Identification of High-Confidence Structural Variants in Domesticated Rainbow Trout Using Whole-Genome Sequencing

Calling Structural Variants with Confidence from Short-Read Data in Wild Bird Populations

Comprehensive characterization of structural variation in natural populations has only become feasible in the last decade. To investigate the population genomic nature of structural variation, reproducible and high-confidence structural variation callsets are first required. We created a population-scale reference of the genome-wide landscape of structural variation across 33 Nordic house sparrows (Passer domesticus). To produce a consensus callset across all samples using short-read data, we compare heuristic-based quality filtering and visual curation (Samplot/PlotCritic and Samplot-ML) approaches. We demonstrate that curation of structural variants is important for reducing putative false positives and that the time invested in this step outweighs the potential costs of analyzing short-read-discovered structural variation data sets that include many potential false positives. We find that even a lenient manual curation strategy (e.g. applied by a single curator) can reduce the proportion of putative false positives by up to 80%, thus enriching the proportion of high-confidence variants. Crucially, in applying a lenient manual curation strategy with a single curator, nearly all (>99%) variants rejected as putative false positives were also classified as such by a more stringent curation strategy using three additional curators. Furthermore, variants rejected by manual curation failed to reflect the expected population structure from SNPs, whereas variants passing curation did. Combining heuristic-based quality filtering with rapid manual curation of structural variants in short-read data can therefore become a time- and cost-effective first step for functional and population genomic studies requiring high-confidence structural variation callsets.

Investigating structural variant, indel and single nucleotide polymorphism differentiation between locally adapted Atlantic salmon populations

Genomic structural variants (SVs) are now recognized as an integral component of intraspecific polymorphism and are known to contribute to evolutionary processes in various organisms. However, they are inherently difficult to detect and genotype from readily available short-read sequencing data, and therefore remain poorly documented in wild populations. Salmonid species displaying strong interpopulation variability in both life history traits and habitat characteristics, such as Atlantic salmon (Salmo salar), offer a prime context for studying adaptive polymorphism, but the contribution of SVs to fine-scale local adaptation has yet to be explored. Here, we performed a comparative analysis of SVs, single nucleotide polymorphisms (SNPs) and small indels (<50 bp) segregating in the Romaine and Puyjalon salmon, two putatively locally adapted populations inhabiting neighboring rivers (Québec, Canada) and showing pronounced variation in life history traits, namely growth, fecundity, and age at maturity and smoltification. We first catalogued polymorphism using a hybrid SV characterization approach pairing both short- (16X) and long-read sequencing (20X) for variant discovery with graph-based genotyping of SVs across 60 salmon genomes, along with characterization of SNPs and small indels from short reads. We thus identified 115,907 SVs, 8,777,832 SNPs and 1,089,321 short indels, with SVs covering 4.8 times more base pairs than SNPs. All three variant types revealed a highly congruent population structure and similar patterns of F ST and density variation along the genome. Finally, we performed outlier detection and redundancy analysis (RDA) to identify variants of interest in the putative local adaptation of Romaine and Puyjalon salmon. Genes located near these variants were enriched for biological processes related to nervous system function, suggesting that observed variation in traits such as age at smoltification could arise from differences in neural development. This study therefore demonstrates the feasibility of large-scale SV characterization and highlights its relevance for salmonid population genomics.

Conserved QTL and chromosomal inversion affect resistance to columnaris disease in 2 rainbow trout (Oncorhyncus mykiss) populations

