Signatures of positive selection after the introduction of genomic selection in the Finnish Ayrshire population.

The Finnish Ayrshire (FAY) belongs to the Nordic Red breeds and is characterized by high milk yield, high milk components, good fertility, and functional conformation. The FAY breeding program is based on genomic selection. Despite the benefits of selection on breeding values, autozygosity in the genome may increase due to selection, and increased autozygosity may cause inbreeding depression in selected traits. However, there is lack of studies concerning selection signatures in the FAY after genomic selection introduction. The aim of this study was to identify signatures of selection in FAY after the introduction of genomic selection. Genomic data included 45,834 SNPs. The genotyped animals were divided into 2 groups: animals born before genomic selection introduction (6,108 cows) and animals born after genomic selection introduction (47,361 cows). We identified the selection signatures using 3 complementary methods: 2 based on identification of selection signatures from runs of homozygosity (ROH) islands and one based on the decay of site-specific extended haplotype between populations at SNP sites (Rsb). In total, we identified 34 ROH islands on chromosomes 1, 3, 6, 8, 12-15, 17, 19, 22, and 26 in FAY animals born before genomic selection (between 1980 and 2011) and 30 ROH islands on chromosomes 1-3, 13-17, 22, and 25-26 in FAY animals born after genomic selection introduction (between 2015 and 2020). We additionally detected 22 ΔROH islands on chromosomes 2-3, 11, 13, 14, 16, 18, 20, and 25-26. Finally, a total of 31 Rsb regions on chromosomes 2, 3, 14, 18, 20, and 25 were identified. Based on the results, genomic selection has favored certain alleles and haplotypes on genomic regions related to traits relevant in the FAY breeding program: milk production, fertility, growth, beef production traits, and feed efficiency. Several genes related to these traits, e.g., PLA2G4A, MECR, CHUK, COX15, RICTOR, SHISA9, and SEMA4G overlapped or partially overlapped the observed selection signature regions. The association of genotypes within these regions and their effects on traits relevant in the FAY breeding program should be studied and genetic regions undergoing selection monitored in the FAY population.

Inheritance of feed intake-based resilience traits and their correlation with production traits in Finnish pig breeds.

High resilience against diseases, changing environmental conditions, and other stress factors and the ability to efficiently recover to normal status, is becoming increasingly important in pig production. Finding new phenotypes that relate to resilience is a crucial step for improving the resilience of pigs through selection. The objective of this study was to extract resilience-related phenotypes based on fluctuations in daily feed intake (DFI, g) and time spent in feeding per day (TPD, min) and to estimate the heritability of these traits and genetic correlations with production traits (PT). Resilience-related traits with high enough heritability and with either favorable or neutral genetic correlation with PT could be used in the selection program to improve the productivity and welfare of pigs. In this study, we used data from 7,347 Finnish Yorkshire, Landrace, and crossbred pigs raised at the test station. Six pig-specific resilience-related phenotypes were extracted from the individual DFI and TPD: root mean square error (RMSE), quantile regression (QR), and coefficient of variation (CV). RMSE was calculated from the differences between the actual DFI (or TPD) and the pig-specific predicted values. QR was based on the number of days that a pig belonged to the group with the lowest 5% of pigs based on DFI (or TPD), and CV was calculated over the daily observations of DFI (or TPD). PT included average daily gain (ADG, g), backfat thickness (BF, mm), and feed conversion rate (FCR, g/g). The heritability estimates for resilience-related traits varied between 0.07 ±â€…0.02 (QRDFI) and 0.20 ±â€…0.03 (RMSETPD). The genetic correlations between resilience-related traits and PT were mostly neutral, but for example, RMSEDFI had a favorable genetic correlation with FCR and BF but an unfavorable correlation with ADG. Lastly, we observed that pigs belonging to the lowest 10% group based on their breeding value (BV) for QRTPD had a lower proportion (10% incidence) of sick days compared to the highest 10% BV group (30% incidence). Therefore, pigs exhibiting small TPD variation (related to high resilience) tend to be less susceptible to sickness than pigs with large TPD variation (related to low resilience). Given its moderate heritability, neutral genetic correlation with PT, and positive effect on health, QRTPD can be considered the most promising resilience-related trait in the Finnish production system.

