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Genetic analysis of a major international collection of cultivated apple varieties reveals previously unknown historic heteroploid and inbred relationships - PubMed

  • ️Mon Jan 01 2018

Genetic analysis of a major international collection of cultivated apple varieties reveals previously unknown historic heteroploid and inbred relationships

Matthew Ordidge et al. PLoS One. 2018.

Abstract

Domesticated apple (Malus x domestica Borkh.) is a major global crop and the genetic diversity held within the pool of cultivated varieties is important for the development of future cultivars. The aim of this study was to investigate the diversity held within the domesticated form, through the analysis of a major international germplasm collection of cultivated varieties, the UK National Fruit Collection, consisting of over 2,000 selections of named cultivars and seedling varieties. We utilised Diversity Array Technology (DArT) markers to assess the genetic diversity within the collection. Clustering attempts, using the software STRUCTURE revealed that the accessions formed a complex and historically admixed group for which clear clustering was challenging. Comparison of accessions using the Jaccard similarity coefficient allowed us to identify clonal and duplicate material as well as revealing pairs and groups that appeared more closely related than a standard parent-offspring or full-sibling relations. From further investigation, we were able to propose a number of new pedigrees, which revealed that some historically important cultivars were more closely related than previously documented and that some of them were partially inbred. We were also able to elucidate a number of parent-offspring relationships that had resulted in a number of important polyploid cultivars. This included reuniting polyploid cultivars that in some cases dated as far back as the 18th century, with diploid parents that potentially date back as far as the 13th century.

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Proportional membership of 2138 accessions within K = 3, K = 4 and K = 25 clusters inferred from STRUCTURE.

Each accession is represented by a vertical bar partitioned into K segments representing the proportional membership of the accession within each cluster. Accessions are ordered by cluster of maximal membership and size of maximal proportion.

Fig 2
Fig 2. Distribution of similarity across the whole collection (2138 accessions) and a series of documented clones of major international cultivars.

1D Density plot as produced in Genstat using a bandwidth of 0.75. All similarity values were calculated using the Jaccard coefficient. Documented clones were as identified in the NFC database and archive. Groups are as follows: (a) all 2138 accessions including clonal samples; (b-i) clonal samples of ‘Cox’s Orange Pippin’, ‘Delicious’, ‘Golden Delicious’, ‘Jonagold’, ‘Jonathan’, ‘McIntosh’, ‘Northern Spy’ and ‘Rome Beauty’.

Fig 3
Fig 3. Distribution of similarity across all non clonal or duplicate members of the collection (1777 accessions) and a series of documented siblings, parent-offspring and full-sibs.

1D Density plot as produced in Genstat using a bandwidth of 0.75. All similarity values were calculated using the Jaccard coefficient. Documented relationships were as identified in the NFC database and archive. Groups are as follows: (a) all 1777 accessions including siblings and parents; (b-g) similarity between documented (half- and full-) sibling offspring of ‘Cox’s Orange Pippin’, ‘Delicious’, ‘Golden Delicious’, ‘Jonathan’, ‘McIntosh’ and ‘Worcester Pearmain’; (h-m) similarity between documented offspring of ‘Cox’s Orange Pippin’, ‘Delicious’, ‘Golden Delicious’, ‘Jonathan’, ‘McIntosh’, ‘Worcester Pearmain’ and their respective parent; (n) similarity between documented full-sibling offspring from crosses between ‘Cox’s Orange Pippin’ and ‘Golden Delicious’, ‘Jonathan’ or ‘McIntosh’ and between ‘Jonathan’ and ‘Delicious’ or ‘Golden Delicious’.

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Grants and funding

This research was funded under award codes GC0143 and GC0147 by the UK Department for Environment, Food and Rural Affairs; all authors received funding. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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