We present a comparative genetic analysis of the quantitative trait loci underlying resistance to warm water columnaris disease in 2 farmed rainbow trout (Oncorhynchus mykiss) populations. We provide evidence for the conservation of a major quantitative trait loci on Omy03, and the putative role played by a chromosomal rearrangement on Omy05. A total of 3,962 individuals from the 2 populations experienced a natural Flavobacterium columnare outbreak. Data for 25,823 genome-wide SNPs were generated for both cases (fatalities) and controls (survivors). F_ST and pairwise additive genetic relationships suggest that, despite being currently kept as separate broodstocks, the 2 populations are closely related. Association analyses identified a major quantitative trait loci on chromosome Omy03 and a second smaller quantitative trait loci on Omy05. Quantitative trait loci on Omy03 consistently explained 3–11% of genetic variation in both populations, whereas quantitative trait loci on Omy05 showed different degree of association across populations and sexes. The quantitative trait loci on Omy05 was found within a naturally occurring, 54.84 cM long inversion which is easy to tag due to a strong linkage disequilibrium between the 375 tagging SNPs. The ancestral haplotype on Omy05 was associated with decreased mortality. Genetic correlation between mortality in the 2 populations was estimated at 0.64, implying that the genetic basis of resistance is partly similar in the 2 populations. Our quantitative trait loci validation identifies markers that can be potentially used to complement breeding value evaluations to increase resistance against columnaris disease, and help to mitigate effects of climate change on aquaculture.

Development of a High-Density 665 K SNP Array for Rainbow Trout Genome-Wide Genotyping

Single nucleotide polymorphism (SNP) arrays, also named « SNP chips », enable very large numbers of individuals to be genotyped at a targeted set of thousands of genome-wide identified markers. We used preexisting variant datasets from USDA, a French commercial line and 30X-coverage whole genome sequencing of INRAE isogenic lines to develop an Affymetrix 665 K SNP array (HD chip) for rainbow trout. In total, we identified 32,372,492 SNPs that were polymorphic in the USDA or INRAE databases. A subset of identified SNPs were selected for inclusion on the chip, prioritizing SNPs whose flanking sequence uniquely aligned to the Swanson reference genome, with homogenous repartition over the genome and the highest Minimum Allele Frequency in both USDA and French databases. Of the 664,531 SNPs which passed the Affymetrix quality filters and were manufactured on the HD chip, 65.3% and 60.9% passed filtering metrics and were polymorphic in two other distinct French commercial populations in which, respectively, 288 and 175 sampled fish were genotyped. Only 576,118 SNPs mapped uniquely on both Swanson and Arlee reference genomes, and 12,071 SNPs did not map at all on the Arlee reference genome. Among those 576,118 SNPs, 38,948 SNPs were kept from the commercially available medium-density 57 K SNP chip. We demonstrate the utility of the HD chip by describing the high rates of linkage disequilibrium at 2–10 kb in the rainbow trout genome in comparison to the linkage disequilibrium observed at 50–100 kb which are usual distances between markers of the medium-density chip.

Identification of Haplotypes Associated With Resistance to Bacterial Cold Water Disease in Rainbow Trout Using Whole-Genome Resequencing

Bacterial cold water disease (BCWD) is an important disease in rainbow trout aquaculture. Previously, we have identified and validated two major QTL (quantitative trait loci) for BCWD resistance, located on chromosomes Omy08 and Omy25, in the odd-year Troutlodge May spawning population. We also demonstrated that marker-assisted selection (MAS) for BCWD resistance using the favorable haplotypes associated with the two major QTL is feasible. However, each favorable haplotype spans a large genomic region of 1.3–1.6 Mb. Recombination events within the haplotype regions will result in new haplotypes associated with BCWD resistance, which will reduce the accuracy of MAS for BCWD resistance over time. The objectives of this study were 1) to identify additional SNPs (single nucleotide polymorphisms) associated with BCWD resistance using whole-genome sequencing (WGS); 2) to validate the SNPs associated with BCWD resistance using family-based association mapping; 3) to refine the haplotypes associated with BCWD resistance; and 4) to evaluate MAS for BCWD resistance using the refined QTL haplotypes. Four consecutive generations of the Troutlodge May spawning population were evaluated for BCWD resistance. Parents and offspring were sequenced as individuals and in pools based on their BCWD phenotypes. Over 12 million SNPs were identified by mapping the sequences from the individuals and pools to the reference genome. SNPs with significantly different allele frequencies between the two BCWD phenotype groups were selected to develop SNP assays for family-based association mapping in three consecutive generations of the Troutlodge May spawning population. Among the 78 SNPs derived from WGS, 77 SNPs were associated with BCWD resistance in at least one of the three consecutive generations. The additional SNPs associated with BCWD resistance allowed us to reduce the physical sizes of haplotypes associated with BCWD resistance to less than 0.5 Mb. We also demonstrated that the refined QTL haplotypes can be used for MAS in the Troutlodge May spawning population. Therefore, the SNPs and haplotypes reported in this study provide additional resources for improvement of BCWD resistance in rainbow trout.

