Estimating genetic parameters with molecular relatedness and pedigree reconstruction for growth traits in early mixed breeding of juvenile turbot
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Abstract: An introduced turbot population was used to establish families and to estimate genetic parameters of the offspring. However, there is a lack of pedigree information, and common environmental effects can be introduced when each full-sib family is raised in a single tank. Therefore, in the genetic evaluation, SSRs (simple sequence repeats) were used to reconstruct the pedigree and to calculate molecular relatedness between individuals, and the early mixed-family culture model was used to remove the impact of the common environmental effects. After 100 d of early mixed culture, twenty SSRs were used to cluster 20 families and to calculate paired molecular relationships (n=880). Additive genetic matrices were constructed using molecular relatedness (MR) and pedigree reconstruction (PR) and were then applied to the same animal model to estimate genetic parameters. Based on PR, the heritabilities for body weight and body length were 0.214±0.124 and 0.117±0.141, and based on MR they were 0.101±0.031 and 0.102±0.034, respectively. Cross validation showed that the accuracies of the estimated breeding values based on MR (body weight and body length of 0.717±0.045 and 0.629±0.141, respectively) were higher than those of PR (body weight and body length of 0.692±0.052 and 0.615±0.060, respectively). The MR method ensure availability of all genotyped selection candidates, thereby improving the accuracy of the breeding value estimation.
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Key words:
- turbot /
- SSR /
- genetic parameter /
- mixed breeding
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Table 1. Characteristics of SSR primers (Ruan et al., 2010)
Loci Primer sequence (5′-3′) Repeats Size/bp Fluorescent dye Temperature/°C YSKr61 F: TCAGTGGGCAGTGAGGTG
R: AAGTCAGAGAAACATCCAGAGTCT 164–173 HEX 62.0 YSKr71 F: TGGGATACATACACATTC
R: AGTGAGTTGACAGACAGAGACGC 172–178 TAMRA 53.4 YSKr72 F: CCAGACAGATAACTACACA
R: GTAAGGCTCGTTAGTCACACGC 132–168 FAM 58.0 YSKr85 F: TACTTACACTGTGTATGTGC
R: GAGAACCGAAGAAATGAGAGTGC 252–290 ROX 56.0 YSKr92 F: CCACGCTGTGTATTTCCTCAT
R: GGTCAACATTCAAACCCAACTGTGC 188–208 HEX 60.0 YSKr101 F: CGGATAGTTAGTACCTCAT
R: GAAAACTGAAGCTGAATGACGC 112–133 TAMRA 56.0 YSKr111 F: AACTGGGACTGGAGTGGAC
R: CTCATTAGAGCCGCTGTATTGCG 340–366 FAM 62.0 YSKr119 F: GCTCTTCCAAGTGCCA
R: TGTAGTGTACCAAATGCACGC 242–271 ROX 54.6 YSKr121 F: CAGAGGACAGCGACGAAGAC
R: AGCATTGCATTGGGTTGAGTACGC 183–188 HEX 62.0 YSKr124 F: CAGCCGTTCTGACCTCGTAG
R: ACCCTCCACTGCTTGTCCTTGGTGC 178–187 TAMRA 62.0 YSKr125 F: ACTTATTTGCCTATGGAGAG
R: TTCATTCACATCACTGGTCCGTG 138–151 FAM 56.0 YSKr6 F: CTAACAAACAACGCAGTCG
R: AGAAACAGGGTAGCATCACCTT 299–313 ROX 62.0 YSKr141 F: TTCTGCTCCCTTCTTCGTGT
R: TCGGTGCTTGTGGAAATCGGCG 171–189 FAM 61.0 YSKr169 F: TAATCTCCTGTTGCCTAATG
R: AACGGACGAGTTCGGTGCAAC 179–185 ROX 62.0 YSKr170 F: GCTACAGTGATGTCGCA
R: ATTTATCCAGTGTTTCGAAC 276–304 HEX 54.6 YSKr173 F: CTGGATTTGCCACGTCAGTAC
R: TCTCGCTAACGCTTCACCTCAAG 323–474 TAMRA 59.0 Table 2. Genetic diversity information of 16 SSR loci
