Image-based morphometric analysis reveals moderate to highly heritable nut shape traits in pecan

Nut shape is an important trait in determining the value of a pecan (Carya illinoensis) nut crop. Nut shape influences attractiveness to consumers, nut filling, ease of mechanical cracking, and is distinctive enough that it is the primary means of cultivar identification. Narrow sense heritability (h2) of a trait is the fraction of phenotypic variance attributed to variation in genes with additive effect. Estimation of h2 is key to breeding programs as it determines the method of selection and amount of genetic gain in each breeding cycle. In the present study, we estimated the heritability of pecan nut shape characters following two different approaches. First, image-based phenotypes of pecan nuts from 34 full-sib families generated from random crosses between 31 different parents were generated and analyzed for 10 different morphometric traits using the computer program Tomato Analyzer. The narrow-sense heritability for each trait was estimated using the mid-parent offspring regression method. Second, a separate set of 19 pecan genotypes were phenotyped for the same shape traits for two years and heritabilities were estimated by variance component analysis. Heritability estimates ranged from 0.41 to 0.83 for the mid-parent offspring regression method and from 0.26 to 0.78 for variance component method. Additionally, elliptical Fourier transform was performed to study the overall variation in nut shape. The first three principal components obtained from Elliptical Fourier transform explained 65.9% of the total variation in shape attributed to the nut’s roundness and angularity of proximal and distal ends. The use of the image-based high-throughput method of phenotyping and the heritability estimates obtained in this study directly benefit pecan breeding programs focusing on nut shape traits.