Power of QTL mapping experiments in commercial Atlantic salmon populations, exploiting linkage and linkage disequilibrium and effect of limited recombination in males

Whereas detection and positioning of genes that affect quantitative traits (quantitative trait loci (QTL)) using linkage mapping uses only information from recombinants in the genotyped generations, linkage disequilibrium (LD) mapping uses historical recombinants. Thus, whereas linkage mapping requires large family sizes to detect and accurately position QTL, LD mapping is more dependent on the number of families sampled from the population. In commercial Atlantic salmon breeding programmes, only a small number of individuals per family are routinely phenotyped for traits such as disease resistance and meat colour. In this paper, we assess the power and accuracy of combined linkage disequilibrium linkage analysis (LDLA) to detect QTL in the commercial population using simulation. When 15 half-sib sire families (each sire mated to 30 dams, each dam with 10 progeny) were sampled from the population for genotyping, we were able to detect a QTL explaining 10% of the phenotypic variance in 85% of replicates and position this QTL within 3 cM of the true position in 70% of replicates. When recombination was absent in males, a feature of the salmon genome, power to detect QTL increased; however, the accuracy of positioning the QTL was decreased. By increasing the number of sire families sampled from the population to be genotyped to 30, we were able to increase both the proportion of QTL detected and correctly positioned (even with no recombination in males). QTL with much smaller effect could also be detected. The results suggest that even with the existing recording structure in commercial salmon breeding programmes, there is considerable power to detect and accurately position QTL using LDLA.     

QTL for body weight and condition factor in Atlantic salmon (Salmo salar): comparative analysis with rainbow trout (Oncorhynchus mykiss) and Arctic charr (Salvelinus alpinus)

Genotypes at 91 microsatellite loci in three full-sib families were used to search for QTL affecting body weight (BW) and condition factor in North American Atlantic salmon (Salmo salar). More than one informative marker was identified on 16-18 linkage groups in each family, allowing at least one chromosomal interval to be analyzed per linkage group. Two significant QTL for BW on linkage groups AS-8 and AS-11, and four significant QTL for condition factor on linkage groups AS-2, AS-5, AS-11, and AS-14 were identified. QTL for both BW and condition factor were located on linkage groups AS-1, 6, 8, 11, and 14 when considering both significant and suggestive QTL effects. The largest QTL effects for BW (AS-8) and for condition factor (AS-14) accounted for 20.1 and 24.9% of the trait variation, respectively. Three of the QTL for BW occur on linkage groups where similar effects have been detected on the homologous regions in either rainbow trout (Oncorhynchus mykiss) or Arctic charr (Salvelinus alpinus).     

Detection of QTL affecting harvest traits in a commercial Atlantic salmon population

Genetic variation in performance and quality traits measured at harvest has previously been demonstrated in Atlantic salmon aquaculture populations. To map major loci underlying this variation, we utilized data from 10 families from a commercial breeding programme. Significant QTL were detected affecting harvest weight and length traits on linkage group 1, and affecting waste weight on linkage group 5. In total, 11 of the 29 linkage groups examined showed at least suggestive evidence for a QTL. These data suggest that major loci affecting economically important harvest characteristics are segregating in commercial salmon populations.     

Detection of Quantitative Trait Loci (QTL) Related to Grilsing and Late Sexual Maturation in Atlantic Salmon (Salmo salar)

