Timothy D. Leeds

RNA-Seq Identifies SNP Markers for Growth Traits in Rainbow Trout

Fast growth is an important and highly desired trait, which affects the profitability of food animal production, with feed costs accounting for the largest proportion of production costs. Traditional phenotype-based selection is typically used to select for growth traits; however, genetic improvement is slow over generations. Single nucleotide polymorphisms (SNPs) explain 90% of the genetic differences between individuals; therefore, they are most suitable for genetic evaluation and strategies that employ molecular genetics for selective breeding. SNPs found within or near a coding sequence are of particular interest because they are more likely to alter the biological function of a protein. We aimed to use SNPs to identify markers and genes associated with genetic variation in growth. RNA-Seq whole-transcriptome analysis of pooled cDNA samples from a population of rainbow trout selected for improved growth versus unselected genetic cohorts (10 fish from 1 full-sib family each) identified SNP markers associated with growth-rate. The allelic imbalances (the ratio between the allele frequencies of the fast growing sample and that of the slow growing sample) were considered at scores >5.0 as an amplification and <0.2 as loss of heterozygosity. A subset of SNPs (n = 54) were validated and evaluated for association with growth traits in 778 individuals of a three-generation parent/offspring panel representing 40 families. Twenty-two SNP markers and one mitochondrial haplotype were significantly associated with growth traits. Polymorphism of 48 of the markers was confirmed in other commercially important aquaculture stocks. Many markers were clustered into genes of metabolic energy production pathways and are suitable candidates for genetic selection. The study demonstrates that RNA-Seq at low sequence coverage of divergent populations is a fast and effective means of identifying SNPs, with allelic imbalances between phenotypes. This technique is suitable for marker development in non-model species lacking complete and well-annotated genome reference sequences.

Rainbow trout resistance to bacterial cold-water disease is moderately heritable and is not adversely correlated with growth.

The objectives of this study were to estimate the heritabilities for and genetic correlations among resistance to bacterial cold-water disease and growth traits in a population of rainbow trout (Oncorhynchus mykiss). Bacterial cold-water disease, a chronic disease of rainbow trout, is caused by Flavobacterium psychrophilum. This bacterium also causes acute losses in young fish, known as rainbow trout fry syndrome. Selective breeding for increased disease resistance is a promising strategy that has not been widely used in aquaculture. At the same time, improving growth performance is critical for efficient production. At the National Center for Cool and Cold Water Aquaculture, reducing the negative impact of diseases on rainbow trout culture and improving growth performance are primary objectives. In 2005, when fish averaged 2.4 g, 71 full-sib families were challenged with F. psychrophilum and evaluated for 21 d. Overall survival was 29.3% and family rates of survival varied from 1.5 to 72.5%. Heritability of postchallenge survival, an indicator of disease resistance, was estimated to be 0.35 +/- 0.09. Body weights at 9 and 12 mo posthatch and growth rate from 9 to 12 mo were evaluated on siblings of the fish in the disease challenge study. Growth traits were moderately heritable, from 0.32 for growth rate to 0.61 for 12-mo BW. Genetic and phenotypic correlations between growth traits and resistance to bacterial cold-water disease were not different from zero. These results suggest that genetic improvement can be made simultaneously for growth and bacterial cold-water disease resistance in rainbow trout by using selective breeding.

Response to selection for bacterial cold water disease resistance in rainbow trout

A family-based selection program was initiated at the National Center for Cool and Cold Water Aquaculture in 2005 to improve resistance to bacterial cold water disease (BCWD) in rainbow trout. The objective of this study was to estimate response to 2 generations of selection. A total of 14,841 juvenile fish (BW = 3.1 g; SD = 1.1 g) from 230 full-sib families and 3 randomly mated control lines were challenged intraperitoneally with Flavobacterium psychrophilum, the bacterium that causes BCWD, and mortalities were observed for 21 d. Selection was applied to family EBV derived from a proportional-hazards frailty (animal) model while constraining rate of inbreeding to <or=1% per generation. After adjusting for nongenetic effects, survival rate of select-line families increased by 24.6 +/- 6.8 and 44.7 +/- 6.7 (cumulative) percentage points after 1 and 2 generations of selection, respectively (P < 0.01). Genetic trend, estimated from a linear animal model that fit genetic group effects, was 19.0 +/- 4.1 percentage points per generation and approached significance (P = 0.07). Heritability estimates from the proportional-hazards frailty model and linear animal model were similar (0.22 and 0.23, respectively), and family EBV from both models were highly correlated (-0.92). Accuracy of selection, estimated as the correlation between mid-parent EBV and progeny survival rate, was 0.20 (P < 0.01) for the proportional-hazards frailty model and 0.18 (P = 0.01) for the linear animal model. Accuracy estimates were not different (P = 0.81) between the models. This study demonstrates that selective breeding can be effective for improving resistance to experimental BCWD challenge in rainbow trout.