Improving resilience, i.e., the capacity to respond to the impacts of stressors and to effectively recover to normal status, is a promising approach to enhancing the well-being of pigs and the productivity of the pig industry. Animals with high resilience can maintain their performance under challenging conditions. However, obtaining heritable measurements and indicators of resilience is challenging. One indicator of resilience is fluctuation in daily feed intake (DFI) and time spent in feeding per day (TPD). In our study, the proportion of days during which a particular pig belongs to the lowest 5% of pigs based on TPD (QRTPD) turned out to be the most promising resilience-related trait. This trait is moderately inheritable and has only a weak genetic correlation with production traits (PTs). Pigs with the most favorable breeding values (BVs) for QRTPD had four times fewer sick days than pigs with less favorable BVs for QRTPD. Overall, selecting QRTPD would improve pig resilience and health without negative effects on PTs.

Effect of carnosine synthesis precursors in the diet on jejunal metabolomic profiling and biochemical compounds in slow-growing Korat chicken.

The slow-growing Korat chicken (KR) has been developed to provide an alternative breed for smallholder farmers in Thailand. Carnosine enrichment in the meat can distinguish KR from other chicken breeds. Therefore, our aim was to investigate the effect of enriched carnosine synthesis, obtained by the ß-alanine and L-histidine precursor supplementation in the diet, on changes to metabolomic profiles and biochemical compounds in slow-growing KR jejunum tissue. Four hundred 21-day-old female KR chickens were divided into 4 experimental groups: a group with a basal diet, a group with a basal diet supplemented with 1.0% ß-alanine, 0.5% L-histidine, and a mix of 1.0% ß-alanine and 0.5% L-histidine. The feeding trial lasted 70 d. Ten randomly selected chickens from each group were slaughtered. Metabolic profiles were analyzed using proton nuclear magnetic resonance spectroscopy. In total, 28 metabolites were identified. Significant changes in the concentrations of these metabolites were detected between the groups. Partial least squares discriminant analysis was used to distinguish the metabolites between the experimental groups. Based on the discovered metabolites, 34 potential metabolic pathways showed differentiation between groups, and 8 pathways (with impact values higher than 0.05, P < 0.05, and FDR < 0.05) were affected by metabolite content. In addition, biochemical changes were monitored using synchrotron radiation-based Fourier transform infrared microspectroscopy. Supplementation of ß-alanine alone in the diet increased the ß-sheets and decreased the α-helix content in the amide I region, and supplementation of L-histidine alone in the diet also increased the ß-sheets. Furthermore, the relationship between metabolite contents and biochemical compounds were confirmed using principal component analysis (PCA). Results from the PCA indicated that ß-alanine and L-histidine precursor group was highly positively correlated with amide I, amide II, creatine, tyrosine, valine, isoleucine, and aspartate. These findings can help to understand the relationships and patterns between the spectral and metabolic processes related to carnosine synthesis.

Thigh muscle metabolic response is linked to feed efficiency and meat characteristics in slow-growing chicken.

The Korat chicken (KR) is a slow-growing Thai chicken breed with relatively poor feed efficiency (FE) but very tasty meat with high protein and low fat contents, and a unique texture. To enhance the competitiveness of KR, its FE should be improved. However, selecting for FE has an unknown effect on meat characteristics. Thus, understanding the genetic basis underlying FE traits and meat characteristics is needed. In this study, 75 male KR birds were raised up to 10 wk of age. For each bird, the feed conversion ratio (FCR), residual feed intake (RFI), and physicochemical properties, flavor precursors, and biological compounds in the thigh meat were evaluated. At 10 wk of age, thigh muscle samples from 6 birds (3 with high FCR and 3 with low FCR values) were selected, and their proteomes were investigated using a label-free proteomic method. Weighted gene coexpression network analysis (WGCNA) was used to screen the key protein modules and pathways. The WGCNA results revealed that FE and meat characteristics significantly correlated with the same protein module. However, the correlation was unfavorable; improving FE may result in a decrease in meat quality through the alteration in biological processes including glycolysis/gluconeogenesis, metabolic pathway, carbon metabolism, biosynthesis of amino acids, pyruvate metabolism, and protein processing in the endoplasmic reticulum. The hub proteins of the significant module (TNNT1, TNNT3, TNNI2, TNNC2, MYLPF, MYH10, GADPH, PGK1, LDHA, and GPI) were also identified to be associated with energy metabolism, and muscle growth and development. Given that the same proteins and pathways are present in FE and meat characteristics but in opposite directions, selection practices for KR should simultaneously consider both trait groups to maintain the high meat quality of KR while improving FE.

