Development, Management and Use of a SNP Map for Rhesus Macaque

描述(申请人提供)：我们将使用最近完成的恒河猴基因组图谱，识别随机分布在恒河猴(Macaca Mulatta)基因组中的大约83,333个单核苷酸多态(SNP)。我们将对来自7个不同地区群体的混合(n=25)DNA样本构建的简化表示文库(RRL)中每个DNA片段的至少10个副本进行测序，然后过滤、解析并与恒河猴草稿序列进行比较，并使用我们之前开发的生物信息学工具来确定83,333个SNP的位置、侧翼序列和次要等位基因频率(MAF)。Iliumina iSelect芯片上的基因分型分析将对印度猕猴和中国恒河猴之间频率差异最大的7600个SNP进行分析，并对192只印度恒河猴和192只中国恒河猴以及678只印度/中国恒河猴的不同比例的印度和中国血统的样本进行基因分型。7,600个SNPs的基因型别将被用来1)确认多世代家庭中SNPs的孟德尔分离，2)评估SNPs在印度/中国杂交种和家系动物中准确估计印度和中国血统的比例的能力，3)寻找祖先信息标记用于QTL的混合定位和进行“气质”的QTL混合定位。我们的SNP地图将通过包括数据库SNP在内的几个渠道公开提供。在长尾猕猴的83,333个SNP中，最有可能提供信息的384个SNP将在6个不同的长尾猕猴种群的96个样本中进行基因分型，以确定每个SNP的最少96个小组，每个小组用于识别原籍国、亲子关系分析和对遗传管理有用的评估参数。化验将由这两块板构建，并提供给NIH调查人员，以提供成本回收。上述SNPs基因分型将用于恒河猴和长尾猕猴区域种群的基因组和种群结构分析。

DESCRIPTION (provided by applicant): We will use the recently completed rhesus macaque genome map, to identify approximately 83,333 single nucleotide polymorphisms (SNPs) randomly distributed throughout the rhesus macaque (Macaca mulatta) genome. At least ten copies of each DNA fragments in reduced representation libraries (RRLs) constructed from pooled (n=25)DNA samples from 7 different regional populations will be sequenced, then filtered, parsed and compared to the rhesus macaque draft sequence and to each other using bioinformatics tools we previously developed to identify the locations, flanking sequences and minor allele frequencies (MAFs) of 83,333 SNPs. Genotyping assays on lliumina iSelect chips will be constructed for the 7,600 SNPs whose frequencies differ most between Indian and Chinese rhesus macaques and genotyped in geographically representative samples of 192 Indian rhesus macaques, and192 Chinese rhesus macaques and in 678 Indian/Chines rhesus macaques with varying proportions of Indian and Chinese ancestry. Genotypes for the 7,600 SNPs will be used to 1) confirm Mendelian segregation of SNPs in multigeneration families, 2) assess the ability of the SNPs to accurately estimate proportions of Indian and Chinese ancestry in Indian/Chinese hybrid, pedigreed animals and 3) identify ancestry informative markers for admixture mapping of QTLs and to conduct admixture mapping of a QTL for "temperament.". Our SNP map will be made publically available through several outlets including dbSNP. The 384 most potentially informative of the 83,333 SNPs for longtail macaques will be genotyped in 96 samples from six different longtail macaque populations to identify minimum panels of 96 SNPs each for identifying country of origin and for parentage analysis and estiinating parameters useful for genetic management. Assays will be constructed of these two panels and made available to NIH investigators, providing cost recovery. The genotypes of SNPs described above will be used for genomic and population structure analyses of regional populations of rhesus and longtail macaques.