Development and validation of the Axiom®Apple480K SNP genotyping array
Development and validation of the Axiom®Apple480K SNP genotyping array
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DOI：
10.1111/tpj.13145
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发表时间：
2016-04-01
期刊：
影响因子：
7.2
通讯作者：
Troggio, Michela
中科院分区：
文献类型：
--
作者：
Bianco, Luca;Cestaro, Alessandro;Troggio, Michela
栽培苹果（Malus x Aesthetica Borkh.）是温带地区最重要的水果作物之一，具有很高的经济和文化价值。苹果基因组是高度杂合的，最近经历了一次重复，加上快速的连锁不平衡衰减，使得很难进行全基因组关联（GWA）研究。单核苷酸多态性阵列以相对低的每个数据点的成本提供高度多路复用的测定，并且可以是用于鉴定与感兴趣的性状相关的标记物的有效工具。在这里，我们描述了苹果487K SNP Affyssin Axiom（R）基因分型阵列的开发和验证，并讨论了其潜在的应用。该阵列是从63个不同品种的高深度重测序中建立的，涵盖了栽培苹果的大部分遗传多样性。通过应用焦点方法来选择SNP以富集基因区域，但也达到非基因区域的均匀覆盖。用Axiom（R）Apple480K对包括两个作图群体的92个后代在内的总共1324个苹果种质进行了基因型分析，以评估阵列的有效性。绝大多数SNP（359994或74%）属于严格的多高分辨率多态性。我们还设计了一个过滤程序，以确定一个子集的275K非常强大的标记，可以安全地用于苹果种质资源调查。Axiom（R）Apple480K现已商业化发布，可供公众和专有使用，很可能成为苹果GWA研究的参考工具。
Cultivated apple (Malus x 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 (R) 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 (R) Apple480K to assess the effectiveness of the array. A large majority of SNPs (359994 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 (R) Apple480K has now been commercially released both for public and proprietary use and will likely be a reference tool for GWA studies in apple.