Morphometrics Reveals Complex and Heritable Apple Leaf Shapes.

Zoë Migicovsky,Daniel H Chitwood,Mao Li,Sean Myles

doi:10.3389/fpls.2017.02185

Abstract

Apple (Malus spp.) is a widely grown and valuable fruit crop. Leaf shape is important for flowering in apple and may also be an early indicator for other agriculturally valuable traits. We examined 9,000 leaves from 869 unique apple accessions using linear measurements and comprehensive morphometric techniques. We identified allometric variation as the result of differing length-to-width aspect ratios between accessions and species of apple. The allometric variation was due to variation in the width of the leaf blade, not the length. Aspect ratio was highly correlated with the first principal component (PC1) of morphometric variation quantified using elliptical Fourier descriptors (EFDs) and persistent homology (PH). While the primary source of variation was aspect ratio, subsequent PCs corresponded to complex shape variation not captured by linear measurements. After linking the morphometric information with over 122,000 genome-wide single nucleotide polymorphisms (SNPs), we found high SNP heritability values even at later PCs, indicating that comprehensive morphometrics can capture complex, heritable phenotypes. Thus, techniques such as EFDs and PH are capturing heritable biological variation that would be missed using linear measurements alone.

Highlights

Apples (Malus spp.) are one of the world’s most widely grown fruit crops, with the third highest global production quantity of over 84 million tons in 2014 (Food Agriculture Organization of the United Nations, 2017)
While the primary axis of variation in apple using elliptical Fourier descriptors (EFDs) and persistent homology (PH) is due to this allometric variation, we find high single nucleotide polymorphisms (SNPs) heritability values even at later principal components, indicating that comprehensive estimates of shape capture heritable variation which would be missed by linear estimates alone
We examined 24 phenotypes related to apple leaf shape and size including length, width, surface area, dry weight, leaf mass per area, within-tree variance, and overall shape estimated using principal component (PC) derived from EFD and PH data

Summary

Introduction

Apples (Malus spp.) are one of the world’s most widely grown fruit crops, with the third highest global production quantity of over 84 million tons in 2014 (Food Agriculture Organization of the United Nations, 2017). Previous studies in apple used linear measurements, such as length and width, to quantify leaf shape (Liebhard et al, 2003; Bassett et al, 2011). The length-to-width aspect ratio is a major source of variation in leaf shape. Differing aspect ratios lead to a disproportionate increase or decrease in length relative to width, resulting in allometric variation, in leaves (Gurevitch, 1992; Chitwood et al, 2013). While linear measurements such as leaf length and width are useful, they fail to capture the full extent of leaf shape diversity. Failing to measure leaf shape comprehensively limits our ability to discern the total underlying genetic contributions

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