Quantifying apple diversity: A phenomic characterization of Canada’s Apple Biodiversity Collection

Watts, Sophie; Migicovsky, Zoë; McClure, Kendra A.; Yu, Cindy H. J.; Amyotte, Beatrice; Baker, Thomas P.; Bowlby, David; Burgher-MacLellan, Karen; Butler, Laura; Donald, Richard; Fan, Lihua; Fillmore, Sherry; Flewelling, John; Gardner, Kyle M.; Hodges, Mark D; Hughes, Tim; Jagadeesan, Vinetha; Lewis, Naomi; MacDonell, Edward; MacVicar, Laura; McElroy, Michel S.; Money, Daniel; O'Hara, M.; Ong, Quang; Palmer, Leslie Campbell; Sawler, Jason; Vinqvist‐Tymchuk, Melinda; Rupasinghe, HP Vasantha; DeLong, John M.; Forney, Charles F.; Song, Jun; Myles, Sean

doi:10.1002/ppp3.10211

Cited by 29 publications

(47 citation statements)

References 62 publications

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“…Further, each variable in PCA should ideally capture an independent biological feature of apples. However, some phenotypes analysed here are correlated, such as harvest date and firmness [ 23 ], and their variation may be driven by the same biological feature [ 27 ]. Therefore, interpreting our PCA as a quantification of the degree of phenotypic differentiation between cultivated and wild apples should take these caveats into consideration.…”

Section: Discussionmentioning

confidence: 99%

“…The phenotype data analysed here were collected from Canada’s Apple Biodiversity Collection (ABC) and were part of previously published work [ 23 ]. Briefly, the ABC is an apple germplasm collection located at the Agriculture and Agri-Food Canada (AAFC) Kentville Research Station in Nova Scotia, Canada (45.071767, -64.480466).…”

Section: Methodsmentioning

confidence: 99%

“…Phenotype data from the ABC were collected in 2016 and 2017 [ 23 ]. Here we focus on 10 phenotypes most relevant for assessing how apples have changed during domestication, breeding and improvement.…”

Section: Methodsmentioning

confidence: 99%

“…Phenotyping large and diverse populations of plants is labour intensive and frequently results in a “phenotyping bottleneck” [ 22 ], leaving crop researchers without powerful fruit quality data for analysis. Recently, comprehensive phenotyping of Canada’s Apple Biodiversity Collection (ABC) generated measurements for fruit phenotypes in a collection of more than 1000 wild and cultivated apple accessions [ 23 ]. In the present work, we explored ten phenotypes from the ABC and determined the degree to which the cultivated apple differed from its primary wild progenitor, M .…”

Section: Introductionmentioning

confidence: 99%

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Phenotypic divergence between the cultivated apple (Malus domestica) and its primary wild progenitor (Malus sieversii)

et al. 2022

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An understanding of the relationship between the cultivated apple (Malus domestica) and its primary wild progenitor species (M. sieversii) not only provides an understanding of how apples have been improved in the past, but may be useful for apple improvement in the future. We measured 10 phenotypes in over 1000 unique apple accessions belonging to M. domestica and M. sieversii from Canada’s Apple Biodiversity Collection. Using principal components analysis (PCA), we determined that M. domestica and M. sieversii differ significantly in phenotypic space and are nearly completely distinguishable as two separate groups. We found that M. domestica had a shorter juvenile phase than M. sieversii and that cultivated trees produced flowers and ripe fruit later than their wild progenitors. Cultivated apples were also 3.6 times heavier, 43% less acidic, and had 68% less phenolic content than wild apples. Using historical records, we found that apple breeding over the past 200 years has resulted in a trend towards apples that have higher soluble solids, are less bitter, and soften less during storage. Our results quantify the significant changes in phenotype that have taken place since apple domestication, and provide evidence that apple breeding has led to continued phenotypic divergence of the cultivated apple from its wild progenitor species.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Phenotypic divergence between the cultivated apple (Malus domestica) and its primary wild progenitor (Malus sieversii)

et al. 2022

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“…On average, elite material is also harvested later than genetic resources, most probably because fruits with a later ripening are more firm (Migicovsky et al 2016) and can be stored longer (Nybom et al 2008). Modern varieties also have a lower phenolic content than genetic resources in general (Ceci et al 2021;Watts et al 2021). A recent pedigree reconstruction study showed that the two populations are separated by approximately 5-10 generations (Muranty et al 2020), which could result in the persistence of marker phase and effects across populations.…”

