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Rainbow trout is one of the most popular aquaculture species worldwide, with a long history of domestication. However, limited information exists about the genetic diversity of farmed rainbow trout populations globally, with most available reports relying on low‐throughput genotyping technologies. Notably, no information exists about the genetic diversity status of farmed rainbow trout in Sweden. Double‐digest restriction‐site‐associated DNA sequencing was performed on more than 500 broodfish from two leading producers in Sweden and from the country's national breeding program. Following the detection of single nucleotide polymorphisms (SNPs), genetic diversity was studied by using either individual SNPs (n = 8680; one SNP retained per 300 bp sequence reads) or through SNP haplotypes (n = 20 558; all SNPs retained in 300 bp sequence reads). Similar amounts of genetic diversity were found amongst the three populations when individual SNPs were used. Furthermore, principal component analysis and discriminant analysis of principal components suggested two genetic clusters with the two industry populations grouped together. Genetic differentiation based on the FST fixation index was ~0.01 between the industry populations and ~0.05 when those were compared with the breeding program. Preliminary estimates of effective population size (Ne) and inbreeding (based on runs of homozygosity; FROH) were similar amongst the three populations (Ne ≈ 50–80; median FROH ≈ 0.11). Finally, the haplotype‐based analysis suggested that animals from the breeding program had higher shared coancestry levels than those from the other two populations. Overall, our study provides novel insights into the genetic diversity and structure of Sweden's three main farmed rainbow trout populations, which could guide their future management. [ABSTRACT FROM AUTHOR]

Routine implementation of genomic information for guiding selection decisions is not yet common in the majority of aquaculture species. Reduced representation sequencing approaches offer a cost‐effective solution for obtaining genome‐wide information in species with a limited availability of genomic resources. In the current study, we implemented double‐digest restriction site‐associated DNA sequencing (ddRAD‐seq) on an Arctic charr strain with the longest known history of selection (approximately 40 years) aiming to improve selection decisions. In total, 1730 animals reared at four different farms in Sweden and spanning from year classes 2013–2017 were genotyped using ddRAD‐seq. Approximately 5000 single nucleotide polymorphisms (SNPs) were identified, genetic diversity‐related metrics were estimated, and genome‐wide association studies (GWAS) for body length at different time points and age of sexual maturation were conducted. Low genetic differentiation amongst animals from the different farms was observed based on both the results from pairwise Fst values and principal component analysis (PCA). The existence of associations was investigated between the mean genome‐wide heterozygosity of each full‐sib family (year class 2017) and the corresponding inbreeding coefficient or survival to the eyed stage. A moderate correlation (−0.33) was estimated between the mean observed heterozygosity of each full‐sib family and the corresponding inbreeding coefficient, while no linear association was obtained with the survival to the eyed stage. GWAS did not detect loci with major effect for any of the studied traits. However, genomic regions explaining more than 1% of the additive genetic variance for either studied traits were suggested across 14 different chromosomes. Overall, key insights valuable for future selection decisions of Arctic charr have been obtained, suggesting ddRAD as an attractive genotyping platform for obtaining genome‐wide information in a cost‐effective manner. [ABSTRACT FROM AUTHOR]

Tilapia hatcheries in Tanzania rely heavily on importing germplasm. Nevertheless, the genetic structure of the imported stocks is poorly understood. In the current study, the level of genetic diversity and differentiation of eight populations of Nile tilapia (Oreochromis niloticus) strains imported in Tanzania was investigated. Four of the studied strains originated from Thailand, three from Uganda, and one from the Netherlands. Double-digest restriction site–associated DNA sequencing (ddRAD-seq) was applied to identify and genotype single nucleotide polymorphisms (SNPs). In total, 2214 SNPs passed all the quality control steps and were utilized for downstream analysis. Mean heterozygosity estimates were higher for the Thailand strains (Ho, 0.23) compared with the strains from Uganda (Ho, 0.12). Low genetic distance was observed amongst populations from the same geographic origin (Fst, 0.01–0.04). However, genetic distance between populations from different geographic origins was substantial (Fst, 0.24–0.44). Bayesian model–based clustering (STRUCTURE) and discriminant analysis of principal components (DAPC) grouped the studied animals into three distinct clusters. A cross-validation approach (where 25% of animals from each population were considered of unknown origin) was conducted in order to test the efficiency of the SNP dataset for identifying the population of origin. The cross-validation procedure was repeated 10 times resulting in approximately 97% of the tested animals being allocated to the correct geographic population of origin. The breeding history and hatchery practices used to manage these stocks prior and after import appear to be the main factors for the genetic diversity observed in this study. Our study will help inform hatchery stock management and future breeding program designs in Tanzania. [ABSTRACT FROM AUTHOR]

