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. 2022 Jul 29;12(8):jkac137.
doi: 10.1093/g3journal/jkac137.

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

Federico C F Calboli  1 , Heikki Koskinen  2 , Antti Nousianen  2 , Clémence Fraslin  3 , Ross D Houston  3 , Antti Kause  1
Affiliations

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

Federico C F Calboli et al. G3 (Bethesda). .

Abstract

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). FST 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.

Keywords: GWAS; QTL; columnaris disease; inversion; rainbow trout.

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Figures

Fig. 1.
Fig. 1.
Genome-wide association analysis across all chromosomes from the MLMA-LOCO (leave-one-chromosome out) approach. For all panels, in blue the chromosome significance P-value, in red the genome-wide significance line, both based on Bonferroni correction. a) Manhattan plot of LUKE female fish. b) Manhattan plot of LUKE male fish. c) Manhattan plot of Savon Taimen female fish. d) Manhattan plot of all fish combined. e) Manhattan plot of Savon Taimen females and LUKE males combined.
Fig. 2.
Fig. 2.
Manhattan plots for chromosome Omy3 from MLMA-LOCO analysis. For all panels, in blue the chromosome significance P-value, in red the genome-wide significance line, both based on Bonferroni correction. a) Manhattan plot of LUKE female fish. b) Manhattan plot of LUKE male fish. c) Manhattan plot of Savon Taimen fish. d) Manhattan plot of all fish combined. e) Manhattan plot of Savon Taimen and LUKE males combined.
Fig. 3.
Fig. 3.
Manhattan plots for chromosome Omy5 from MLMA-LOCO analysis. For all panels, in blue the chromosome significance P-value, in red the genome-wide significance line, both based on Bonferroni correction. The red dots correspond to the P-values of SNPs marked as tagging SNPs for the large inversion complex on Omy5. a) Manhattan plot of LUKE female fish. b) Manhattan plot of LUKE male fish. c) Manhattan plot of Savon Taimen fish. d) Manhattan plot of all fish combined. e) Manhattan plot of Savon Taimen and LUKE males combined.
See this image and copyright information in PMC

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