Section: Potential Of Combining Populationsmentioning

confidence: 99%

Combining genetic resources and elite material populations to improve the accuracy of genomic prediction in apple

Cazenave

Petit

Laurens

et al. 2021

Preprint

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Genomic selection is an attractive strategy for apple breeding that could reduce the length of breeding cycles. A possible limitation to the practical implementation of this approach lies in the creation of a training set large and diverse enough to ensure accurate predictions. In this study, we investigated the potential of combining two available populations, i.e. genetic resources and elite material, in order to obtain a large training set with a high genetic diversity. We compared the predictive ability of genomic predictions within-population, across-population or when combining both populations, and tested a model accounting for population-specific marker effects in this last case. The obtained predictive abilities were moderate to high according to the studied trait and were always highest when the two populations were combined into a unique training set. We also investigated the potential of such a training set to predict hybrids resulting from crosses between the two populations, with a focus on the method to design the training set and the best proportion of each population to optimize predictions. The measured predictive abilities were very similar for all the proportions, except for the extreme cases where only one of the two populations was used in the training set, in which case predictive abilities could be lower than when using both populations. Using an optimization algorithm to choose the genotypes in the training set also led to higher predictive abilities than when the genotypes were chosen at random. Our results provide guidelines to initiate breeding programs that use genomic selection when the implementation of the training set is a limitation.

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Meta‐analysis of apple (Malus × domestica Borkh.) fruit and juice quality traits for potential use in hard cider production

VanderWeide

Nocker

Gottschalk

2022

Plants People Planet

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Societal Impact Statement The production of hard cider is a burgeoning industry in North America. However, traditional European cider‐specific apples are largely unsuitable for production in modern systems and have not been widely adopted. Evaluation of the biochemical variability in apples can provide a better characterization of varieties for use in hard cider production. Many varieties exhibited extensive variability in biochemical traits. Varieties with high phenolics and acidity displayed greater plasticity of these traits between seasons, which supports the concept of “vintage quality” and opens new marketing opportunities. This study provides valuable insight for apple producers to integrate cider‐specific and nonspecific varieties into their production systems. Summary The North American fermented beverage market has undergone extensive growth in the fermented apple juice (hard cider) sector over the last decade. Traditional hard cider producing regions such as England, France, and Spain have historically utilized cider‐specific apples that have desirable balances between sugar, organic acid, and phenolics. However, in North America, culinary apples (lower acidity and phenolics) are predominantly used, and information distinguishing the varieties with novel use for hard cider production is lacking. In this study, we evaluated variation of four major apple biochemical traits (total soluble solids, pH, titratable acidity, and total phenolics) as they relate to use for hard cider production by using a meta‐analysis approach. We analyzed the variation in cider quality traits across 47 published works and more than 800 unique apple varieties, including an additional analysis of 142 varieties from cider apple germplasms in the United States. The biochemical traits of many varieties exhibited plasticity, and the characterization of a subset of varieties using two cider classification system revealed that most belonged to the “sweet” or “sharp” (acidic) categories rather than “bitter” (high phenolic content). We also compared the classification of a subset of varieties from two US germplasm resources across two seasons and found varieties that have high percent phenolics and/or malic acid experienced greater biochemical plasticity and potential classification change across vintages. Ultimately, this work provides information regarding the variability in apple biochemical traits and also suggests a unique opportunity for producers to market “vintage” quality.

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Quantifying apple diversity: A phenomic characterization of Canada’s Apple Biodiversity Collection

Abstract: This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.

Cited by 29 publications

References 62 publications

Phenotypic divergence between the cultivated apple (Malus domestica) and its primary wild progenitor (Malus sieversii)

Phenotypic divergence between the cultivated apple (Malus domestica) and its primary wild progenitor (Malus sieversii)

Combining genetic resources and elite material populations to improve the accuracy of genomic prediction in apple

Meta‐analysis of apple (Malus × domestica Borkh.) fruit and juice quality traits for potential use in hard cider production

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