A population genomics approach for unraveling the genetic bases of differentiation between dessert and cider apples

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Understanding the processes that occurred during domestication remains one of the central questions in genetics. In addition to fundamental importance, it can indeed provide knowledge on the genetic bases for further crop improvement. As an example, apple is one of the most important fruit crops in temperate regions, having both an economic and a cultural value. Dessert apples are used for consumption as fruits while cider apples are used to produce cider. Yet few traits are known to be different, despite overlapping between dessert and cider apples, namely fruit size and bitterness. A population genomics approach was used for detecting loci involved in the differentiation between cider and dessert apples, on two core collections of old cultivars, one for dessert apples and one for cider apples. A set of 96 gene fragments, localized in 6 areas of the apple genome bearing QTLs for traits of agronomic interest, was re-sequenced and the Illumina 8K SNP chip was used to genotype these two collections. The low estimates of per locus differentiation (ie Fst) between dessert and cider apples indicated that these two pools recently derive from common ancestors, except for 2 genomic regions exhibiting higher Fst values and potentially involved in selective processes. Departure from neutrality was also tested for each “population” using Tajima’s D and Fu and Li’s D and several areas of the genome were found to have significant decrease of both. Such knowledge could be helpful in new selection programs, bringing their efficiency to a higher level.

Malus x domestica
genetic structure
signatures of selection
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