Computational protocol: Genetic Mapping and QTL Analysis of Growth-Related Traits in Pinctada fucata Using Restriction-Site Associated DNA Sequencing

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Protocol publication

[…] Pearson correlation coefficients were used to determine the linear correlation between pairs of growth-related traits, using software SPSS version 16.0 (SPSS Inc., USA). The mean size of growth-related traits was compared in the large and small subpopulation using the Student’s t-test in SPSS version 16.0. The significance level was set to 0.05. The QTL mapping was performed using MapQTL 5 software and the KW non-parametric test was performed to determine the significant relationship between the regions of the genome and growth-related traits. We used the nonparametric KW analysis because the growth-related traits of the individuals used in this study deviated from a normal distribution, and no assumptions were being made about the probability distributions of the quantitative traits. The KW test ranks all individuals in accordance with the quantitative trait and classifies them in accordance with their marker genotype. A KW value larger than the thresholds given by the KW test (χ2 test, P<0.005) and a degree of correlation between loci and traits that was equal to or greater than four asterisks were used to identify QTL-peak loci . The genotype frequency difference between the large subpopulation and the small subpopulation was compared using the Chi-square test in SPSS version 16.0. The significance level was set to 0.05. […]

Pipeline specifications

Software tools SPSS, MapQTL
Applications Miscellaneous, WGS analysis