Estimating inbreeding rate and effective population size in the Finnish Ayrshire population in the era of genomic selection.

Genomic selection has been applied in dairy cattle breeding over the last decade. Using genomic information may speed up genetic gain as breeding values can be predicted reasonably accurately directly after birth. However, genetic diversity may decrease if the inbreeding rate per generation increases and the effective population size decreases. Despite many positive qualities of the Finnish Ayrshire, for example, high average protein yield and fertility, over time the breed has lost its place as the most common dairy breed in Finland. Thus, maintaining the genetic variability of the breed is becoming more important. The aim of our research was to estimate the impact of genomic selection on inbreeding rate and effective population size using both pedigree and genomic data. The genomic data included 46,914 imputed single nucleotide polymorphism (SNP) variants from 75,038 individuals, and the pedigree data included 2,770,025 individuals. All animals in the data were born between 2000 and 2020. Genomic inbreeding coefficients were estimated as the proportion of SNPs in runs of homozygosity (ROH) out of the total number of SNPs. The inbreeding rate was estimated by regressing the mean genomic inbreeding coefficients on birth years. Effective population size was then estimated based on the inbreeding rate. Additionally, effective population size was estimated from the mean increase in individual inbreeding using pedigree data. Introduction of genomic selection was assumed to have taken place gradually; years 2012-2014 were treated as a transition period from the traditional phenotype-based breeding value estimation to genomic-based estimation. The median length of the identified homozygous segments was 5.5 Mbp, and a slight increase in the proportion of segments over 10 Mbp was observed after 2010. The inbreeding rate decreased from 2000 to 2011 and subsequently increased slightly. The pedigree- and genomic-based estimates of inbreeding rate were similar to each other. The estimates of effective population size based on the regression method were very sensitive to the number of years considered; thus, the estimates were not very reliable. The effective population size estimated from the mean increase in individual inbreeding reached its highest value of 160 in 2011 and decreased to 150 after that. In addition, the generation interval in the sire path has decreased from 5.5 years to 3.5 years after genomic selection was implemented. Based on our results, after the implementation of genomic selection, the proportion of long ROH stretches has increased, the generation interval in the sire path has decreased, the inbreeding rate has increased and the effective population size has decreased. However, the effective population size is still at a good level, allowing for an efficient selection scheme in the Finnish Ayrshire breed.

Comparative proteomics revealed duodenal metabolic function associated with feed efficiency in slow-growing chicken.

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.

Single-step genomic evaluation of Russian dairy cattle using internal and external information.

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 Black & White 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.

Correction to: Genome-wide SNP data unveils the globalization of domesticated pigs.

An amendment to this paper has been published and can be accessed via the original article.

Estimation of heritability of feeding behaviour traits and their correlation with production traits in Finnish Yorkshire pigs.

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.

Genome-wide SNP data unveils the globalization of domesticated pigs.

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.

Whole-genome association analysis of pork meat pH revealed three significant regions and several potential genes in Finnish Yorkshire pigs.

BACKGROUND: One of the most commonly used quality measurements of pork is pH measured 24 h after slaughter. The most probable mode of inheritance for this trait is oligogenic with several known major genes, such as PRKAG3. In this study, we used whole-genome SNP genotypes of over 700 AI boars; after a quality check, 42,385 SNPs remained for association analysis. All the boars were purebred Finnish Yorkshire. To account for relatedness of the animals, a pedigree-based relationship matrix was used in a mixed linear model to test the effect of SNPs on pH measured from loin. A bioinformatics analysis was performed to identify the most promising genes in the significant regions related to meat quality. RESULTS: Genome-wide association study (GWAS) revealed three significant chromosomal regions: one on chromosome 3 (39.9 Mb-40.1 Mb) and two on chromosome 15 (58.5 Mb-60.5 Mb and 132 Mb-135 Mb including PRKAG3). A conditional analysis with a significant SNP in the PRKAG3 region, MARC0083357, as a covariate in the model retained the significant SNPs on chromosome 3. Even though linkage disequilibrium was relatively high over a long distance between MARC0083357 and other significant SNPs on chromosome 15, some SNPs retained their significance in the conditional analysis, even in the vicinity of PRKAG3. The significant regions harbored several genes, including two genes involved in cyclic AMP (cAMP) signaling: ADCY9 and CREBBP. Based on functional and transcription factor-gene networks, the most promising candidate genes for meat pH are ADCY9, CREBBP, TRAP1, NRG1, PRKAG3, VIL1, TNS1, and IGFBP5, and the key transcription factors related to these genes are HNF4A, PPARG, and Nkx2-5. CONCLUSIONS: Based on SNP association, pathway, and transcription factor analysis, we were able to identify several genes with potential to control muscle cell homeostasis and meat quality. The associated SNPs can be used in selection for better pork. We also showed that post-GWAS analysis reveals important information about the genes' potential role on meat quality. The gained information can be used in later functional studies.

