Bianco Luca, Cestaro Alessandro, Linsmith Gareth, Muranty Hélène, Denancé Caroline, Théron Anthony, Poncet Charles, Micheletti Diego, Kerschbamer Emanuela, Di Pierro Erica A, Larger Simone, Pindo Massimo, Van de Weg Eric, Davassi Alessandro, Laurens François, Velasco Riccardo, Durel Charles-Eric, Troggio Michela
Research and Innovation Centre, Fondazione Edmund Mach, via Edmund Mach 1, 38010, San Michele all'Adige, Trento, Italy.
Institut de Recherche en Horticulture et Semences - UMR1345, Institut National de la Recherche Agronomique (INRA), SFR 4207 QUASAV, 42 Rue Georges Morel, F-49071, Beaucouzé, France.
Plant J. 2016 Apr;86(1):62-74. doi: 10.1111/tpj.13145.
Cultivated apple (Malus × domestica Borkh.) is one of the most important fruit crops in temperate regions, and has great economic and cultural value. The apple genome is highly heterozygous and has undergone a recent duplication which, combined with a rapid linkage disequilibrium decay, makes it difficult to perform genome-wide association (GWA) studies. Single nucleotide polymorphism arrays offer highly multiplexed assays at a relatively low cost per data point and can be a valid tool for the identification of the markers associated with traits of interest. Here, we describe the development and validation of a 487K SNP Affymetrix Axiom(®) genotyping array for apple and discuss its potential applications. The array has been built from the high-depth resequencing of 63 different cultivars covering most of the genetic diversity in cultivated apple. The SNPs were chosen by applying a focal points approach to enrich genic regions, but also to reach a uniform coverage of non-genic regions. A total of 1324 apple accessions, including the 92 progenies of two mapping populations, have been genotyped with the Axiom(®) Apple480K to assess the effectiveness of the array. A large majority of SNPs (359 994 or 74%) fell in the stringent class of poly high resolution polymorphisms. We also devised a filtering procedure to identify a subset of 275K very robust markers that can be safely used for germplasm surveys in apple. The Axiom(®) Apple480K has now been commercially released both for public and proprietary use and will likely be a reference tool for GWA studies in apple.
栽培苹果（Malus × domestica Borkh.）是温带地区最重要的水果作物之一，具有巨大的经济和文化价值。苹果基因组高度杂合，且最近经历了一次复制，再加上连锁不平衡快速衰减，使得进行全基因组关联（GWA）研究变得困难。单核苷酸多态性阵列能以相对较低的每个数据点成本提供高度多重的检测，并且可以成为识别与感兴趣性状相关标记的有效工具。在此，我们描述了一种用于苹果的487K SNP Affymetrix Axiom(®) 基因分型阵列的开发与验证，并讨论其潜在应用。该阵列基于对63个不同品种的高深度重测序构建而成，这些品种涵盖了栽培苹果的大部分遗传多样性。通过应用聚焦点方法选择单核苷酸多态性，以富集基因区域，同时也能实现非基因区域的均匀覆盖。共有1324份苹果种质，包括两个作图群体的92个后代，已使用Axiom(®) Apple480K进行基因分型，以评估该阵列的有效性。绝大多数单核苷酸多态性（359994个或74%）属于严格类别的多高分辨率多态性。我们还设计了一种筛选程序，以识别出275K个非常稳健的标记子集，这些标记可安全地用于苹果种质资源调查。Axiom(®) Apple480K现已商业发布，可供公共和专有使用，并且很可能成为苹果GWA研究的参考工具。