In Atlantic salmon aquaculture, early sexual maturation represents a major problem for producers. This is especially true for grilse, which mature after one sea winter before reaching a desirable harvest weight, rather than after two sea winters. Salmon maturing as grilse have a much lower market value than later maturing individuals. For this reason, most companies desire fish that grow fast and mature late. Marker-assisted selection has the potential to improve the efficiency of selection against early maturation and for late sexual maturation; however, studies identifying age of sexual maturation-related genetic markers are lacking for Atlantic salmon. Therefore, we used a 6.5K single-nucleotide polymorphism (SNP) array to genotype five families from the Mainstream Canada broodstock program and search for SNPs associated with early (grilsing) or late sexual maturation. There were 529 SNP loci that were variable across all five families, and this was the set that was used for quantitative trait loci (QTL) analysis. GridQTL identified two chromosomes, Ssa10 and Ssa21, containing QTL related to grilsing. In contrast, only one QTL, on Ssa18, was found linked to late maturation in Atlantic salmon. Our previous work on these five families did not identify genome-wide significant growth-related QTL on Ssa10, Ssa21, or Ssa18. Therefore, taken together, these results suggest that both grilsing and late sexual maturation are controlled independently of one another and also from growth-related traits. The identification of genomic regions associated with grilsing or late sexual maturation provide an opportunity to incorporate this information into selective breeding programs that will enhance Atlantic salmon farming.     

Mapping of quantitative trait loci for flesh colour and growth traits in Atlantic salmon (Salmo salar)

Background

Flesh colour and growth related traits in salmonids are both commercially important and of great interest from a physiological and evolutionary perspective. The aim of this study was to identify quantitative trait loci (QTL) affecting flesh colour and growth related traits in an F2 population derived from an isolated, landlocked wild population in Norway (Byglands Bleke) and a commercial production population.

Methods

One hundred and twenty-eight informative microsatellite loci distributed across all 29 linkage groups in Atlantic salmon were genotyped in individuals from four F2 families that were selected from the ends of the flesh colour distribution. Genotyping of 23 additional loci and two additional families was performed on a number of linkage groups harbouring putative QTL. QTL analysis was performed using a line-cross model assuming fixation of alternate QTL alleles and a half-sib model with no assumptions about the number and frequency of QTL alleles in the founder populations.

Results

A moderate to strong phenotypic correlation was found between colour, length and weight traits. In total, 13 genome-wide significant QTL were detected for all traits using the line-cross model, including three genome-wide significant QTL for flesh colour (Chr 6, Chr 26 and Chr 4). In addition, 32 suggestive QTL were detected (chromosome-wide P < 0.05). Using the half-sib model, six genome-wide significant QTL were detected for all traits, including two for flesh colour (Chr 26 and Chr 4) and 41 suggestive QTL were detected (chromosome-wide P < 0.05). Based on the half-sib analysis, these two genome-wide significant QTL for flesh colour explained 24% of the phenotypic variance for this trait.

Conclusions

A large number of significant and suggestive QTL for flesh colour and growth traits were found in an F2 population of Atlantic salmon. Chr 26 and Chr 4 presented the strongest evidence for significant QTL affecting flesh colour, while Chr 10, Chr 5, and Chr 4 presented the strongest evidence for significant QTL affecting growth traits (length and weight). These QTL could be strong candidates for use in marker-assisted selection and provide a starting point for further characterisation of the genetic components underlying flesh colour and growth.     

Major quantitative trait loci affect resistance to infectious pancreatic necrosis in Atlantic salmon (Salmo salar)

Infectious pancreatic necrosis (IPN) is a viral disease currently presenting a major problem in the production of Atlantic salmon (Salmon salar). IPN can cause significant mortality to salmon fry within freshwater hatcheries and to smolts following transfer to seawater, although challenged populations show clear genetic variation in resistance. To determine whether this genetic variation includes loci of major effect, a genomewide quantitative trait loci (QTL) scan was performed within 10 full-sib families that had received a natural seawater IPN challenge. To utilize the large difference between Atlantic salmon male and female recombination rates, a two-stage mapping strategy was employed. Initially, a sire-based QTL analysis was used to detect linkage groups with significant effects on IPN resistance, using two to three microsatellite markers per linkage group. A dam-based analysis with additional markers was then used to confirm and position any detected QTL. Two genomewide significant QTL and one suggestive QTL were detected in the genome scan. The most significant QTL was mapped to linkage group 21 and was significant at the genomewide level in both the sire and the dam-based analyses. The identified QTL can be applied in marker-assisted selection programs to improve the resistance of salmon to IPN and reduce disease-related mortality.     

