High Density Rice Array (HDRA6.4) developed by the McCouch-Rice Lab at Cornell University. Oryza sativa

A High Density Rice Array (HDRA) was developed as an Affymetrix Custom GeneChip Array by the McCouch Rice Lab at Cornell University. The HDRA assays 700,000 SNPs, or approximately one SNP every 0.54 Kb across the rice genome (genome size = 380 Mb). It was designed to capture most of the haplotype variation observed in a discovery panel consisting of 16M SNPs (generated by sequencing 125 rice genomes at ~7X genome coverage) and to maximize the inclusion of non-synonymous SNPs. Six probes per SNP target were designed as 3 A-allele and 3 B-allele probes at offsets from center ranging from -6 to +6. A small fraction of SNPs have only 4 probes (2-A, 2-B). For all SNPs, the “A” allele is the reference allele (Os-Nipponbare-Reference-IRGSP-1.0 assembly). Additionally, we designed 23,656 x 25-bp probes complimentary to invariant regions of the genome that were used to normalize systematic differences between samples. An estimated 45% of HDRA SNPs map within genes, hitting all 39,045 unique, non-TE rice gene models (MSUv7 rice genome annotation, GFF3 file, Feb. 7, 2012, http://rice.plantbiology.msu.edu/), while 55% of SNPs map to intergenic regions. Non-synonymous are found in 91% of unique, non-TE gene models, and 57% of genic SNPs are distributed within exons, 36% within introns, 5% within 5’ UTRs and 2% within 3’ UTRs. Of the intergenic SNPs, 40% are located in putative regulatory regions within 2 Kb of a transcriptional start site. Overall design: Using the HDRA, SNP variation was assayed in a collection of 1,568 diverse O. stiva accessions and the resulting genotypic dataset was analyzed for population structure and used for Genome Wide Association Studies (GWAS).

康奈尔大学McCouch水稻实验室开发了一款Affymetrix定制基因芯片，即高密度水稻基因芯片（High Density Rice Array, HDRA）。该HDRA可检测70万个单核苷酸多态性（Single Nucleotide Polymorphism, SNP），在水稻基因组（基因组大小为380 Mb）上平均每0.54 Kb即存在1个SNP。该芯片的设计初衷是覆盖由16M个SNP构成的发现集（该发现集通过对125份水稻基因组进行~7倍基因组覆盖度测序获得）中观测到的绝大多数单倍型变异，并最大化纳入非同义单核苷酸多态性。每个SNP靶标设计了6条探针，其中3条为A等位基因探针、3条为B等位基因探针，探针相对于靶标中心的偏移范围为-6至+6；小部分SNP仅配有4条探针（2条A等位、2条B等位）。所有SNP的“A”等位基因为参考等位基因，对应Os-Nipponbare参考基因组IRGSP-1.0组装版本。此外，研究团队还设计了23656条25 bp长度的探针，用于与基因组的保守区域互补结合，以标准化不同样本间的系统差异。据估算，45%的HDRA检测SNP可定位至基因区域，覆盖了MSUv7水稻基因组注释（GFF3格式文件，2012年2月7日发布，来源：http://rice.plantbiology.msu.edu/）中全部39045个非转座因子（Transposable Element, TE）的独特非TE水稻基因模型；剩余55%的SNP定位于基因间区。91%的独特非TE基因模型中存在非同义SNP；基因区内的SNP中，57%分布于外显子区域、36%分布于内含子区域、5%分布于5'非翻译区（5' Untranslated Region, 5' UTR）、2%分布于3'非翻译区（3' Untranslated Region, 3' UTR）。对于基因间区的SNP，40%位于转录起始位点上下游2 Kb范围内的推定调控区域。整体实验设计方案为：使用HDRA对1568份多样性丰富的O. stiva种质资源进行SNP变异检测，对获得的基因型数据集进行群体结构分析，并用于全基因组关联研究（Genome-Wide Association Study, GWAS）。