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Genomic heritability estimation for the early life-history transition related to propensity to migrate in wild rainbow and steelhead trout populations.

Hu G, Wang C, Da Y - Ecol Evol (2014)

Bottom Line: Applying genomic heritability estimation using the same dataset, we found that smoltification in the UYR population were almost completely determined by additive effects, with 95.5% additive heritability and 4.5% dominance heritability, whereas smoltification in the UMC population had substantial dominance effects, with 0% additive heritability and 39.3% dominance heritability.Dominance test detected one SNP marker (R30393) with significant dominance effect on smoltification (P = 1.98 × 10(-7)).These results suggested that blocking the free access to the ocean may have reduced genetic diversity and increased genomic similarity associated with the early life-history transition related to propensity to migrate.

View Article: PubMed Central - PubMed

Affiliation: Heilongjiang River Fishery Research Institute, Chinese Academy of Fishery Sciences Harbin, 150070, China ; Department of Animal Science, University of Minnesota Saint Paul, Minnesota, 55108.

ABSTRACT
A previous genomewide association study (GWAS) identified SNP markers associated with propensity to migrate of rainbow and steelhead trout (Oncorhynchus mykiss) in a connected population with free access to the ocean in Upper Yakima River (UYR) and a population in Upper Mann Creek (UMC) that has been sequestered from its access to the ocean for more than 50 years. Applying genomic heritability estimation using the same dataset, we found that smoltification in the UYR population were almost completely determined by additive effects, with 95.5% additive heritability and 4.5% dominance heritability, whereas smoltification in the UMC population had substantial dominance effects, with 0% additive heritability and 39.3% dominance heritability. Dominance test detected one SNP marker (R30393) with significant dominance effect on smoltification (P = 1.98 × 10(-7)). Genomic-predicted additive effects completely separated migratory and nonmigratory fish in the UYR population, whereas genomic-predicted dominance effects achieved such complete separation in the UMC population. The UMC population had higher genomic additive and dominance correlations than the UYR population, and fish between these two populations had the least genomic correlations. These results suggested that blocking the free access to the ocean may have reduced genetic diversity and increased genomic similarity associated with the early life-history transition related to propensity to migrate.

No MeSH data available.


Related in: MedlinePlus

Patterns of genomic prediction for smoltification in blocked population. (A) Genomic-predicted additive effects (GBLUP_a) of all individuals were nearly “0” for all individuals. (B) Enlarged GBLUP_a values surprisingly separated all Smolt fish from Resident fish, although the original GBLUP_a values were nearly zero. (C) Genomic-predicted dominance effects (GBLUP_d) separated Smolt fish from Resident fish. (D) Genomic-predicted genetic values (GBLUP_g) had virtually identical patterns as GBLUP_d.
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fig02: Patterns of genomic prediction for smoltification in blocked population. (A) Genomic-predicted additive effects (GBLUP_a) of all individuals were nearly “0” for all individuals. (B) Enlarged GBLUP_a values surprisingly separated all Smolt fish from Resident fish, although the original GBLUP_a values were nearly zero. (C) Genomic-predicted dominance effects (GBLUP_d) separated Smolt fish from Resident fish. (D) Genomic-predicted genetic values (GBLUP_g) had virtually identical patterns as GBLUP_d.

Mentions: Genomic prediction of SMOLT had patterns in parallel to the estimated genomic contributions to SMOLT. In the UYR population, additive genomic prediction (GBLUP_a) completely separated migrate and nonmigrate fish (Fig. 1A), and dominance genomic prediction (GBLUP_d) was nearly zero for all individuals (Fig. 1B) but the enlarged GBLUP_d distinguished most migrate fish from nonmigrate fish (Fig. 1C), and genomic-predicted total genetic value (GBLUP_g = GBLUP_a + GBLUP_d) separated migrate and nonmigrate fish with least variations (Fig. 1D). The patterns of GBLUP_a and GBLUP_g showed that the UYR population had a genomic stratification with two nonoverlapping groups (Figs 1A and D). In the UMC population, GBLUP_a values for all individuals were virtually “0”, about 10−59 (Fig. 2A). However, enlarged GBLUP_a surprisingly separated migratory fish from nonmigratory fish completely, with GBLUP_a > 0 for migratory (Smolt) fish, and GBLUP_a < 0 for nonmigratory (Resident) fish (Fig. 2B). GBLUP_d and GBLUP_g distinguished migratory fish from nonmigratory fish completely (Fig. 2C and D). The patterns of genomic predictions discussed above were consistent with the results of genomic heritability estimates.