QTL and association analysis for skin and fibre pigmentation in sheep provides evidence of a major causative mutation and epistatic effects

The pursuits of white features and white fleeces free of pigmented fibre have been important selection objectives for many sheep breeds. The cause and inheritance of non‐white colour patterns in sheep has been studied since the early 19th century. Discovery of genetic causes, especially those which predispose pigmentation in white sheep, may lead to more accurate selection tools for improved apparel wool. This article describes an extended QTL study for 13 skin and fibre pigmentation traits in sheep. A total of 19 highly significant, 10 significant and seven suggestive QTL were identified in a QTL mapping experiment using an Awassi × Merino × Merino backcross sheep population. All QTL on chromosome 2 exceeded a LOD score of greater than 4 (range 4.4–30.1), giving very strong support for a major gene for pigmentation on this chromosome. Evidence of epistatic interactions was found for QTL for four traits on chromosomes 2 and 19. The ovine TYRP1 gene on OAR 2 was sequenced as a strong positional candidate gene. A highly significant association (P < 0.01) of grandparental haplotypes across nine segregating SNP/microsatellite markers including one non‐synonymous SNP with pigmentation traits could be shown. Up to 47% of the observed variation in pigmentation was accounted for by models using TYRP1 haplotypes and 83% for models with interactions between two QTL probabilities, offering scope for marker‐assisted selection for these traits.     

Single nucleotide polymorphisms in the insulin‐like growth factor 1 (IGF1) gene are associated with growth‐related traits in farmed Atlantic salmon

Understanding the genetic basis of variation in traits related to growth and fillet quality in Atlantic salmon is of importance to the aquaculture industry. Several growth‐related QTL have been identified via the application of genetic markers. The IGF1 gene is considered a highly conserved and crucial growth‐regulating gene in salmonid species. However, the association between polymorphisms in the IGF1 gene and growth‐related traits in Atlantic salmon is unknown. Therefore, in this study, regions of the Atlantic salmon IGF1 gene were sequenced, aligned and compared across individuals. Three SNPs were identified in the putative promoter (SNP1, g.5763G>T; GenBank no. AGKD01012745 ), intron 1 (SNP2, g.7292C>T; GenBank no. AGKD01012745 ) and intron 3 (SNP3, g.4671A>C; GenBank no. AGKD01133398 ) regions respectively. These SNPs were genotyped in a population of 4800 commercial Atlantic salmon with data on several weight and fillet traits measured at harvest (at approximately 3 years of age). In a mixed model, association analysis of individual SNPs, SNP1 and SNP3 were both significantly associated with several weight traits (P < 0.05). The estimated additive effect on overall harvest weight was approximately 35 and 110 g for SNPs 1 and 3 respectively. A haplotype analysis confirmed the association between genetic variation in the IGF1 gene with overall body weight (P < 0.05) and fillet component traits (P < 0.05). Our findings suggest the identified nucleotide polymorphisms of the IGF1 gene may either affect farmed Atlantic salmon growth directly or be in population‐wide linkage disequilibrium with causal variation, highlighting their possible utility as candidates for marker‐assisted selection in the aquaculture industry.     

Quantitative trait loci for body weight, condition factor and age at sexual maturation in Arctic charr (Salvelinus alpinus): comparative analysis with rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar)

In salmonid fishes, life-history changes may often be coupled to early individual growth trajectories. We identified quantitative trait loci (QTL) for body weight (BW), condition factor (K) and age at sexual maturation (MT) in two full-sib families of Arctic charr (Salvelinus alpinus) to ascertain if QTL for MT were confounded with BW QTL intervals. Three significant QTL for BW, three QTL for MT and one significant QTL for K were identified. A BW QTL with major effect was localized to linkage group 8 (AC-8) and explained more than 34% of the phenotypic variation. Markers on AC-8 have previously been identified as being associated with variation in fork length and BW in this species. Similarly, a major QTL (PEV = 23%) with an influence on the female MT was localized to AC-23. Some of these regions are homologous to those in the genomes of rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar), where similar QTL effects have been detected. Our results also suggest the conservation of MT QTL on the homeologous linkage group pair AC-3/24 in Arctic charr. We further identified chromosomal regions that harbor QTL for multiple traits. In particular, markers on AC-4, -20 and -36 had detectable QTL for all traits studied. Significant MT QTL detected on AC-23, -24, and -27 were autonomous of any BW QTL regions, suggesting that the regulation of MT may be more independent of BW control within this species than in other species of salmonids.     