Loci K n HObs HExp PIC NE-1P NE-2P NE-PP NE-I NE-SI HW F (Null) YSKr61 3 909 0.359 0.498 0.437 0.876 0.746 0.606 0.313 0.580 *** 0.175 0 YSKr71 9 715 0.815 0.762 0.727 0.625 0.447 0.258 0.092 0.392 *** 0.042 9 YSKr72 10 909 0.792 0.831 0.813 0.495 0.325 0.146 0.047 0.346 *** 0.026 3 YSKr85 14 904 0.885 0.848 0.831 0.462 0.299 0.128 0.040 0.336 *** 0.021 4 YSKr92 9 907 0.882 0.801 0.774 0.566 0.388 0.205 0.067 0.366 *** –0.050 0 YSKr101 10 901 0.685 0.708 0.674 0.683 0.502 0.302 0.119 0.426 *** 0.018 5 YSKr111 14 901 0.921 0.861 0.848 0.428 0.271 0.106 0.033 0.328 *** 0.035 7 YSKr119 11 899 0.871 0.843 0.823 0.483 0.315 0.144 0.044 0.340 *** 0.014 7 YSKr121 8 906 0.925 0.824 0.801 0.523 0.349 0.172 0.054 0.352 *** 0.060 3 YSKr124 10 905 0.783 0.753 0.731 0.614 0.428 0.223 0.083 0.394 *** 0.023 1 YSKr125 6 909 0.674 0.706 0.654 0.715 0.546 0.369 0.139 0.432 *** 0.029 9 YSKr6 6 903 0.858 0.762 0.720 0.646 0.468 0.290 0.098 0.394 *** 0.061 9 YSKr141 6 902 0.627 0.619 0.571 0.788 0.622 0.442 0.193 0.489 *** 0.008 8 YSKr169 4 901 0.615 0.627 0.554 0.793 0.649 0.489 0.212 0.490 *** 0.013 2 YSKr170 13 888 0.555 0.826 0.805 0.510 0.338 0.158 0.051 0.350 *** 0.197 1 YSKr173 25 867 0.780 0.902 0.894 0.331 0.198 0.063 0.018 0.304 *** 0.072 8 Note: Number of individuals, 931; number of loci, 16; mean number of alleles per locus, 9.875 0; mean proportion of loci typed, 0.955 0; mean expected heterozygosity, 0.760 8; mean polymorphic information content (PIC), 0.728 5; combined non-exclusion probability (first parent), 0.000 157; combined non-exclusion probability (second parent), 0.000 000 55; combined non-exclusion probability (parent pair), 2.396×10–11; combined non-exclusion probability (identity), 1.366×10–18; combined non-exclusion probability (sib identity), 0.000 000 28. K, number of alleles at the locus; n, number of individuals typed at the locus; HObs, observed heterozygosity; HExp, expected heterozygosity; PIC, polymorphic information content; NE-1P, average non-exclusion probability for one candidate parent; NE-2P, average non-exclusion probability for one candidate parent given the genotype of a known parent of the opposite sex; NE-PP, average non-exclusion probability for a candidate parent pair; NE-I, average non-exclusion probability for identity of two unrelated individuals; NE-SI, average non-exclusion probability for identity of two siblings; HW, significance of deviation from Hardy-Weinberg equilibrium; F (Null), estimated null allele frequency. ***, significant at the 0.1% level. The significance level includes a Bonferroni correction if the Bonferroni correction option was selected. Table 3. Variance component of body weight
$ {\sigma }_{a}^{2} $ $ {\sigma }_{d}^{2} $ $ {\sigma }_{e}^{2} $ $ {\sigma }_{p}^{2} $ $ {h}^{2} $±SE PR 0.326±0.172 0.705±0.303 0.488±0.124 1.519±0.298 0.214±0.121 MR 0.139±0.036 0.631±0.251 0.608±0.033 1.379±0.253 0.101±0.031 Note: $ {\sigma }_{a}^{2} $, additive genetic variance (g2); $ {\sigma }_{d}^{2} $, maternal common environmental variance (g2); $ {\sigma }_{e}^{2} $, residual variance (g2); $ {\sigma }_{p}^{2} $, phenotypic variance (g2); h2, heritability; SE, stardard error. Table 4. Variance component of body length
$ {\sigma }_{a}^{2} $ $ {\sigma }_{d}^{2} $ $ {\sigma }_{e}^{2} $ $ {\sigma }_{p}^{2} $ $ {h}^{2} $±SE PR 0.038±0.046 0.126±0.052 0.162±0.034 0.327±0.053 0.117±0.141 MR 0.031±0.001 0.106±0.045 0.169±0.001 0.306±0.045 0.102±0.034 Note: $ {\sigma }_{a}^{2} $, additive genetic variance (cm2); $ {\sigma }_{d}^{2} $, maternal common environmental variance (cm2); $ {\sigma }_{e}^{2} $, residual variance (cm2); $ {\sigma }_{p}^{2} $, phenotypic variance (cm2); h2, heritability; SE, stardard error. Table 5. Genetic correlation and phenotypic correlation of body weight (BW) and body length (BL) based on pedigree reconstruction (PR) and molecular relatedness (MR)
Correlation coefficient Genetic correlation Phenotypic correlation MR 0.856 0.668 PR 0.723 0.624 Table 6. Results of cross validation between observations and predicted values
Pearson correlation
coefficient of
body weightPearson correlation
coefficient of
body lengthMolecular relatedness 0.717±0.045 0.629±0.058 Pedigree reconstruction 0.692±0.052 0.615±0.060 -
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