Genetic diversity patterns in farmed rainbow trout (Oncorhynchus mykiss) populations using genome-wide SNP and haplotype data.

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.

Protein content and HvNAM alleles in Nordic barley (Hordeum vulgare) during a century of breeding.

BACKGROUND: Barley has been bred for more than a century in the Nordic countries, with dramatic improvements of yield traits. In this study we investigate if this has come at the cost of lower grain protein and micronutrient (iron, zinc) content, by analysing 80 accessions representing four different improvement stages. We further re-sequenced the two grain protein content associated genes HvNAM-1 and HvNAM-2 in full and performed expression analyses of the same genes to search for genetic associations with nutrient content. RESULTS: We found higher thousand grain weight in barley landraces and in accessions from the late improvement group compared to accessions from the mid of the twentieth century. Straw length was much reduced in late stage accessions. No significant temporal decrease in grain protein, iron or zinc content during twentieth century Nordic crop improvement could be detected. Out of the 80 accessions only two deviant HvNAM-1 sequences were found, represented by one accession each. These do not appear to be correlated to grain protein content. The sequence of HvNAM-2 was invariable in all accessions and no correlations between expression levels of HvNAM-1 and HvNAM-2 and with grain protein content was found. CONCLUSIONS: In contrast to studies in wheat, where a strong negative correlation between straw length and grain protein and micronutrient content has been found, we do not see this relationship in Nordic barley. The last 60 years of breeding has reduced straw length but, contrary to expectations, not protein and micronutrient content. Variation in grain protein and micronutrient content was found among the Nordic barley accessions, but it is not explained by variation of HvNAM genes. This means that HvNAM is an unexploited source of genetic variation for nutrient content in Nordic barley.

Flowering time adaption in Swedish landrace pea (Pisum sativum L.).

BACKGROUND: Cultivated crops have repeatedly faced new climatic conditions while spreading from their site of origin. In Sweden, at the northernmost fringe of Europe, extreme conditions with temperature-limited growth seasons and long days require specific adaptation. Pea (Pisum sativum L.) has been cultivated in Sweden for millennia, allowing for adaptation to the local environmental conditions to develop. To study such adaptation, 15 Swedish pea landraces were chosen alongside nine European landraces, seven cultivars and three wild accessions. Number of days to flowering (DTF) and other traits were measured and the diversity of the flowering time genes HIGH RESPONSE TO PHOTOPERIOD (HR), LATE FLOWERING (LF) and STERILE NODES (SN) was assessed. Furthermore, the expression profiles of LF and SN were obtained. RESULTS: DTF was positively correlated with the length of growing season at the site of origin (GSO) of the Swedish landraces. Alleles at the HR locus were significantly associated with DTF with an average difference of 15.43 days between the two detected haplotypes. LF expression was found to have a significant effect on DTF when analysed on its own, but not when HR haplotype was added to the model. HR haplotype and GSO together explained the most of the detected variation in DTF (49.6 %). CONCLUSIONS: We show local adaptation of DTF, primarily in the northernmost accessions, and links between genetic diversity and diversity in DTF. The links between GSO and genetic diversity of the genes are less clear-cut and flowering time adaptation seems to have a complex genetic background.

Re-sequencing of the casein genes in Swedish Red cattle giving milk with diverse protein profiles and extreme rennet coagulation properties.

Impaired rennet coagulation properties in milk could lead to prolonged processing times and production losses. Heritability for milk coagulation has previously been estimated to be 0.28 to 0.45, indicating that genetic selection can be used to manipulate this trait. The CN proteins are expressed by the genes CSN1S1, CSN2, CSN1S2, and CSN3 and are located on bovine chromosome 6. To better understand the effect of genetic variation in the CN genes on milk coagulation, blood and milk samples from 30 Swedish Red Dairy Cattle (RDC) with divergent coagulation properties were investigated. DNA from the 30 cows was sequenced for the CN genes to determine the theoretical AA sequence and to look for genetic variation in the untranslated regions. The aim is to confirm the protein genetic variants previously reported, while searching for additional genetic variation in the CN genes of 30 RDC. We observed genetic variation in 116 SNPs in the known CN genes where 10% of the SNPs are exon variants and the remaining 90% are intron variants. A total of 2.5% of the SNPs are found in the 5'- or 3'-untranslated region (UTR) regions of the exons; 2% are synonymous variants and 6% are missense variants that concurred with the known protein variants for CSN1S1, CSN2, and CSN3. Furthermore, 6% of the SNPs are splice polypyrimidine tract intron variants. The 2 genetic variants in the 5'- and 3'-UTR in CSN1S1 and CSN3 are found with protein variants CSN1S1C and CSN3B. Because both UTR variants are associated with gain and loss of micro RNA and transcription factors, this could explain differences in expression of the genetic protein variants. Preliminary chi-squared analysis and comparison with previous GWAS studies showed potential connections between the identified SNPs and coagulation properties of milk. By advancing the knowledge of the connection between the DNA sequence and the functional properties of the CN proteins, we hope to learn more about the cheese coagulation properties of milk from RDC.

