Development and validation of a 20K single nucleotide polymorphism (SNP) whole genome genotyping array for apple (Malus × domestica Borkh).
Development and validation of a 20K single nucleotide polymorphism (SNP) whole genome genotyping array for apple (Malus × domestica Borkh).
复制标题
DOI：
10.1371/journal.pone.0110377
复制
发表时间：
2014
期刊：
影响因子：
3.7
通讯作者：
Troggio M
中科院分区：
文献类型：
--
作者：
Bianco L;Cestaro A;Sargent DJ;Banchi E;Derdak S;Di Guardo M;Salvi S;Jansen J;Viola R;Gut I;Laurens F;Chagné D;Velasco R;van de Weg E;Troggio M
高密度SNP阵列用于全基因组等位基因变异的评估使得作物种质的高分辨率遗传表征成为可能。一个中密度的苹果芯片，IRSC 8 K SNP阵列，已成功地开发和用于双亲本群体的筛选。然而，由于连锁不平衡的快速衰减，该阵列上包含的稳健且分布良好的标记的数量不足以在更广泛的种质集中进行全基因组关联分析，或以高精度进行基于谱系的分析。我们描述了一个Illumina Infinium阵列靶向20 K SNP的发展。根据13个海棠品种和1个海棠品种的基因组重测序数据预测了SNP。微苹果属）。设计了用于SNP选择的管道，其避免了与包括旁系同源序列变体相关的陷阱，支持构建稳健的多等位基因SNP单倍体，并在±5 kb的狭窄基因组区域（称为焦点（FP））内选择多达11个条目。广泛的基因组覆盖率是通过将FP以1 cM的间隔放置在共有遗传图谱上，用FP补充它们以富集每条染色体的末端，以及通过桥接大于400 Kbps的物理间隔来实现的。该选择还包括来自IRSC 8 K阵列的3.7K验证的SNP。该阵列已被用于其他研究，其中每个全同胞家庭平均有15.8K SNP标记，每个全同胞家庭平均有16.8K SNP。新开发的阵列具有高密度的多态性验证SNP，预计将在基于谱系的分析和基因组选择中发挥重要作用。这也将是一个有价值的工具，以帮助剖析控制重要的果实品质性状的遗传机制，并帮助识别适合应用标记辅助选择在苹果育种计划的标记-性状协会。
High-density SNP arrays for genome-wide assessment of allelic variation have made high resolution genetic characterization of crop germplasm feasible. A medium density array for apple, the IRSC 8K SNP array, has been successfully developed and used for screens of bi-parental populations. However, the number of robust and well-distributed markers contained on this array was not sufficient to perform genome-wide association analyses in wider germplasm sets, or Pedigree-Based Analysis at high precision, because of rapid decay of linkage disequilibrium. We describe the development of an Illumina Infinium array targeting 20K SNPs. The SNPs were predicted from re-sequencing data derived from the genomes of 13 Malus × domestica apple cultivars and one accession belonging to a crab apple species (M. micromalus). A pipeline for SNP selection was devised that avoided the pitfalls associated with the inclusion of paralogous sequence variants, supported the construction of robust multi-allelic SNP haploblocks and selected up to 11 entries within narrow genomic regions of ±5 kb, termed focal points (FPs). Broad genome coverage was attained by placing FPs at 1 cM intervals on a consensus genetic map, complementing them with FPs to enrich the ends of each of the chromosomes, and by bridging physical intervals greater than 400 Kbps. The selection also included ∼3.7K validated SNPs from the IRSC 8K array. The array has already been used in other studies where ∼15.8K SNP markers were mapped with an average of ∼6.8K SNPs per full-sib family. The newly developed array with its high density of polymorphic validated SNPs is expected to be of great utility for Pedigree-Based Analysis and Genomic Selection. It will also be a valuable tool to help dissect the genetic mechanisms controlling important fruit quality traits, and to aid the identification of marker-trait associations suitable for the application of Marker Assisted Selection in apple breeding programs.
登录
查看更多内容
影响因子：
4.4
作者：
Kumar S;Garrick DJ;Bink MC;Whitworth C;Chagné D;Volz RK
通讯作者：
Volz RK
影响因子：
3.7
作者：
Baird NA;Etter PD;Atwood TS;Currey MC;Shiver AL;Lewis ZA;Selker EU;Cresko WA;Johnson EA
通讯作者：
Johnson EA
影响因子：
3.7
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
通讯作者：
Peace C
影响因子：
3.7
作者：
Derrien T;Estellé J;Marco Sola S;Knowles DG;Raineri E;Guigó R;Ribeca P
通讯作者：
Ribeca P
影响因子：
4.4
作者：
Chutimanitsakun Y;Nipper RW;Cuesta-Marcos A;Cistué L;Corey A;Filichkina T;Johnson EA;Hayes PM
通讯作者：
Hayes PM