B-mode, real-time ultrasound for estimating carcass measures in live sheep: Accuracy of ultrasound measures and their relationships with carcass yield and value,

Accuracy and repeatability of live-animal ultrasound measures, and the relationships of these measures with subprimal yields and carcass value, were investigated using data from 172 wethers. Wethers were F(1) progeny from the mating of 4 terminal sire breeds to Rambouillet ewes and were finished in a feedlot to a mean BW of 62.9 kg (SD = 9.5 kg). Before transport to slaughter, LM area, LM depth, and backfat thickness were measured from transverse ultrasound images taken between the 12th and 13th ribs. After slaughter, these measures were taken on each carcass. Carcasses were fabricated into subprimal cuts, and weights were recorded. Ultrasound accuracy and repeatability were assessed using bias, SE of prediction, SE of repeatability, and simple correlations. Relationships among ultrasound and carcass measures, and between these measures and carcass yield and value, were evaluated using residual correlations and linear prediction models. Ultrasound bias approached 0 for LM area, and backfat thickness was overestimated by only 0.69 mm. The SE of prediction and r were 1.55 cm(2) and 0.75 for LM area, and 1.4 mm and 0.81 for backfat thickness, respectively. The SE of repeatability was 1.31 cm(2) and 0.75 mm for LM area and backfat thickness, respectively. At a standardized BW and backfat thickness, wethers with larger LM area and LM depth yielded larger and more valuable carcasses, and these relationships were detectable with ultrasound. For each SD increase in carcass LM area, dressing percentage increased 1.57 percentage points, gross carcass value increased US

Assessment of Genetic Correlation between Bacterial Cold Water Disease Resistance and Spleen Index in a Domesticated Population of Rainbow Trout: Identification of QTL on Chromosome Omy19

5.12, and boxed carcass value increased US

Evaluation of Columbia, USMARC-Composite, Suffolk, and Texel rams as terminal sires in an extensive rangeland production system: I. Ewe productivity and crossbred lamb survival and preweaning growth

6.84 (P < 0.001). For each SD increase in ultrasound LM area, dressing percentage increased 0.95 percentage points, gross carcass value increased US

Evaluation of Genome-Enabled Selection for Bacterial Cold Water Disease Resistance Using Progeny Performance Data in Rainbow Trout: Insights on Genotyping Methods and Genomic Prediction Models

3.15, and boxed carcass value increased US

Genome-Wide Association Study for Identifying Loci that Affect Fillet Yield, Carcass, and Body Weight Traits in Rainbow Trout (Oncorhynchus mykiss)

3.86 (P < 0.001). When LM area effects were adjusted for carcass weight, the response in boxed carcass value attributed to disproportionate increases in high-value subprimal cut weights was small. Associations of dressing percentage and carcass value with ultrasound and carcass LM depth were significant (P < 0.01) but smaller than corresponding associations with LM area. These data indicate biological and economical incentives for increasing LM area in wethers, and live-animal ultrasound can provide reliable estimates of carcass measures. These results are applicable to terminal sire breeders and producers who market sheep using carcass-merit pricing systems.

Evidence of major genes affecting resistance to bacterial cold water disease in rainbow trout using Bayesian methods of segregation analysis.