Relative production of Atlantic salmon from fluvial and lacustrine habitats estimated from analyses of scale characteristics

Empirical and back-calculated growth of Atlantic salmon parr were compared between fish reared in fluvial and lacustrine habitats of Conne River, Newfoundland. Length at age was significantly higher for lacustrine parr. Various classification and maximum likelihood estimators indicated that 75% or more of the fish used lakes for rearing. Lacustrine use is another aspect of the inherent variability and plasticity of Atlantic salmon life-history traits. As most Newfoundland river systems include lakes, estimates of regional spawning targets and potential smolt production will need to take lake habitat into account.     

Determination of body shape variation in Irish hatchery‐reared and wild Atlantic salmon

Discriminant function analysis was used to distinguish morphologically between samples of parr, smolts and adult Atlantic salmon Salmo salar from several hatchery and river systems in Ireland. The effect of habitat shift was investigated in Atlantic salmon parr. Parr grown from the eyed‐egg stage with a non‐sibling group in a hatchery environment, came to resemble the mean body shape of their host hatchery Atlantic salmon stock more closely than that of a full sibling group grown at their natal hatchery. Wild Atlantic salmon smolts differed in shape from hatchery‐reared smolts. This difference was less pronounced, but still statistically significant when wild adults were compared with hatchery‐reared adults captured in the coastal drift‐net fishery after a year spent at sea. Rearing conditions had a significant impact on the production and growth of fish body shape. This in turn may have affected adaptability and survivorship of ranched Atlantic salmon in the marine environment.     

Growth of Atlantic Salmon parr in fluvial and lacustrine habits

The growth of naturally recruited Atlantic salmon Salmo salar parr in fluvial and lacustrine habitats was investigated in three northern Norwegian watercourses. Salmon parr were sampled in autumn with small mesh gillnets in lakes, and by electrofishing in streams. In three northern Norwegian watercourses, lacustrine Atlantic salmon Salmo salar parr were larger in length and weight at age than fluvial parr. Back-calculated lengths indicated that lacustrine salmon parr were recruited from the fastest growing part of the populations and they had larger growth (length) increments between age intervals than fluvial parr. There was no consistent pattern in growth comparisons between parr from the inlet and outlet streams. Temperature regime alone could not explain the growth difference observed between parr from the different habitats.     

水产养殖动物遗传连锁图谱及QTL定位研究进展

自1997年美国农业部启动5种水产养殖动物基因组计划以来,在不到10年的时间里,世界各国都相继开展了本国主要水产养殖动物基因组研究。截至2005年底,有近17种海淡水养殖动物公布了遗传连锁图谱：属于高密度连锁图谱的有虹鳟和大西洋鲑（标记数超过1000）;属于中密度遗传连锁图谱的有罗非鱼、沟鲶、黑虎虾、日本牙鲆和欧洲海鲈（标记数为400-1000）;属于低密度遗传连锁图谱的有泰国的胡鲶,中国的栉孔扇贝、鲤鱼,日本的黄尾鲕,美国的牡蛎等近10种养殖种类（标记数少于400）。水产养殖动物遗传连锁图谱的构建和发展,促进了一些与经济性状（如生长、抗逆、发育等）相关的数量性状位点（QTL）的定位研究。然而,QTL定位研究目前只在具有中高密度遗传连锁图谱的鲑科鱼类（虹鳟、大西洋鲑和北极嘉鱼）、罗非鱼、沟鲶和日本牙鲆等种类中开展,而且定位研究仍处在初级水平。遗传连锁图谱的高分辨率和QTL在图谱上的精确定位,是今后能否实现对主要水产养殖动物的经济性状进行遗传操作的技术保证,同时也是实现分子标记或基因辅助育种在水产养殖动物中成功运用的制胜法宝。     

