Abstract
Image-based phenotyping methodologies are powerful tools to determine quality parameters for fruit breeders and processors. The fruit size and shape of American cranberry (Vaccinium macrocarpon L.) are particularly important characteristics that determine the harvests’ processing value and potential end-use products (e.g., juice vs. sweetened dried cranberries). However, cranberry fruit size and shape attributes can be difficult and time consuming for breeders and processors to measure, especially when relying on manual measurements and visual ratings. Therefore, in this study, we implemented image-based phenotyping techniques for gathering data regarding basic cranberry fruit parameters such as length, width, length-to-width ratio, and eccentricity. Additionally, we applied a persistent homology algorithm to better characterize complex shape parameters. Using this high-throughput artificial vision approach, we characterized fruit from 351 progeny from a full-sib cranberry population over three field seasons. Using a covariate analysis to maximize the identification of well-supported quantitative trait loci (QTL), we found 252 single QTL in a 3-year period for cranberry fruit size and shape descriptors from which 20% were consistently found in all years. The present study highlights the potential for the identified QTL and the image-based methods to serve as a basis for future explorations of the genetic architecture of fruit size and shape in cranberry and other fruit crops.
Highlights
The American cranberry (Vaccinium macrocarpon L.) is a perennial fruit crop native to North America (Eck, 1990), which has gained importance worldwide because of itsHow to cite this article Diaz-Garcia et al (2018), Image-based phenotyping for identification of quantitative trait loci (QTL) determining fruit shape and size in American cranberry (Vaccinium macrocarpon L.)
Persistent homology and correlation with other basic descriptors In total, we analyzed 1,053 pictures from 351 full-sib individuals taken over a 3-year period; each picture contained at least 25 cranberry fruit (Fig. 1A)
We found 17 different QTL that collocated consistently in the 2014–2016 period; LW had the most collocated QTL with 4, width, area, eccentricity and PC1 had 3 each, length had 1, Figure 2 Correlation among cranberry traits and heritability estimates. (A) Pearson correlation between all persistent homology-based and basic descriptors; both circle size and color illustrate the correlation between pairs of traits; circles were omitted for non-significant correlation; best linear unbiased predictors (BLUP) were used for calculating correlations. (B) Genomic heritability (h2) by trait calculated on a per-year-basis using genomic relationships between individuals
Summary
The American cranberry (Vaccinium macrocarpon L.) is a perennial fruit crop native to North America (Eck, 1990), which has gained importance worldwide because of its. How to cite this article Diaz-Garcia et al (2018), Image-based phenotyping for identification of QTL determining fruit shape and size in American cranberry (Vaccinium macrocarpon L.). Many studies have characterized the cranberry genome, but few studies have studied the genetic architecture governing important horticultural traits. Next-generation sequencing has been used to assemble and study the cranberry plastid (Fajardo et al, 2013), mitochondrial (Fajardo et al, 2014), and nuclear (Polashock et al, 2014) genomes. The recent development of several biparental populations in cranberry (e.g., GRYG and CNJ populations) have allowed the construction of simple sequence repeat based (Georgi et al, 2013; Schlautman et al, 2015b) and single nucleotide polymorphism based genetic maps (Covarrubias-Pazaran et al, 2016; Daverdin et al, 2017; Schlautman et al, 2017)
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