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

<div><p>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 <i>Flavobacterium psychrophilum</i>, 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 (<i>h²</i> = 0.56±0.18) and odd-year (<i>h²</i> = 0.60±0.15) lines. A significant genetic correlation between SI and BCWD resistance was observed in the even-year line (<i>r_g</i> = 0.45±0.20, <i>P</i> = 0.03) but not in the odd-year line (<i>r_g</i> = 0.16±0.12, <i>P</i> = 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.</p></div

Significant and suggestive QTL for BCWD traits using half-sib family regression analysis¹ in rainbow trout family 2008132.

1<p>Footnotes are the same as for <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075749#pone-0075749-t003" target="_blank">Table 3</a>.</p

Family phenotypic correlation between naïve-animal spleen index (SI) and survival following challenge with <i>F. psychrophilum</i>.

<p>(A) Trait correlation in fifteen 2007 year-class families selected based on BCWD resistance phenotype. Families were created using parents whose full-sibs were BCWD challenged in 2005 and identified as highly disease “resistant” (R) or “susceptible” (S) families. Five RxR (blue), RxS (green) and SxS (red) crosses were assayed for both survival (n = 200 fish per family, mean age 118 days,) and SI (n = 20 per family, mean age 128 days). (B) Trait correlation in 2008 year-class families. Fifteen families were created from fish whose full-sibs were evaluated in 2006 for SI and categorized as high SI (H) and low SI (L). Five HxH (blue), HxL (green) and LxL (red) crosses assayed for both survival (n = 120 fish per family, mean age 114 days,) and SI (n = 20 per family, mean age 145 days). (C) Stability of SI in HxH, HxL and LxL cross types. Values represent an average (±1 SEM) of 5 families per cross type. (D) Equivalent growth rates of the F₁ SI QTL (2008) families.</p

Significant and suggestive QTL for SI using half-sib family regression analysis¹ in rainbow trout family 2008132.

1<p>Half-sib regression interval mapping was performed with web-based software GridQTL <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075749#pone.0075749-Seaton1" target="_blank">[24]</a>.</p>2<p>Rainbow trout chromosome number <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075749#pone.0075749-Rexroad1" target="_blank">[21]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075749#pone.0075749-Palti1" target="_blank">[22]</a>.</p>3<p>The chromosome location with the highest estimated <i>F</i>-value was defined as the most likely QTL location. The map cM units are based on genetic maps developed for this QTL genome scan study.</p>4<p>The likelihood ratio test statistic was estimated as where <i>L₀</i> is the log likelihood of polygenic model and <i>L₁</i> is the log likelihood of the QTL model at the tested location (cM).</p>5<p>Asymptotically <i>F-</i>test statistic with the degrees of freedom(DF) being the number of sires or dams included for the numerator, and the total number of offspring minus twice the number of sires or dams for the denominator <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075749#pone.0075749-Knott1" target="_blank">[25]</a>. The QTL with <i>F</i>-value ≥ <i>F_{ChromWide P = 0.05}</i> was defined as suggestive QTL (*) and QTL with <i>F</i>-value ≥ <i>F_{ExperWide P = 0.05}</i> was defined as significant QTL (**).</p>6<p>Chromosome-wide <i>F</i>-value at <i>P</i> = 0.05 was estimated using 10,000 permutations with GridQTL <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075749#pone.0075749-Seaton1" target="_blank">[24]</a>.</p>7<p>Experiment-wide <i>F_{ExperWide P = 0.05}</i> was estimated using 10,000 bootstraps with re-sampling with GridQTL <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075749#pone.0075749-Seaton1" target="_blank">[24]</a>.</p>8<p>The proportion of phenotypic variance explained by the QTL was calculated as where <i>MSE_full</i> and <i>MSE_reduced</i> are the mean squared error of the full and reduced model, respectively <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075749#pone.0075749-Knott1" target="_blank">[25]</a>. The estimated was corrected for selective genotyping according to Darvasi and Soller <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075749#pone.0075749-Darvasi1" target="_blank">[61]</a>.</p>9<p>The 95% confidence intervals for each suggestive and significant QTL was determined using 10,000 bootstraps with re-sampling with software GridQTL <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075749#pone.0075749-Seaton1" target="_blank">[24]</a>.</p>10<p>The closest markers flanking (left and right) the chromosome location with the highest estimated <i>F</i>-value in the QTL scan.</p

Plot of Omy19 showing QTL intervals for SI and BCWD resistance traits.

<p>The location and designation of microsattalite markers used to identify the QTL are listed above the figure. The 95% confidence interval for each QTL is indicated below the graph by an individual line for each trait. Data for both SI and BCWD QTL fit a single QTL model with no evidence for a second QTL.</p

Quantitative trait loci for SI identified by half-sib (HS) family regression interval mapping in rainbow trout family 2008132.

<p>(A) Plot of QTL for dam alleles showing all chromosomes. A major QTL was identified on Omy19. (B) Plots of quantitative trait loci for sire allels showing all chromosomes. Major QTL were identified on Omy5 and Omy16.</p

Association of alleles with spleen size and BCWD survival traits.

1<p>Allele effect is estimated by regression of SI, survival days, or survival status with the dam allele. The two alleles from the dam are listed, and for convenience, the effect on phenotype is listed in positive units.</p>2<p>Null allele.</p>3<p>n.s. indicates non-significant test (<i>P</i>>0.05).</p

Rainbow trout families with divergent spleen indices: family with high average SI, 2008132, and low average SI, 2008140.

<p>(A) Four randomly selected fish and respective spleens. (B) SI phenotype distribution of families 2008132 and 2008140. (C) Average body weights (not statistically different). (D) Survival following laboratory injection challenge with <i>F. psychrophilum</i> (<i>P</i><0.001, results are an average from triplicate tanks, n = 40 fish per tank).</p