Assessing footprints of selection in commercial Atlantic salmon populations using microsatellite data

Relatively large rates of response to traits of economic importance have been observed in different selection experiments in salmon. Several QTL have been mapped in the salmon genome, explaining unprecedented levels of phenotypic variation. Owing to the relatively large selection intensity, individual loci may be indirectly selected, leaving molecular footprints of selection, together with increased inbreeding, as its likely relatives will share the selected loci. We used population differentiation and levels of linkage disequilibrium in chromosomes known to be harbouring QTL for body weight, infectious pancreatic necrosis resistance and infectious salmon anaemia resistance to assess the recent selection history at the genomic level in Atlantic salmon. The results clearly suggest that the marker SSA0343BSFU on chromosome 3 (body weight QTL) showed strong evidence of directional selection. It is intriguing that this marker is physically mapped to a region near the coding sequence of DVL2 , making it an ideal candidate gene to explain the rapid evolutionary response of this chromosome to selection for growth in Salmo salar. Weak evidence of diversifying selection was observed in the QTL associated with infectious pancreatic necrosis and infectious salmon anaemia resistance. Overall, this study showed that artificial selection has produced important changes in the Atlantic salmon genome, validating QTL in commercial salmon populations used for production purposes according to the recent selection history.     

An integrated linkage map reveals candidate genes underlying adaptive variation in Chinook salmon (Oncorhynchus tshawytscha)

Salmonids are an important cultural and ecological resource exhibiting near worldwide distribution between their native and introduced range. Previous research has generated linkage maps and genomic resources for several species as well as genome assemblies for two species. We first leveraged improvements in mapping and genotyping methods to create a dense linkage map for Chinook salmon Oncorhynchus tshawytscha by assembling family data from different sources. We successfully mapped 14 620 SNP loci including 2336 paralogs in subtelomeric regions. This improved map was then used as a foundation to integrate genomic resources for gene annotation and population genomic analyses. We anchored a total of 286 scaffolds from the Atlantic salmon genome to the linkage map to provide a framework for the placement 11 728 Chinook salmon ESTs. Previously identified thermotolerance QTL were found to colocalize with several candidate genes including HSP70, a gene known to be involved in thermal response, as well as its inhibitor. Multiple regions of the genome with elevated divergence between populations were also identified, and annotation of ESTs in these regions identified candidate genes for fitness related traits such as stress response, growth and behaviour. Collectively, these results demonstrate the utility of combining genomic resources with linkage maps to enhance evolutionary inferences.     

Size variability of juvenile Atlantic salmon: links to environmental conditions

Climate change models predict a 2 to 6° C increase in air temperature within the next 100 years in the Maritime Provinces of eastern Canada. Higher air temperatures are expected to contribute to increased water temperatures, alterations in stream flow conditions, and ultimately reductions in fish growth. Mean annual size-at-age of juvenile Atlantic salmon Salmo salar decreased in the Northwest Miramichi and Southwest Miramichi Rivers between 1971–1999. Lengths-at-age of juveniles were significantly correlated between the two rivers. For Atlantic salmon parr, stronger associations between inter-cohort fork length ( L _F) than intra-cohort L _F were observed, suggesting that environmental conditions in the current year of growth have the more significant effects on size of age 2 year parr than conditions encountered the previous year by age 1 year parr of the same cohort. Fork lengths of parr were significantly and negatively associated with spring air and water temperatures. In the Miramichi River, increases in air and water temperature as predicted from climate change models may adversely affect growth of juvenile Atlantic salmon parr, reducing the overall productivity of the Atlantic salmon populations in this region.     