Understanding population structure and genetic diversity within and between local Nile tilapia lines cultured in Tanzania is important for sustainable aquaculture production. This study investigated the genetic structure and diversity among seven Nile tilapia populations in Tanzania (Karanga, Igunga, Ruhila, Fisheries Education and Training Agency, Tanzania Fisheries Research Institute, Kunduchi, and Lake Victoria). Double-digest restriction site-associated DNA (ddRAD) libraries were prepared from 140 individual fish (20 per population) and sequenced using an Illumina HiSeq 4000 resulting in the identification of 2,180 informative single nucleotide polymorphisms (SNPs). Pairwise Fst values revealed strong genetic differentiation between the closely related populations; FETA, Lake Victoria, and Igunga and those from TAFIRI and Karanga with values ranging between 0.45 and 0.55. Population structure was further evaluated using Bayesian model-based clustering (STRUCTURE) and discriminant analysis of principal components (DAPC). Admixture was detected among Karanga, Kunduchi, and Ruhila populations. A cross-validation approach (25% of individual fish from each population was considered of unknown origin) was conducted in order to test the efficiency of the SNP markers to correctly assign individual fish to the population of origin. The cross-validation procedure was repeated 10 times resulting in 77% of the tested individual fish being allocated to the correct population. Overall our results provide a new database of informative SNP markers for both conservation management and aquaculture activities of Nile tilapia strains in Tanzania. [ABSTRACT FROM AUTHOR]

Because mastitis is very frequent and unavoidable, adding recovery information into the analysis for genetic evaluation of mastitis is of great interest from economical and animal welfare point of view. Here we have performed genome-wide association studies (GWAS) to identify associated single nucleotide polymorphisms (SNPs) and investigate the genetic background not only for susceptibility to - but also for recoverability from mastitis. Somatic cell count records from 993 Danish Holstein cows genotyped for a total of 39378 autosomal SNP markers were used for the association analysis. Single SNP regression analysis was performed using the statistical software package DMU. Substitution effect of each SNP was tested with a t-test and a genome-wide significance level of P-value < 10-4 was used to declare significant SNP-trait association. A number of significant SNP variants were identified for both traits. Many of the SNP variants associated either with susceptibility to - or recoverability from mastitis were located in or very near to genes that have been reported for their role in the immune system. Genes involved in lymphocyte developments (e.g., MAST3 and STAB2) and genes involved in macrophage recruitment and regulation of inflammations (PDGFD and PTX3) were suggested as possible causal genes for susceptibility to - and recoverability from mastitis, respectively. However, this is the first GWAS study for recoverability from mastitis and our results need to be validated. The findings in the current study are, therefore, a starting point for further investigations in identifying causal genetic variants or chromosomal regions for both susceptibility to - and recoverability from mastitis. [ABSTRACT FROM AUTHOR]

Background: The development of a reliable method to predict heterosis would greatly improve the efficiency of commercial crossbreeding schemes. Extending heterosis prediction from the line level to the individual sire level would take advantage of variation between sires from the same pure line, and further increase the use of heterosis in crossbreeding schemes. We aimed at deriving the theoretical expectation for heterosis due to dominance in the crossbred offspring of individual sires, and investigating how much extra variance in heterosis can be explained by predicting heterosis at the individual sire level rather than at the line level. We used 53 421 SNP (single nucleotide polymorphism) genotypes of 3427 White Leghorn sires, allele frequencies of six White Leghorn dam-lines and cage-based records on egg number and egg weight of ~210 000 crossbred hens. Results: We derived the expected heterosis for the offspring of individual sires as the between- and within-line genome-wide heterozygosity excess in the offspring of a sire relative to the mean heterozygosity of the pure lines. Next, we predicted heterosis by regressing offspring performance on the heterozygosity excess. Predicted heterosis ranged from 7.6 to 16.7 for egg number, and from 1.1 to 2.3 grams for egg weight. Between-line differences accounted for 99.0% of the total variance in predicted heterosis, while within-line differences among sires accounted for 0.7%. Conclusions: We show that it is possible to predict heterosis at the sire level, thus to distinguish between sires within the same pure line with offspring that show different levels of heterosis. However, based on our data, variation in genome-wide predicted heterosis between sires from the same pure line was small; most differences were observed between lines. We hypothesise that this method may work better if predictions are based on SNPs with identified dominance effects. [ABSTRACT FROM AUTHOR]

