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

Matthew Ordidge,Edward P Venison,Pianpool Kirdwichai,M Fazil Baksh,J George Gibbings,Jim M Dunwell,Dario Cantu

doi:10.1371/journal.pone.0202405

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.

Highlights

The domesticated apple (Malus x domestica Borkh.) is one of the world’s most widely cultivated temperate fruit, the genetic basis of its domestication continues to be a subject of debate [1,2,3,4,5,6,7,8,9,10,11,12]
Comparison of the log probability of the data for cluster numbers ranging from 1–40 suggested that a set of 20–30 clusters might be most appropriate to capture the major structure in the data, and it was noted that a smaller peak in ΔK was clearly present at K = 25
Heteroploid and inbred relationships in apple patterns were consistent across all clustering alternatives: clonal accessions were clustered together, and a set of major international cultivars and their clones tended to associate with their documented offspring

Summary

Introduction

The domesticated apple (Malus x domestica Borkh.) is one of the world’s most widely cultivated temperate fruit, the genetic basis of its domestication continues to be a subject of debate [1,2,3,4,5,6,7,8,9,10,11,12]. Heteroploid and inbred relationships in apple 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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