Figure 1.
Workflow used for discovery of SNPs associated with growth traits in the rainbow trout transcriptome.
SNPs identified in RNA-Seq reads were called and filtered using Alpheus pipeline. The SNP detection stringency conditions include at least 4 reads calling the variant, >20% reads calling the variant and >20 Quality score. SNP putatively associated with fast growth were considered at allelic imbalances scores >5.0 as an amplification and <0.2 as loss of heterozygosity. SNPs were validated by individually genotyping the discovery panel. Putative SNPs were genotyped for association analysis on 778 fish (40 families).
Figure 2.
Variation in average family body weight (BW) measured in grams at approximately 6, 7, 9 and 12 months post-hatching (Weight1, Weight2, Weight3 and Weight4). CV (SD/mean) indicates the phenotypic coefficients of variation.
Color intensities (green, blue and red) reflect changes in mean of BWs of different families at Weight1, Weigh2 and Weight3, respectively. Up/right/down arrows indicate families’ mean BWs lie within top, middle and bottom 33% of the population at each age, respectively.
Table 1.
Association of nuclear SNPs with growth traits1 using family-based association analysis2.
Table 2.
Family-based association analysis of nuclear SNPs with growth traits1 using the R package GWAF2.
Table 3.
Association of nuclear SNPs with weight1 using family-based quantitative trait linkage disequilibrium (QTLD) analysis, the measured genotype test and the quantitative disequilibrium test (QTDT) 2.
Table 4.
Summary of nuclear markers significantly associated/linked1 to growth traits and their annotations.
Table 5.
Association of mitochondrial SNPs with weight1 using population-based association analysis2.
Table 6.
Summary of mitochondrial markers significantly associated 1 with growth traits and their annotations1.
Table 7.
Polymorphism of significantly associated/linked markers to growth traits in three aquaculture broodstocks.
Figure 3.
NCCCWA genetic/physical map with positions of 19 nuSNPs polymorphic markers. nuSNPs were genotyped on mapping families from the NCCCWA.
Linkage groups were determined and nuSNPs were added to the NCCCWA genetic map [32]. Closest markers from the published map were determined using two-point linkage analyses.