A candidate chromosome inversion in Arctic charr (Salvelinus alpinus) identified by population genetic analysis techniques

The "genomics era" has allowed questions to be asked about genome organization and genome architecture of non-model species at a rate not previously seen. Analyses of these genome-wide datasets have documented many examples of novel structural variants (SVs) such as chromosomal inversions, copy number variants, and chromosomal translocations, many of which have been linked to adaptation. The salmonids are a taxonomic group with abundant genome-wide datasets due to their importance in aquaculture and fisheries. However, the number of documented SVs in salmonids is surprisingly low and is most likely due to removing loci in high linkage disequilibrium when analyzing structure and gene flow. Here we re-analyze RAD-seq data from several populations of Arctic charr (Salvelinus alpinus) and document a novel ∼1.2 MB SV at the distal end of LG12. This variant contains 15 protein-coding genes connected to a wide-range of functions including cell adhesion and signal transduction. Interestingly, we studied the frequency of this polymorphism in four disjointed populations of charr-one each from Nunavut, Newfoundland, Eastern Russia, and Scotland-and found evidence of the variant only in Nunavut, Canada, suggesting the polymorphism is novel and recently evolved.

A 104-bp Structural Variation of the ADPRHL1 Gene Is Associated With Growth Traits in Chickens

Analyzing marker-assisted breeding is an important method utilized in modern molecular breeding. Recent studies have determined that a large number of molecular markers appear to explain the impact of "lost heritability" on human height. Therefore, it is necessary to locate molecular marker sites in poultry and investigate the possible molecular mechanisms governing their effects. In this study, we found a 104-bp insertion/deletion polymorphism in the 5'UTR of the ADPRHL1 gene through resequencing. In cross-designed F₂ resource groups, the indel was significantly associated with weight at 0, 2, 4, 6, and 10 weeks and a number of other traits [carcass weight (CW), semi-evisceration weight (SEW), evisceration weight (EW), claw weight (CLW), wings weight (DWW), gizzard weight (GW), pancreas weight (PW), chest muscle weight (CMW), leg weight (LW), leg muscle weight (LMW), shedding Weight (SW), liver rate (LR), and leg muscle rate (LMR)] (P < 0.05). In brief, the insertion-insertion (II) genotype was significantly associated with the greatest growth traits and meat quality traits, whereas the values associated with the insertion-deletion (ID) genotype were the lowest in the F₂ reciprocal cross chickens. The mutation sites were genotyped in 4,526 individuals from 12 different chicken breeds and cross-designed F₂ resource groups. The II genotype is the most important genotype in commercial broilers, and the I allele frequency observed in these breeds is relatively high. Deletion mutations tend to be fixed in commercial broilers. However, there is still considerable great potential for breeding in dual-purpose chickens and commercial laying hens. A luciferase reporter assay showed that the II genotype of the ADPRHL1 gene possessed 2.49-fold higher promoter activity than the DD genotype (P < 0.05). We hypothesized that this indel might affect the transcriptional activity of ADPRHL1, thereby affecting the growth traits of chickens. These findings may help to elucidate the function of the ADPRHL1 gene and facilitate enhanced reproduction in the chicken industry.