Whole-genome re-sequencing provides key genomic insights in farmed Arctic charr (Salvelinus alpinus) populations of anadromous and landlocked origin from Scandinavia.

Arctic charr (Salvelinus alpinus) is a niche-market high-value species for Nordic aquaculture. Similar to other salmonids, both anadromous and landlocked populations are encountered. Whole-genome re-sequencing (22X coverage) was performed on two farmed populations of anadromous (Sigerfjord; n = 24) and landlocked (Arctic Superior; n = 24) origin from Norway and Sweden respectively. More than 5 million SNPs were used to study their genetic diversity and to scan for selection signatures. The two populations were clearly distinguished through principal component analysis, with the mean fixation index being ~0.12. Furthermore, the levels of genomic inbreeding estimated from runs of homozygosity were 6.23% and 8.66% for the Norwegian and the Swedish population respectively. Biological processes that could be linked to selection pressure associated primarily with the anadromous background and/or secondarily with domestication were suggested. Overall, our study provided insights regarding the genetic composition of two main strains of farmed Arctic charr from Scandinavia. At the same time, ample genomic resources were produced in the magnitude of millions of SNPs that could assist the transition of Nordic Arctic charr farming in the genomics era.

The genetic basis of adaptive population differentiation: a quantitative trait locus analysis of fitness traits in two wild barley populations from contrasting habitats.

We used a quantitative trait locus (QTL) approach to study the genetic basis of population differentiation in wild barley, Hordeum spontaneum. Several ecotypes are recognized in this model species, and population genetic studies and reciprocal transplant experiments have indicated the role of local adaptation in shaping population differences. We derived a mapping population from a cross between a coastal Mediterranean population and a steppe inland population from Israel and assessed F3 progeny fitness in the natural growing environments of the two parental populations. Dilution of the local gene pool, estimated as the proportion of native alleles at 96 marker loci in the recombinant lines, negatively affected fitness traits at both sites. QTLs for fitness traits tended to differ in the magnitude but not in the direction of their effects across sites, with beneficial alleles generally conferring a greater fitness advantage at their native site. Several QTLs showed fitness effects at one site only, but no opposite selection on individual QTLs was observed across the sites. In a common-garden experiment, we explored the hypothesis that the two populations have adapted to divergent nutrient availabilities. In the different nutrient environments of this experiment, but not under field conditions, fitness of the F3 progeny lines increased with the number of heterozygous marker loci. Comparison of QTL-effects that underlie genotype x nutrient interaction in the common-garden experiment and genotype x site interaction in the field suggested that population differentiation at the field sites may have been driven by divergent nutrient availabilities to a limited extent. Also in this experiment no QTLs were observed with opposite fitness effects in contrasting environments. Our data are consistent with the view that adaptive differentiation can be based on selection on multiple traits changing gradually along ecological gradients. This can occur without QTLs showing opposite fitness effects in the different environments, that is, in the absence of genetic trade-offs in performance between environments.

Development of microsatellite markers for the wood cricket, Nemobius sylvestris (Orthoptera: Gryllidae).

Thirty-four novel microsatellite markers developed for wood cricket (Nemobius sylvestris) were tested and optimized. Twenty-five microsatellite loci were polymorphic, exhibiting between two and nine alleles. Observed heterozygosities ranged from 0.038 to 0.925. The microsatellites were also tested in a species belonging to another genus of the Gryllidae family (Gryllus bimaculatus). Two markers produced clear banding patterns with the expected product size. These markers will be used to study the effects of forest fragmentation on genetic connectivity using wood cricket as a model species.

A genetic analysis of relative growth rate and underlying components in Hordeum spontaneum.

Species from productive and unproductive habitats differ inherently in their relative growth rate (RGR) and a wide range of correlated quantitative traits. We investigated the genetic basis of this trait complex, and specifically assessed whether it is under the control of just one or a few genes that can act as 'master switches' by simultaneously affecting a range of traits in the complex. To address this problem, we crossed two Hordeum spontaneum lines originating from two habitats that differ in productivity. The F3 offspring, in which parental alleles are present in different combinations due to recombination and segregation, was analysed for RGR and its underlying components (leaf area ratio, unit leaf rate, photosynthesis, respiration), as well as a number of other physiological and morphological parameters. For this intra-specific comparison, we found a complex of positively and negatively correlated traits, which was quite similar to what is generally observed across species. A quantitative trait loci (QTL) analysis showed three major and one minor QTL for RGR. Most other variables of the growth-trait complex showed fewer QTLs that were typically scattered over various locations on the genome. Thus, at least in H. spontaneum, we found no evidence for regulation of the trait complex by one or two master switches.