Genome-wide SNP detection, validation, and development of an 8K SNP array for apple.
Genome-wide SNP detection, validation, and development of an 8K SNP array for apple.
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DOI：
10.1371/journal.pone.0031745
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Peace C
中科院分区：
文献类型：
--
作者：
Chagné D;Crowhurst RN;Troggio M;Davey MW;Gilmore B;Lawley C;Vanderzande S;Hellens RP;Kumar S;Cestaro A;Velasco R;Main D;Rees JD;Iezzoni A;Mockler T;Wilhelm L;Van de Weg E;Gardiner SE;Bassil N;Peace C
由于高通量遗传标记筛选系统是一系列遗传学研究和植物育种应用的关键，国际RosBREED SNP联合会(IRSC)利用Illumina Infinium®II系统开发了一种中高通量SNP筛选工具，用于对苹果(Malus×home tica)育种种质的等位基因变异进行全基因组范围的评估。为了在全基因组范围内发现SNP，选择了27个苹果品种作为世界范围内的育种种质，并用Illumina Genome Analyzer II在低覆盖率下进行了重新测序。将这些序列与‘金冠’全基因组序列进行比对后，利用SoapSNP对SNP进行了鉴定。共检测到2,113,120个SNP，相当于基因组每288个碱基对应一个SNP。然后使用Illumina GoldenGate®分析来验证具有一系列特征的144个SNPs的子集，使用了一组160个苹果材料。这项验证测试使Illumina Infinium®II系统的SNPs最终子集得以微调。制定了一套严格的筛选标准，允许选择一组SNPs，这些SNPs不仅在苹果基因组中表现出均匀的分布和一系列次要等位基因频率，以确保在种质中的有效性，而且还位于假定的外显子区域，以最大限度地提高基因分型成功率。对IRSC苹果8K SNP阵列v1共构建了7867个SNP，其中5554个SNP在分离家系和种质资源中表现为多态。这一公开可用的基因组学资源将提供史无前例的SNP单倍型解析，这将使标记-座位-性状关联发现、数量性状遗传结构描述、遗传变异(中性和功能性)研究以及基因组选择成为可能。
As high-throughput genetic marker screening systems are essential for a range of genetics studies and plant breeding applications, the International RosBREED SNP Consortium (IRSC) has utilized the Illumina Infinium® II system to develop a medium- to high-throughput SNP screening tool for genome-wide evaluation of allelic variation in apple (Malus×domestica) breeding germplasm. For genome-wide SNP discovery, 27 apple cultivars were chosen to represent worldwide breeding germplasm and re-sequenced at low coverage with the Illumina Genome Analyzer II. Following alignment of these sequences to the whole genome sequence of ‘Golden Delicious’, SNPs were identified using SoapSNP. A total of 2,113,120 SNPs were detected, corresponding to one SNP to every 288 bp of the genome. The Illumina GoldenGate® assay was then used to validate a subset of 144 SNPs with a range of characteristics, using a set of 160 apple accessions. This validation assay enabled fine-tuning of the final subset of SNPs for the Illumina Infinium® II system. The set of stringent filtering criteria developed allowed choice of a set of SNPs that not only exhibited an even distribution across the apple genome and a range of minor allele frequencies to ensure utility across germplasm, but also were located in putative exonic regions to maximize genotyping success rate. A total of 7867 apple SNPs was established for the IRSC apple 8K SNP array v1, of which 5554 were polymorphic after evaluation in segregating families and a germplasm collection. This publicly available genomics resource will provide an unprecedented resolution of SNP haplotypes, which will enable marker-locus-trait association discovery, description of the genetic architecture of quantitative traits, investigation of genetic variation (neutral and functional), and genomic selection in apple.
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DOI：
10.1111/j.1365-313x.2006.02964.x
发表时间：
2007-02
期刊：
The Plant journal : for cell and molecular biology
影响因子：
--
作者：
Espley RV;Hellens RP;Putterill J;Stevenson DE;Kutty-Amma S;Allan AC
通讯作者：
Allan AC
影响因子：
3.4
作者：
Illa E;Sargent DJ;Lopez Girona E;Bushakra J;Cestaro A;Crowhurst R;Pindo M;Cabrera A;van der Knaap E;Iezzoni A;Gardiner S;Velasco R;Arús P;Chagné D;Troggio M
通讯作者：
Troggio M
影响因子：
3.7
作者：
Myles S;Chia JM;Hurwitz B;Simon C;Zhong GY;Buckler E;Ware D
通讯作者：
Ware D
影响因子：
5.4
作者：
Maliepaard, C;Alston, FH;King, GJ
通讯作者：
King, GJ
影响因子：
4.4
作者：
Chagne, David;Gasic, Ksenija;Korban, Schuyler S.
通讯作者：
Korban, Schuyler S.