Rostoks Nils, Mudie Sharon, Cardle Linda, Russell Joanne, Ramsay Luke, Booth Allan, Svensson Jan T, Wanamaker Steve I, Walia Harkamal, Rodriguez Edmundo M, Hedley Peter E, Liu Hui, Morris Jenny, Close Timothy J, Marshall David F, Waugh Robbie
Genome Dynamics, Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA, UK.
Mol Genet Genomics. 2005 Dec;274(5):515-27. doi: 10.1007/s00438-005-0046-z. Epub 2005 Oct 22.
More than 2,000 genome-wide barley single nucleotide polymorphisms (SNPs) were developed by resequencing unigene fragments from eight diverse accessions. The average genome-wide SNP frequency observed in 877 unigenes was 1 SNP per 200 bp. However, SNP frequency was highly variable with the least number of SNP and SNP haplotypes observed within European cultivated germplasm reflecting effects of breeding history on genetic diversity. More than 300 SNP loci were mapped genetically in three experimental mapping populations which allowed the construction of an integrated SNP map incorporating a large number of RFLP, AFLP and SSR markers (1,237 loci in total). The genes used for SNP discovery were selected based on their transcriptional response to a variety of abiotic stresses. A set of known barley abiotic stress QTL was positioned on the linkage map, while the available sequence and gene expression information facilitated the identification of genes potentially associated with these traits. Comparison of the sequenced SNP loci to the rice genome sequence identified several regions of highly conserved gene order providing a framework for marker saturation in barley genomic regions of interest. The integration of genome-wide SNP and expression data with available genetic and phenotypic information will facilitate the identification of gene function in barley and other non-model organisms.
通过对八个不同种质的单基因片段进行重测序，开发出了2000多个全基因组大麦单核苷酸多态性（SNP）。在877个单基因中观察到的全基因组平均SNP频率为每200 bp 1个SNP。然而，SNP频率变化很大，在欧洲栽培种质中观察到的SNP和SNP单倍型数量最少，这反映了育种历史对遗传多样性的影响。在三个实验性作图群体中对300多个SNP位点进行了遗传定位，从而构建了一个整合的SNP图谱，该图谱包含大量的RFLP、AFLP和SSR标记（总共1237个位点）。用于SNP发现的基因是根据它们对各种非生物胁迫的转录反应来选择的。一组已知的大麦非生物胁迫QTL被定位在连锁图谱上，同时可用的序列和基因表达信息有助于鉴定可能与这些性状相关的基因。将测序的SNP位点与水稻基因组序列进行比较，确定了几个基因顺序高度保守的区域，为感兴趣的大麦基因组区域的标记饱和提供了一个框架。将全基因组SNP和表达数据与可用的遗传和表型信息整合起来，将有助于鉴定大麦和其他非模式生物中的基因功能。