Background Boar taint is an offensive urine or faecal-like odour, affecting the smell and taste of cooked pork from some mature non-castrated male pigs. Androstenone and skatole in fat are the molecules responsible. In most pig production systems, males, which are not required for breeding, are castrated shortly after birth to reduce the risk of boar taint. There is evidence for genetic variation in the predisposition to boar taint. A genome-wide association study (GWAS) was performed to identify loci with effects on boar taint. Five hundred Danish Landrace boars with high levels of skatole in fat (>0.3 μg/g), were each matched with a litter mate with low levels of skatole and measured for androstenone. DNA from these 1,000 non-castrated boars was genotyped using the Illumina PorcineSNP60 Beadchip. After quality control, tests for SNPs associated with boar taint were performed on 938 phenotyped individuals and 44,648 SNPs. Empirical significance thresholds were set by permutation (100,000). For androstenone, a 'regional heritability approach' combining information from multiple SNPs was used to estimate the genetic variation attributable to individual autosomes. Results A highly significant association was found between variation in skatole levels and SNPs within the CYP2E1 gene on chromosome 14 (SSC14), which encodes an enzyme involved in degradation of skatole. Nominal significance was found for effects on skatole associated with 4 other SNPs including a region of SSC6 reported previously. Genome-wide significance was found for an association between SNPs on SSC5 and androstenone levels and nominal significance for associations with SNPs on SSC13 and SSC17. The regional analyses confirmed large effects on SSC5 for androstenone and suggest that SSC5 explains 23% of the genetic variation in androstenone. The autosomal heritability analyses also suggest that there is a large effect associated with androstenone on SSC2, not detected using GWAS. Conclusions Significant SNP associations were found for skatole on SSC14 and for androstenone on SSC5 in Landrace pigs. The study agrees with evidence that the CYP2E1 gene has effects on skatole breakdown in the liver. Autosomal heritability estimates can uncover clusters of smaller genetic effects that individually do not exceed the threshold for GWAS significance. [ABSTRACT FROM AUTHOR]

Field cress (Lepidium campestre L.), despite its potential as a sustainable alternative oilseed plant, has been underutilized, and no prior attempts to characterize the genome at the genetic or molecular cytogenetic level have been conducted. Genetic maps are the foundation for anchoring and orienting annotated genome assemblies and positional cloning of candidate genes. Our principal goal was to construct a genetic map using integrated approaches of genetic, comparative and cytogenetic map analyses. In total, 503 F2 interspecific hybrid individuals were genotyped using 7,624 single nucleotide polymorphism markers. Comparative analysis demonstrated that ~57% of the sequenced loci in L. campestre were congruent with Arabidopsis thaliana (L.) genome and suggested a novel karyotype, which predates the ancestral crucifer karyotype. Aceto-orcein chromosome staining and fluorescence in situ hybridization (FISH) analyses confirmed that L. campestre, L. heterophyllum Benth. and their hybrids had a chromosome number of 2n = 2x = 16. Flow cytometric analysis revealed that both species possess 2C roughly 0.4 picogram DNA. Integrating linkage and comparative maps with cytogenetic map analyses assigned two linkage groups to their particular chromosomes. Future work could incorporate FISH utilizing A. thaliana mapped BAC clones to allow the chromosomes of field cress to be identified reliably. [ABSTRACT FROM AUTHOR]