Selective breeding of animals for increased disease resistance is an effective strategy to reduce mortality in aquaculture. However, implementation of selective breeding programs is limited by an incomplete understanding of host resistance traits. We previously reported results of a rainbow trout selection program that demonstrated increased survival following challenge with Flavobacterium psychrophilum, the causative agent of bacterial cold water disease (BCWD). Mechanistic study of disease resistance identified a positive phenotypic correlation between post-challenge survival and spleen somatic-index (SI). Herein, we investigated the hypothesis of a genetic correlation between the two traits influenced by colocalizing QTL. We evaluated the inheritance and calculated the genetic correlation in five year-classes of odd- and even-year breeding lines. A total of 322 pedigreed families (n = 25,369 fish) were measured for disease resistance, and 251 families (n = 5,645 fish) were evaluated for SI. Spleen index was moderately heritable in both even-year (h2 = 0.56±0.18) and odd-year (h2 = 0.60±0.15) lines. A significant genetic correlation between SI and BCWD resistance was observed in the even-year line (rg = 0.45±0.20, P = 0.03) but not in the odd-year line (rg = 0.16±0.12, P = 0.19). Complex segregation analyses of the even-year line provided evidence of genes with major effect on SI, and a genome scan of a single family, 2008132, detected three significant QTL on chromosomes Omy19, 16 and 5, in addition to ten suggestive QTL. A separate chromosome scan for disease resistance in family 2008132 identified a significant BCWD QTL on Omy19 that was associated with time to death and percent survival. In family 2008132, Omy19 microsatellite alleles that associated with higher disease resistance also associated with increased spleen size raising the hypothesis that closely linked QTL contribute to the correlation between these traits. To our knowledge, this is the first estimation of spleen size heritability and evidence for genetic linkage with specific disease resistance in a teleost fish.

Rainbow trout (Oncorhynchus mykiss) resistance to columnaris disease is heritable and favorably correlated with bacterial cold water disease resistance.

A 3-yr study was conducted to comprehensively evaluate Columbia, Suffolk, USMARC-Composite (Composite), and Texel breeds as terminal sires in an extensive rangeland production system. The objective was to estimate breed-of-ram effects on ewe fertility, prolificacy, and dystocia, and sire breed effects on lamb survival and growth until weaning at approximately 132 d of age. Data were from 22 Columbia, 22 Composite, 21 Suffolk, and 17 Texel rams with 957 exposures to 574 adult Rambouillet ewes (3- to 7-yr-old at lambing), 908 lambings, and 1,834 lambs. Ram breed did not affect ewe fertility (mean = 94.9%; p = 0.73), total number born per ewe lambing (mean = 2.02 lambs; p = 0.20), number born alive per ewe lambing (mean = 1.90 lambs; p = 0.24), or number weaned per ewe lambing (mean = 1.45 lambs, p = 0.94). Dystocia rates were different (p = 0.01) for ewes mated to Columbia (12.2%), Composite (13.5%), Suffolk (25.7%), and Texel rams (31.9%) during 1 yr of the study, but differences among ram breeds were not repeatable (p ≥ 0.38) during the other 2 yr. Suffolk-sired lambs were heavier (p ≥ 0.02) at birth (5.5 kg) and weaning (40.3 kg) than lambs sired by the other breeds, which did not differ (p ≥ 0.34) for birth weight (mean = 5.3 kg). Texel-sired lambs (37.4 kg) were lighter (p ≥ 0.02) at weaning than Columbia- (38.8 kg) and Composite-sired (38.4 kg) lambs, which did not differ (p = 0.40) for weaning weight. Sire breed effect approached significance (p = 0.06) for lamb survival to weaning; estimated survival probabilities were 0.87 (Columbia), 0.89 (Composite), 0.93 (Suffolk), and 0.86 (Texel) for lambs reared by their birth dam. Interaction between sire breeds and birth weight affected (p < 0.001) lamb survival and revealed that lightweight Columbia- and Suffolk-sired lambs had a greater risk of death than lightweight lambs sired by Composite and Texel rams, but risk of death did not increase substantially for heavyweight lambs from any of the breeds. When mated to adult Rambouillet ewes in an extensive rangeland production system, the use of Suffolk rams is warranted to improve preweaning growth of market lambs and is not predicted to affect ewe fertility, ewe prolificacy, dystocia, or lamb survival compared with the other sire breeds we tested.