Genomic heritability estimation for the early life-history transition related to propensity to migrate in wild rainbow and steelhead trout populations.

Hu G, Wang C, Da Y - Ecol Evol (2014)

Patterns of genomic prediction for smoltification in blocked population. (A) Genomic-predicted additive effects (GBLUP_a) of all individuals were nearly “0” for all individuals. (B) Enlarged GBLUP_a values surprisingly separated all Smolt fish from Resident fish, although the original GBLUP_a values were nearly zero. (C) Genomic-predicted dominance effects (GBLUP_d) separated Smolt fish from Resident fish. (D) Genomic-predicted genetic values (GBLUP_g) had virtually identical patterns as GBLUP_d.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4020697&req=5

fig02: Patterns of genomic prediction for smoltification in blocked population. (A) Genomic-predicted additive effects (GBLUP_a) of all individuals were nearly “0” for all individuals. (B) Enlarged GBLUP_a values surprisingly separated all Smolt fish from Resident fish, although the original GBLUP_a values were nearly zero. (C) Genomic-predicted dominance effects (GBLUP_d) separated Smolt fish from Resident fish. (D) Genomic-predicted genetic values (GBLUP_g) had virtually identical patterns as GBLUP_d.
Mentions: Genomic prediction of SMOLT had patterns in parallel to the estimated genomic contributions to SMOLT. In the UYR population, additive genomic prediction (GBLUP_a) completely separated migrate and nonmigrate fish (Fig. 1A), and dominance genomic prediction (GBLUP_d) was nearly zero for all individuals (Fig. 1B) but the enlarged GBLUP_d distinguished most migrate fish from nonmigrate fish (Fig. 1C), and genomic-predicted total genetic value (GBLUP_g = GBLUP_a + GBLUP_d) separated migrate and nonmigrate fish with least variations (Fig. 1D). The patterns of GBLUP_a and GBLUP_g showed that the UYR population had a genomic stratification with two nonoverlapping groups (Figs 1A and D). In the UMC population, GBLUP_a values for all individuals were virtually “0”, about 10−59 (Fig. 2A). However, enlarged GBLUP_a surprisingly separated migratory fish from nonmigratory fish completely, with GBLUP_a > 0 for migratory (Smolt) fish, and GBLUP_a < 0 for nonmigratory (Resident) fish (Fig. 2B). GBLUP_d and GBLUP_g distinguished migratory fish from nonmigratory fish completely (Fig. 2C and D). The patterns of genomic predictions discussed above were consistent with the results of genomic heritability estimates.

Bottom Line: Applying genomic heritability estimation using the same dataset, we found that smoltification in the UYR population were almost completely determined by additive effects, with 95.5% additive heritability and 4.5% dominance heritability, whereas smoltification in the UMC population had substantial dominance effects, with 0% additive heritability and 39.3% dominance heritability.Dominance test detected one SNP marker (R30393) with significant dominance effect on smoltification (P = 1.98 × 10(-7)).These results suggested that blocking the free access to the ocean may have reduced genetic diversity and increased genomic similarity associated with the early life-history transition related to propensity to migrate.

View Article: PubMed Central - PubMed

Affiliation: Heilongjiang River Fishery Research Institute, Chinese Academy of Fishery Sciences Harbin, 150070, China ; Department of Animal Science, University of Minnesota Saint Paul, Minnesota, 55108.

ABSTRACT
A previous genomewide association study (GWAS) identified SNP markers associated with propensity to migrate of rainbow and steelhead trout (Oncorhynchus mykiss) in a connected population with free access to the ocean in Upper Yakima River (UYR) and a population in Upper Mann Creek (UMC) that has been sequestered from its access to the ocean for more than 50 years. Applying genomic heritability estimation using the same dataset, we found that smoltification in the UYR population were almost completely determined by additive effects, with 95.5% additive heritability and 4.5% dominance heritability, whereas smoltification in the UMC population had substantial dominance effects, with 0% additive heritability and 39.3% dominance heritability. Dominance test detected one SNP marker (R30393) with significant dominance effect on smoltification (P = 1.98 × 10(-7)). Genomic-predicted additive effects completely separated migratory and nonmigratory fish in the UYR population, whereas genomic-predicted dominance effects achieved such complete separation in the UMC population. The UMC population had higher genomic additive and dominance correlations than the UYR population, and fish between these two populations had the least genomic correlations. These results suggested that blocking the free access to the ocean may have reduced genetic diversity and increased genomic similarity associated with the early life-history transition related to propensity to migrate.

No MeSH data available.


Related in: MedlinePlus