QTL for live weight traits in Père David's x red deer interspecies hybrids

Interspecies hybrids between Père David's deer (Elaphurus davidianus) and red deer (Cervus elaphus) have proved to be a powerful resource in the search for quantitative trait loci (QTL) in deer. Several regions of the genome with significant effects on live weight and growth rates in backcross hybrids were detected. These include putative QTL for 6-month live weight (LOD 3.90) on linkage group 12, for 14-month live weight (LOD 3.19) on linkage group 1, three putative QTL for growth rate from 3 to 6 months (LOD 4.19 on linkage group 12, LOD 3.92 on linkage group 12, and LOD 3.34 on linkage group 5). In addition, linkage groups 20 and 1 appear to be associated with live weight traits between 9 and 16 months. The variance in traits explained by these QTL ranged between 5.3% and 11.2%. Allele substitution with Père David's alleles at different loci had both positive and negative effects on live weights and growth rates.     

A linkage map for brown trout (Salmo trutta): chromosome homeologies and comparative genome organization with other salmonid fish

We report on the construction of a linkage map for brown trout (Salmo trutta) and its comparison with those of other tetraploid-derivative fish in the family Salmonidae, including Atlantic salmon (Salmo salar), rainbow trout (Oncorhynchus mykiss), and Arctic char (Salvelinus alpinus). Overall, we identified 37 linkage groups (2n = 80) from the analysis of 288 microsatellite polymorphisms, 13 allozyme markers, and phenotypic sex in four backcross families. Additionally, we used gene-centromere analysis to approximate the position of the centromere for 20 linkage groups and thus relate linkage arrangements to the physical morphology of chromosomes. Sex-specific maps derived from multiple parents were estimated to cover 346.4 and 912.5 cM of the male and female genomes, respectively. As previously observed in other salmonids, recombination rates showed large sex differences (average female-to-male ratio was 6.4), with male crossovers generally localized toward the distal end of linkage groups. Putative homeologous regions inherited from the salmonid tetraploid ancestor were identified for 10 pairs of linkage groups, including five chromosomes showing evidence of residual tetrasomy (pseudolinkage). Map alignments with orthologous regions in Atlantic salmon, rainbow trout, and Arctic char also revealed extensive conservation of syntenic blocks across species, which was generally consistent with chromosome divergence through Robertsonian translocations.     

QTL mapping reveals the genetic architecture of loci affecting pre- and post-zygotic isolating barriers in Louisiana Iris

ABSTRACT: BACKGROUND: Hybridization among Louisiana Irises has been well established and the genetic architecture of reproductive isolation is known to affect the potential for and the directionality of introgression between taxa. Here we use co-dominant markers to identify regions where QTL are located both within and between backcross maps to compare the genetic architecture of reproductive isolation and fitness traits across treatments and years. RESULTS: QTL mapping was used to elucidate the genetic architecture of reproductive isolation between Iris fulva and Iris brevicaulis. Homologous co-dominant EST-SSR markers scored in two backcross populations between I. fulva and I. brevicaulis were used to generate genetic linkage maps. These were used as the framework for mapping QTL associated with variation in 11 phenotypic traits likely responsible for reproductive isolation and fitness. QTL were dispersed throughout the genome, with the exception of one region of a single linkage group (LG) where QTL for flowering time, sterility, and fruit production clustered. In most cases, homologous QTL were not identified in both backcross populations, however, homologous QTL for flowering time, number of growth points per rhizome, number of nodes per inflorescence, and number of flowers per node were identified on several linkage groups. CONCLUSION: Two different traits affecting reproductive isolation, flowering time and sterility, exhibit different genetic architectures, with numerous QTL across the Iris genome controlling flowering time and fewer, less distributed QTL affecting sterility. QTL for traits affecting fitness are largely distributed across the genome with occasional overlap, especially on LG 4, where several QTL increasing fitness and decreasing sterility cluster. Given the distribution and effect direction of QTL affecting reproductive isolation and fitness, we have predicted genomic regions where introgression may be more likely to occur (those regions associated with an increase in fitness and unlinked to loci controlling reproductive isolation) and those that are less likely to exhibit introgression (those regions linked to traits decreasing fitness and reproductive isolation).