Heritability of hypothyroidism in the Finnish Hovawart population.

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.

A combination of two variants in PRKAG3 is needed for a positive effect on meat quality in pigs.

BACKGROUND: Color and pH of meat measured 24 h post mortem are common selection objectives in pig breeding programs. Several amino acid substitutions in PRKAG3 have been associated with various meat quality traits. In our previous study ASGA0070625, a SNP next to PRKAG3, had the most significant association with meat quality traits in the Finnish Yorkshire. However, the known amino acid substitutions, including I199V, did not show any association. The aims of this study were to characterize further variation in PRKAG3 and its promoter region, and to test the association between these variants and the pH and color of pork meat. RESULTS: The data comprised of 220 Finnish Landrace and 230 Finnish Yorkshire artificial insemination boars with progeny information. We sequenced the coding and promoter region of PRKAG3 in these and in three additional wild boars. Genotypes from our previous genome-wide scans were also included in the data. Association between SNPs or haplotypes and meat quality traits (deregressed estimates of breeding values from Finnish national breeding value estimation for pH, color lightness and redness measured from loin or ham) was tested using a linear regression model. Sequencing revealed several novel amino acid substitutions in PRKAG3, including K24E, I41V, K131R, and P134L. Linkage disequilibrium was strong among the novel variants, SNPs in the promoter region and ASGA0070625, especially for the Yorkshire. The strongest associations were observed between ASGA0070625 and the SNPs in the promoter region and pH measured from loin in the Yorkshire and between I199V and pH measured from ham in the Landrace. In contrast, ASGA0070625 was not significantly associated with meat quality traits in the Landrace and I199V not in the Yorkshire. Haplotype analysis showed a significant association between a haplotype consisting of 199I and 24E alleles (or g.-157C or g.-58A alleles in the promoter region) and pH measured from loin and ham in both breeds (P-values varied from 1.72 × 10⁻4 to 1.80 × 10⁻8). CONCLUSIONS: We conclude that haplotype g.-157C - g.-58A - 24E - 199I in PRKAG3 has a positive effect on meat quality in pigs. Our results are readily applicable for marker-assisted selection in pigs.

Ectopic KIT copy number variation underlies impaired migration of primordial germ cells associated with gonadal hypoplasia in cattle (Bos taurus).

Impaired 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.

An exonic insertion within Tex14 gene causes spermatogenic arrest in pigs.

BACKGROUND: Male infertility is an increasing problem in all domestic species including man. Localization and identification of genes involved in defects causing male infertility provide valuable information of specific events in sperm development. Sperm development is a complex process, where diploid spermatogonia develop into haploid, highly specialized spermatozoa. Correct expression and function of various genes and their protein products are required for production of fertile sperm. We have identified an infertility defect in Finnish Yorkshire boars caused by spermatogenic arrest. The aim of this study was to locate the disease associated region using genome wide screen with the PorcineSNP60 Beadchip and identify the causal mutation by candidate gene approach. RESULTS: In the Finnish Yorkshire pig population the spermatogenic arrest (SA) defect appears to be of genetic origin and causes severe degeneration of germ cells and total absence of spermatozoa. Genome wide scan with the PorcineSNP60 Beadchip localized the SA defect to porcine chromosome 12 in a 2 Mbp region. Sequencing of a candidate gene Tex14 revealed a 51 bp insertion within exon 27, which caused differential splicing of the exon and created a premature translation stop codon. The expression of Tex14 was markedly down regulated in the testis of a SA affected boar compared to control boars and no protein product was identified by Western blotting. The SA insertion sequence was also found within intron 27 in all analyzed animals, thus the insertion appears to be a possible duplication event. CONCLUSION: In this study we report the identification of a causal mutation for infertility caused by spermatogenic arrest at an early meiotic phase. Our results highlight the role of TEX14 specifically in spermatogenesis and the importance of specific genomic remodeling events as causes for inherited defects.

