Genomic basis of the differences between cider and dessert apple varieties

Abstract

Unraveling the genomic processes at play during variety diversification is of fundamental interest for understanding evolution, but also of applied interest in crop science. It can indeed provide knowledge on the genetic bases of traits for crop improvement and germplasm diversity management. Apple is one of the most important fruit crops in temperate regions, having both great economic and cultural values. Sweet dessert apples are used for direct consumption, while bitter cider apples are used to produce cider. Several important traits are known to differentiate the two variety types, in particular fruit size, biennial versus annual fruit bearing, and bitterness, caused by a higher content in polyphenols. Here, we used an Illumina 8k SNP chip on two core collections, of 48 dessert and 48 cider apples, respectively, for identifying genomic regions responsible for the differences between cider and dessert apples. The genome-wide level of genetic differentiation between cider and dessert apples was low, although 17 candidate regions showed signatures of divergent selection, displaying either outlier FST values or significant association with phenotypic traits (bitter versus sweet fruits). These candidate regions encompassed 420 genes involved in a variety of functions and metabolic pathways, including several colocalizations with QTLs for polyphenol compounds.

Genetic Diversity, Population Structure, Parentage Analysis, and Construction of Core Collections in the French Apple Germplasm Based on SSR Markers

“…The results are also consistent with the very weak differentiation between dessert and cider apples, as already shown by Cornille et al (2012) on a partially redundant set of accessions. A recent study by our group also underlined the difficulties in finding loci involved in the dessert vs. cider differentiation at the genome level (Leforestier et al 2015).…”

“…These core collections are already used for various goals as exemplified by the study of the differentiation between dessert and cider apples (Leforestier et al 2015). The dessert apple core collection is also currently being phenotyped for various agronomical traits and SNP genotyped within the framework of the European project FruitBreedomics (Laurens et al 2010).…”

Development and validation of the Axiom®Apple480K SNP genotyping array

“…An r 2 below 0.2 within 100 kbp was in fact reported by Leforestier et al . () in two core collections of unrelated accessions of dessert and cider apples, while Kumar et al . () reported an r ² below 0.13 within 100 kbp in a diverse population of apple accessions.…”

“…A number of studies have reported the use of the two medium-density Infinium â arrays for the generation of a number of saturated genetic linkage maps and QTL detection (Antanaviciute et al, 2012;Clark et al, 2014;Falginella et al, 2015) in bi-parental full-sib families, for pedigree-based analysis (PBA) on multiple pedigreed families (Guan et al, 2015;Allard et al, 2016) or for GWA analysis in a family-based design (Kumar et al, 2013). However, GWA studies using the 8K SNP array in collections of unre-lated apple accessions (Kumar et al, 2014;Leforestier et al, 2015) highlighted the limitations of the arrays available to date, which provide a low density of markers for GWA studies as LD decays quite quickly in apple. An r 2 below 0.2 within 100 kbp was in fact reported by Leforestier et al (2015) in two core collections of unrelated accessions of dessert and cider apples, while Kumar et al (2014) reported an r² below 0.13 within 100 kbp in a diverse population of apple accessions.…”

“…However, GWA studies using the 8K SNP array in collections of unre-lated apple accessions (Kumar et al, 2014;Leforestier et al, 2015) highlighted the limitations of the arrays available to date, which provide a low density of markers for GWA studies as LD decays quite quickly in apple. An r 2 below 0.2 within 100 kbp was in fact reported by Leforestier et al (2015) in two core collections of unrelated accessions of dessert and cider apples, while Kumar et al (2014) reported an r² below 0.13 within 100 kbp in a diverse population of apple accessions. Moreover, even the 20K apple Infinium â array was based on a restricted number of accessions (13) in the discovery panel, and although this tool perfectly suits the needs of PBA investigations (Allard et al, 2016), its application to GWA studies is limited by the restricted genetic background on which it is based (Gross et al, 2014).…”