysis, despite their potential increase in power of mapping. We describe here a Bayesian method for QTL mapping in complex plant populations and reported the results from its application to a (previously analysed) potato data set. This Bayesian method was originally developed for human genetics data, and we have proved that it is useful for complex plant populations as well, based on a sensitivity analysis that was performed here. The method accommodates robustness to complex structures in pedigree data, full flexibility in the estimation of the number of QTL across multiple chromosomes, thereby accounting for uncertainties in the transmission of QTL and marker alleles due to incomplete marker information, and the simultaneous inclusion of non-genetic factors affecting the quantitative trait.

A Bayesian method for multipoint oligogenic analysis of quantitative and qualitative traits is presented. This method can be applied to general pedigrees, which do not necessarily have to be “peelable” and can have large numbers of markers. The number of quantitative/qualitative trait loci (QTL), their map positions in the genome, and phenotypic effects (mode of inheritances) are all estimated simultaneously within the same framework. The summaries of the estimated parameters are based on the marginal posterior distributions that are obtained through Markov chain Monte Carlo (MCMC) methods. The method uses founder alleles together with segregation indicators in order to determine the genotypes of the trait loci of all individuals in the pedigree. To improve mixing properties of the sampler, we propose (1) joint sampling of map position and segregation indicators, (2) omitting data augmentation for untyped or uninformative markers (homozygous parent), and (3) updating several markers jointly within a single block. The performance of the method was tested with two replicate GAW10 data sets (considering two levels of available marker information). The results were concordant and similar to those presented earlier with other methods. These analyses clearly illustrate the utility and wide applicability of the method. Genet. Epidemiol. 21:224–242, 2001. © 2001 Wiley-Liss, Inc.

Based on epidemiological data and genetic association studies, neonatal respiratory distress syndrome (RDS) is a complex disease with a multigenic background. The genes coding for surfactant proteins (SP) A and B have been assigned as the most likely genes in the etiology of RDS. The major factor predisposing to RDS is prematurity, and thus the phenotype of a very premature newborn infant that does not develop the disease can be regarded as hypernormal. Altogether 107 father-mother-offspring trios were divided into two sets according to the proband's phenotype, to evaluate familial segregation of candidate gene polymorphisms by the transmission disequilibrium test. A set of 76 trios were analyzed for transmission disequilibrium from parents to affected offspring. Another set of 31 trios were studied for allele transmission from parents to hypernormal offspring born very prematurely before the gestational age of 32 weeks. SP-A1-A2 haplotype 6A(2)-1A(0) showed significant excess transmission to affected infants and SP-A1 allele 6A(2) decreased transmission to the hypernormals. The present family study provides strong support for a direct or indirect role of the SP-A alleles as genetic predisposers to RDS in premature infants. The inclusion of parent-hypernormal offspring trios in transmission disequilibrium test is a useful approach to test for genetic protection against a disease.

A Bayesian method for multipoint mapping of disease genes based on Markov chain Monte Carlo algorithms was applied to the simulated GAW11 data (Study 2). The method is based on repeated Gibbs and more general Metropolis-Hastings steps. For simplicity we assumed a single disease locus model with two alleles. A normal distribution for the underlying latent variable of the qualitative phenotype was assumed. Based on a single replicate of the data no clear evidence of any of the genes underlying the simulated disease was found. However, when three replicates were combined the method was able to locate the locus C correctly on chromosome 3.

A stochastic simulation was used to investigate the value of crossbreeding information in a two line crossbreeding system in poultry under different genetic scenarios. Populations consisted of 25 sires and 250 dams, which were mated to produce both purebred and crossbred progeny. The next generation parents were selected either based on purebred information (PLS) (sib means, and own performance for females) or additional crossbred sib means were included (CCPS). The trait under selection was controlled by 20 loci with varying degree of dominance. Pure lines differed in initial allele frequencies. If the trait was controlled by loci with partial dominance, little or no extra benefit was obtained from including crossbred information over the pure line information. Under complete dominance and overdominance CCPS outperformed PLS. As a practical rule, CCPS is better than PLS if the ratio between dominance variance and total genetic variance is around 0·3 or higher. In this case the most probable cause of the dominance variation is loci with full or overdominance.

Sensitivity of segregation analysis for data structure and data transformation was studied using data from two trials in which mice were challenged at three months of age with a cloned isolate of Trypanosoma congolense and survival time was recorded. Data included records from three inbred strains (C57BL/6 (tolerant), A/J, and BALB/c (both susceptible)) and their crosses. Data were standardized and normalized using a modified power transformation. Segregation analysis was applied to both untransformed and transformed data to determine the genetic inheritance of trypanotolerance in these mice. Data from the two trials were analysed separately and combined. Four genetic models were compared; a one locus model, a polygenic model, a mixed model with common variance, and a mixed model with different variances for each major genotype. Even though the separate data sets and the combined data set all supported the hypothesis of a major gene (or a tightly linked cluster of genes) with different variances within each genotype, parameter estimates were highly sensitive to data transformation and several sets of parameter estimates gave similar likelihood values because of high dependency between parameters. Based on the results segregation analysis can be very sensitive to data structure in a crossbreeding design and to data transformation. Interpretation of the results can be misleading if the entire parameter space is not studied carefully.

