Accurate genomic predictions for BCWD resistance in rainbow trout are achieved using low‐density SNP panels: Evidence that long‐range LD is a major contributing factor

Abstract

Previously accurate genomic predictions for Bacterial cold water disease (BCWD) resistance in rainbow trout were obtained using a medium-density single nucleotide polymorphism (SNP) array. Here, the impact of lower-density SNP panels on the accuracy of genomic predictions was investigated in a commercial rainbow trout breeding population. Using progeny performance data, the accuracy of genomic breeding values (GEBV) using 35K, 10K, 3K, 1K, 500, 300 and 200 SNP panels as well as a panel with 70 quantitative trait loci (QTL)-flanking SNP was compared. The GEBVs were estimated using the Bayesian method BayesB, single-step GBLUP (ssGBLUP) and weighted ssGBLUP (wssGBLUP). The accuracy of GEBVs remained high despite the sharp reductions in SNP density, and even with 500 SNP accuracy was higher than the pedigree-based prediction (0.50-0.56 versus 0.36). Furthermore, the prediction accuracy with the 70 QTL-flanking SNP (0.65-0.72) was similar to the panel with 35K SNP (0.65-0.71). Genomewide linkage disequilibrium (LD) analysis revealed strong LD (r ≥ 0.25) spanning on average over 1 Mb across the rainbow trout genome. This long-range LD likely contributed to the accurate genomic predictions with the low-density SNP panels. Population structure analysis supported the hypothesis that long-range LD in this population may be caused by admixture. Results suggest that lower-cost, low-density SNP panels can be used for implementing genomic selection for BCWD resistance in rainbow trout breeding programs.

Genome-wide patterns of population structure and linkage disequilibrium in farmed Nile tilapia (Oreochromis niloticus)

“…Thus, the minimum number of markers for a high power genomic analysis should be at 351 least,8,300,6,700 and 4,200 for POP A,POP B and POP C,respectively;numbers 352 slightly lower than those suggested by Vallejo et al (2018) and Barria et al (2018a) for also depend on other factors such as the number of individuals genotyped and 356 phenotyped in the training population and the heritability and number of loci affecting 357 the trait (Daetwyler et al, 2008;Goddard, 2009). In preliminary studies of genomic 358 prediction for Nile tilapia, we found high accuracies of GEBV (results not show) for 359 complex traits, using a similar number of markers but a smaller number of animals 360 suggested by Meuwissen (2009).…”

“…The LD estimation for POP A resulted in slightly different values at 317 small distance compared to POP B and POP C, whereas at large distance the differences 318 were more evident for POP C (Figure 4). These results were reflected in smaller Ne of 319 many generations ago for POP A and smaller Ne in the recent past for POP C (Figure 320 smaller Ne was found for for rainbow trout (Vallejo et al, 2018) and Atlantic salmon 330 from North America, Europe (Barria et al, 2018c) and Tasmania (Kijas et al, 2016). 331…”

“…To date, the most widely used measures of LD between two loci are r 2 and Lewontin's 103 et al, 2017), rainbow trout (Rexroad and Vallejo, 2009;Vallejo et al, 2018), coho 116 salmon (Barria et al, 2018a) and Atlantic salmon (Barria et al, 2018c;Gutierrez et al, 117 2015;Hayes et al, 2006;Kijas et al, 2016). However, to date there is scarce 118 information about population genomic structure and LD in farmed Nile tilapia assessed 119 by the use of dense SNP panels.…”

Potential of genomic selection for improvement of resistance to ostreid herpesvirus in Pacific oyster (Crassostrea gigas)

“…Moreover, a high-density linkage map containing 20 000 SNPs has recently been created and aligned with the physical reference genome assembly (Zhang et al 2012;Gutierrez et al 2018a). Using such arrays, several studies have demonstrated that genomic selection for aquaculture species results in improved accuracy compared with traditional pedigree-based approaches; for example in Atlantic salmon (Robledo et al 2018), coho salmon (Barr ıa et al 2018), rainbow trout (Vallejo et al 2018), common carp (Palaiokostas et al 2018b) and Pacific oyster (Gutierrez et al 2018b).…”

Assessing thermal adaptation using family‐based association andFSToutlier tests in a threatened trout species

“…In outbred natural populations of rainbow trout, LD typically spans thousands of bases (<10 kb, Chen, Farrell, Matala, Hoffman, & Narum, ), and average LD in natural European eel ( Anguilla Anguilla ) populations suggest a similar distance, with LD = 10–20 kb (Pujolar et al, ). Genome‐wide LD analysis on an inbred hatchery line of rainbow trout revealed much stronger LD ( r 2 ≥ 0.25) spanning on average over 1 Mb across the genome (Vallejo et al, ). The close mapping distance of the two significant markers observed here presents a target for future research.…”