Whole-genome SNP association analysis of reproduction traits in the Finnish Landrace pig breed.

BACKGROUND: Good genetic progress for pig reproduction traits has been achieved using a quantitative genetics-based multi-trait BLUP evaluation system. At present, whole-genome single nucleotide polymorphisms (SNP) panels provide a new tool for pig selection. The purpose of this study was to identify SNP associated with reproduction traits in the Finnish Landrace pig breed using the Illumina PorcineSNP60 BeadChip. METHODS: Association of each SNP with different traits was tested with a weighted linear model, using SNP genotype as a covariate and animal as a random variable. Deregressed estimated breeding values of the progeny tested boars were used as the dependent variable and weights were based on their reliabilities. Statistical significance of the associations was based on Bonferroni-corrected P-values. RESULTS: Deregressed estimated breeding values were available for 328 genotyped boars. Of the 62,163 SNP in the chip, 57,868 SNP had a call rate > 0.9 and 7,632 SNP were monomorphic. Statistically significant results (P-value < 2.0E-06) were obtained for total number of piglets born in first and later parities and piglet mortality between birth and weaning in later parity, and suggestive associations (P-value < 4.0E-06) for piglet mortality between birth and weaning in first parity, number of stillborn piglets in later parity, first farrowing interval and second farrowing interval. Two of the statistically significant regions for total number of piglets born in first and later parities are located on chromosome 9 around 95 and 79 Mb. The estimated SNP effect in these regions was approximately one piglet between the two homozygote classes. By combining the two most significant SNP in these regions, favourable double homozygote animals are expected to have 1.3 piglets (P-value = 1.69E-08) more than unfavourable double homozygote animals. A region on chromosome 9 (66 Mb) was statistically significant for piglet mortality between birth and weaning in later parity (0.44 piglets between homozygotes, P-value = 6.94E-08). CONCLUSIONS: Three separate regions on chromosome 9 gave significant results for litter size and pig mortality. The frequencies of favourable alleles of the significant SNP are moderate in the Finnish Landrace population and these SNP are thus valuable candidates for possible marker-assisted selection.

Mapping of QTL affecting incidence of blood and meat inclusions in egg layers.

BACKGROUND: Occurrence of blood and meat inclusions is an internal egg quality defect. Mass candling reveals most of the spots, but because brown eggshell hampers selection in brown chicken lines it has not been possible to eliminate the defect by selection. Estimated frequency of blood and meat inclusions in brown layers is about 18% whereas it is 0.5% in white egg layers. Several factors are known to increase the incidence of this fault: genetic background, low level of vitamin A and/or D, stress or infections, for instance. To study the genetic background of the defect, a mapping population of 1599 F2 hens from a cross of White Rock and Rhode Island Red lines was set up. RESULTS: Our histopathological analyses show that blood spots consist of mainly erythrocytes and that meat spots are accumulations of necrotic material. Linkage analysis of 27 chromosomes with 162 microsatellite markers revealed one significant quantitative trait locus (QTL) affecting blood spot and meat spot frequency. We sequenced a fragment of a candidate gene within the region, ZO-2, coding for a tight junction protein. Nine polymorphisms were detected and two of them were included in fine-mapping and association analysis. Fine-mapping defined the QTL result. To further verify the QTL, association analyses were carried out in two independent commercial breeding lines with the marker MCW241 and surrounding SNPs. Association was found mainly in a 0.8 Mb-wide chromosomal area on GGAZ. CONCLUSIONS: There was good agreement between the location of the QTL region on chromosome Z and the association results in the commercial breeds analyzed. Variations found in tight junction protein ZO-2 and microRNA gga-mir-1556 may predispose egg layers to blood and meat spot defects. This paper describes the first results of detailed QTL analyses of the blood and meat spots trait(s) in chickens.