mpaired migration of primordial germ cells during embryonic development causes hereditary gonadal hypoplasia in both sexes of Northern Finncattle and Swedish Mountain cattle. The affected gonads exhibit a lack of or, in rare cases, a reduced number of germ cells. Most affected animals present left-sided gonadal hypoplasia. However, right-sided and bilateral cases are also found. This type of gonadal hypoplasia prevails in animals with white coat colour. Previous studies indicated that gonadal hypoplasia is inherited in an autosomal recessive fashion with incomplete penetrance. In order to identify genetic regions underlying gonadal hypoplasia, a genome-wide association study (GWAS) and a copy number variation (CNV) analysis were performed with 94 animals, including 21 affected animals, using bovine 777,962 SNP arrays. The GWAS and CNV results revealed two significantly associated regions on bovine chromosomes (BTA) 29 and 6, respectively (P=2.19 x 10-13 and P=5.65 x 10-6). Subsequent cytogenetic and PCR analyses demonstrated that homozygosity of a ~500 kb chromosomal segment translocated from BTA6 to BTA29 (Cs29 allele) is the underlying genetic mechanism responsible for gonadal hypoplasia. The duplicated segment includes the KIT gene that is known to regulate the migration of germ cells and precursors of melanocytes. This duplication is also one of the two translocations associated with colour sidedness in various cattle breeds. ISSN:1932-6203

Summary Three simple statistical tests (Bartlett test, log-anova test, and the mixture test, a model that fits a mixture of normal distributions to data) for detecting major genes in hierarchical data structures in outbred livestock populations were investigated. The power of the tests was evaluated when the major gene had 2–3 alleles and in the presence of a skewed distribution of polygenic phenotypes or a non-genetic mixture of normal distributions. The most powerful test, but also the most sensitive to skewness, was the mixture test. The Bartlett test was more powerful than the log-anova test, but was sensitive to skewness of the data and to an underlying non-genetic mixture of distributions. All tests were able to detect a dominant major gene with a difference of 1.5 phenotypic standard deviations between homozygotes from a data set of 5000 records if the frequency of the dominant allele was less than 0.9. The most suitable robust simple test for major gene detection under a hierarchical data structure is the log-anova test. Zusammenfassung Machtigkeit und Sensitivitat einiger einfacher Tests auf das Vorliegen von Hauptgenen in tier-zuchterischen Populationen Es wurden drei einfache statistische Tests auf das Vorliegen von Hautgenen in hierarchisch strukturierten tierzuchterischen Datensatzen untersucht: der Bartlett-Test, der Log-anova-Test und der Mixture-Test, welcher die Daten an eine Mischung von Normalverteilungen anpast. Die Machtigkeit dieser Tests wurde unter einem Hauptgenmodell mit zwei oder drei Allelen untersucht, sowie unter der Annahme einer schiefen Verteilung der polygenen Phanotypen und einer nicht-genetischen Mischung von Normalverteilungen. Der machtigste Test war der Mixture-Test, welcher allerdings auch auf eine Schiefe der Daten am sensitivsten reagierte. Der Bartlett-Test war machtiger als der Log-anova-Test, reagierte jedoch sehr sensitiv auf Schiefe und eine nicht-genetische Mischung von Verteilungen. Alle Tests waren in der Lage, ein dominantes Hauptgen mit einem Unterschied von 1,5 phanotypischen Standardabweichungen zwischen den homozygoten Genotypen in einem Datensatz mit 5 000 Individuen zu entdecken, wenn die Frequenz des dominanten Allels kleiner als 0,9 war. Der geeignetste robuste Test auf das Vorliegen von Hautgenen in hierarchisch strukturierten tierzuchterischen Datensatzen ist der Log-anova-Test.

Osteochondrosis (OC) is a major factor causing joint problems that affect animal welfare and pork production profitability. Strong bones are also important in the slaughtering process, especially as broken bones can lead to rejections of parts of the carcass. In this study, 326 Finnish Yorkshire and 464 Finnish Landrace test station pigs were examined post mortem for bone strength and osteochondral lesions. The objective was to estimate genetic parameters for OC and bone strength and their genetic and phenotypic correlations with carcass meat percentage. Two formulas were used for lean meat percentage, the first one (Hennessy meat-%) comprising two fat thickness measurements and one muscle depth measurement, and the second one (test station meat-%) also including the weight of lean meat in ham. Finnish Yorkshire had stronger bones than Finnish Landrace on average, but also more OC in the proximal end of the humerus (36%) and the distal end of the femur (51%) than Finnish Landrace (29% and 31% OC in the humerus and femur, respectively). By using the data on both breeds, the OC heritability estimated was 0.05 in the humerus and 0.26 in the femur. The estimated heritability of bone strength was also moderate (0.26). Test station meat-% showed higher heritability (0.40) than meat-% based on the Hennessy formula (0.29). Genetic correlations between meat percentage and the other studied traits were weak and associated with high standard errors. The results show that a mild form of OC is common in both Finnish pig breeds; bone strength and OC in the distal end of the femur are moderately heritable and can be improved through selection; and selection for high meat percentage does not seem to affect bone strength or OC.