Arctic charr (Salvelinus alpinus) is a species of high economic value for the aquaculture industry, and of high ecological value due to its Holarctic distribution in both marine and freshwater environments. Novel genome sequencing approaches enable the study of population and quantitative genetic parameters even on species with limited or no prior genomic resources. Low coverage genotyping by sequencing (GBS) was applied in a selected strain of Arctic charr in Sweden originating from a landlocked freshwater population. For the needs of the current study, animals from year classes 2013 (171 animals, parental population) and 2017 (759 animals; 13 full sib families) were used as a template for identifying genome wide single nucleotide polymorphisms (SNPs). GBS libraries were constructed using the PstI and MspI restriction enzymes. Approximately 14.5K SNPs passed quality control and were used for estimating a genomic relationship matrix. Thereafter a wide range of analyses were conducted in order to gain insights regarding genetic diversity and investigate the efficiency of the genomic information for parentage assignment and breeding value estimation. Heterozygosity estimates for both year classes suggested a slight excess of heterozygotes. Furthermore, FST estimates among the families of year class 2017 ranged between 0.009 - 0.066. Principal components analysis (PCA) and discriminant analysis of principal components (DAPC) were applied aiming to identify the existence of genetic clusters among the studied population. Results obtained were in accordance with pedigree records allowing the identification of individual families. Additionally, DNA parentage verification was performed, with results in accordance with the pedigree records with the exception of a putative dam where full sib genotypes suggested a potential recording error. Breeding value estimation for juvenile growth through the usage of the estimated genomic relationship matrix clearly outperformed the pedigree equivalent in terms of prediction accuracy (0.51 opposed to 0.31). Overall, low coverage GBS has proven to be a cost-effective genotyping platform that is expected to boost the selection efficiency of the Arctic charr breeding program. [ABSTRACT FROM AUTHOR]

Imputation is a cost-effective approach to augment marker data for genomic selection and genome-wide association studies. However, most imputation studies have focused on autosomes. Here, we assessed the imputation of markers on the X chromosome in Holstein cattle for nongenotyped animals and animals genotyped with low-density (Illumina BovineLD, Illumina Inc., San Diego, CA) chips, using animals genotyped with medium-density (Illumina BovineSNP50) chips. A total of 26,884 genotyped Holstein individuals genotyped with medium-density chips were used in this study. Imputation was carried out using FImpute V2.2. The following parameters were examined: treating the pseudoautosomal region as autosomal or as X specific, different sizes of reference groups, different male/female proportions in the reference group, and cumulated degree of relationship between the reference group and target group. The imputation accuracy of markers on the X chromosome was improved if the pseudoautosomal region was treated as autosomal. Increasing the proportion of females in the reference group improved the imputation accuracy for the X chromosome. Imputation for nongenotyped animals in general had lower accuracy compared with animals genotyped with the low-density single nucleotide polymorphism array. In addition, higher cumulative pedigree relationships between the reference group and the target animal led to higher imputation accuracy. In the future, better marker coverage of the X chromosome should be developed to facilitate genomic studies involving the X chromosome. [ABSTRACT FROM AUTHOR]

Using targeted genetical genomics, a quantitative trait locus (QTL) affecting the initial postmortem pH value of chicken breast muscle (Pectoralis major) on chromosome 1 (GGA1) recently was fine-mapped. Thirteen genes were present in the QTL region of approximately 1 Mb. In this study, 10 birds that were inferred to be homozygous for either the high (QQ) or low (qq) QTL allele were selected for resequencing. After enrichment for 1 Mb around the QTL region, >500 x coverage for the QTL region in each of the 10 birds was obtained. In total 5056 single-nucleotide polymorphisms (SNPs) were identified for which the genotypes were consistent with one of the QTL genotypes. We used custom tools to identify putative causal mutations in the mapped QTL region from these SNPs. Four nonsynonymous SNPs differentiating the two QTL genotype groups were identified within four local genes (PRDX4, EIF2S3, PCYT1B, and E1BTD2). Although these are likely candidate SNPs to explain the QTL effect, 54 additional consensus SNPs were detected within gene-related regions (untranslated regions, splicing sites CpG island, and promoter regions) for the QQ birds and 71 for the qq birds. These could also play a role explaining the observed QTL effect. The results provide an important step for prioritizing among a large amount of candidate mutations and significantly contribute to the understanding of the genetic mechanisms affecting the initial postmortem pH value of chicken muscle. [ABSTRACT FROM AUTHOR]