Knobbed acrosome defect is associated with a region containing the genes STK17b and HECW2 on porcine chromosome 15.

BACKGROUND: Male infertility is an increasing problem in all domestic species including man. Localization and identification of genes involved in defects causing male infertility provide valuable information of specific events in sperm development. Correct condensation of the sperm head and development of the acrosome are required for fertile sperm. In the Finnish Yorkshire pig population a knobbed acrosome defect (KAD) has been reported which appears to be of genetic origin. In previous studies we have shown that a large number of affected spermatozoa have a cystic swelling anterior to the apical part of the acrosome. RESULTS: Characterization of the knobbed acrosome affected sperm revealed that both the acrosomal granules and chromatin are affected. This type of KAD appears to be a previously unknown and serious form of the defect. A genome wide scan with PorcineSNP60 Genotyping BeadChip defined the KAD associated region within 0.7 Mbp on porcine chromosome 15. Two genes, STK17b and HECW2, located within this region were sequenced. The expression of these genes appeared comparable in KA-affected and control boars. The known function of HECW2 in acrosome development highlighted this gene as a good candidate responsible for the KAD. One nonsynonymous SNP was identified within the HECW2 gene. However, as this mutation was found in homozygous state in individuals with normal sperm, this is not likely to be the causal mutation. CONCLUSIONS: In this study we identified two candidate genes for a severe defect affecting both the sperm acrosome and chromatin that causes infertility. One of these genes, HECW2, plays an important role in ubiquitination, a prerequisite for chromatin remodelling and acrosome formation, highlighting the involvement of this gene in the knobbed acrosome defect and male infertility.

Spermine analogue-regulated expression of spermidine/spermine N1-acetyltransferase and its effects on depletion of intracellular polyamine pools in mouse fetal fibroblasts.

SSAT (Spermidine/spermine N1-acetyltransferase, also known as SAT1), the key enzyme in the catabolism of polyamines, is turned over rapidly and there is only a low amount present in the cell. In the present study, the regulation of SSAT by spermine analogues, the inducers of the enzyme, was studied in wild-type mouse fetal fibroblasts, expressing endogenous SSAT, and in the SSAT-deficient mouse fetal fibroblasts transiently expressing an SSAT-EGFP (enhanced green fluorescent protein) fusion gene. In both cell lines treatments with DENSpm (N(1),N(11)-diethylnorspermine), CPENSpm (N(1)-ethyl-N(11)-[(cyclopropyl)-methy]-4,8-diazaundecane) and CHENSpm (N(1)-ethyl-N(11)-[(cycloheptyl)methy]-4,8-diazaundecane) led to high, moderate or low induction of SSAT activity respectively. The level of activity detected correlated with the presence of SSAT and SSAT-EGFP proteins, the latter localizing both in the cytoplasm and nucleus. RT-PCR (reverse transcription-PCR) results suggested that the analogue-affected regulation of SSAT-EGFP expression occurred, mainly, after transcription. In wild-type cells, DENSpm increased the amount of SSAT mRNA, and both DENSpm and CHENSpm affected splicing of the SSAT pre-mRNA. Depleted intracellular spermidine and spermine levels inversely correlated with detected SSAT activity. Interestingly, the analogues also reduced polyamine levels in the SSAT-deficient cells expressing the EGFP control. The results from the present study show that the distinct SSAT regulation by different analogues involves regulatory actions at multiple levels, and that the spermine analogues, in addition to inducing SSAT, lower intracellular polyamine pools by SSAT-independent mechanisms.

Type 2 diabetes whole-genome association study in four populations: the DiaGen consortium.

Type 2 diabetes (T2D) is a common, polygenic chronic disease with high heritability. The purpose of this whole-genome association study was to discover novel T2D-associated genes. We genotyped 500 familial cases and 497 controls with >300,000 HapMap-derived tagging single-nucleotide-polymorphism (SNP) markers. When a stringent statistical correction for multiple testing was used, the only significant SNP was at TCF7L2, which has already been discovered and confirmed as a T2D-susceptibility gene. For a replication study, we selected 10 SNPs in six chromosomal regions with the strongest association (singly or as part of a haplotype) for retesting in an independent case-control set including 2,573 T2D cases and 2,776 controls. The most significant replicated result was found at the AHI1-LOC441171 gene region.