I have a lot of plant-breeding data (tens of thousands of results) that are composed of phenotypes of parents and offspring. The plants however went trough years of selection and it is not balanced. Moreover, I have a lot of inbreeding data. What is the best way to estimate heritability from this type of data, having the exact pedigree relations and the phenotypes (But no accurate environmental data). Moreover, how would you estimate heritability from nominal traits (like color or resistance)?

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    $\begingroup$ The (biometric) heritability of a trait is the slope of the regression line of the mean phenotype of offspring on their mid-parent. When you have multiple traits, you need to use a general linear model rather than a simple linear regression. The GLM accounts for underlying genetic correlations among traits. Nominal data poses no problem, you simply assign numeric values to each category. For example, red = 1, blue = 0. For the relevant theory, I would consult Falconer & Mackay (1996) "Introduction to quantitative genetics". Also look up the 'multivariate breeder's equation'. $\endgroup$ – Michael Andrew Bentley May 15 '16 at 23:31
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    $\begingroup$ d.umn.edu/~jetterso/Ecological%20Genetics/documents/… $\endgroup$ – rg255 May 16 '16 at 7:00
  • $\begingroup$ Thank you very much, it was very helpful. I went on trying with the REML/MCMC methods, and will check how it goes. $\endgroup$ – Dror Hilman May 17 '16 at 8:45

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