Russell Joanne, Booth Allan, Fuller John, Harrower Brian, Hedley Peter, Machray Gordon, Powell Wayne
Scottish Crop Research Institute, Invergowrie, Dundee, Scotland, UK.
Genome. 2004 Apr;47(2):389-98. doi: 10.1139/g03-125.
Direct estimates of sequence diversity provides an abundant source of DNA polymorphisms based on single nucleotide polymorphisms (SNPs). The frequency and distribution of nucleotide diversity within 23 genes associated with grain germination in barley were determined in a sample of accessions representing European cultivars, landraces, and wild barley accessions from throughout the fertile crescent. The overall nucleotide diversity ranged from 0.0021 to 0.0189 with a single nucleotide change being detected every 78 bp and insertion-deletion events being observed every 680 bp. Within the cultivated (H. vulgare) genepool, a small number of haplotypes were detected, the total number of haplotypes observed in H. spontaneum was almost double that detected in H. vulgare (46 and 26, respectively). Distinct haplotypes were observed in the H. spontaneum and landrace genepools, which are highly divergent from H. vulgare. A comparison of SNP-based haplotype data with EST-derived SSRs and genomic SSRs revealed a similar trend of decreasing variability in the cultivated genepool. However, the number of unique alleles identified in the cultivated sample was much greater with genomic SSRs (18%) compared with only 2.1% for SNPs and 3.8% for EST-derived SSRs. The potential utility of SNPs and EST-derived SSRs for association mapping in barley is discussed.
基于单核苷酸多态性（SNP）对序列多样性的直接估计提供了丰富的DNA多态性来源。在一个代表欧洲栽培品种、地方品种以及来自整个新月沃地的野生大麦种质的样本中，测定了与大麦种子萌发相关的23个基因内核苷酸多样性的频率和分布。总体核苷酸多样性范围为0.0021至0.0189，每78个碱基对检测到一个单核苷酸变化，每680个碱基对观察到插入-缺失事件。在栽培的（H. vulgare）基因库中，检测到少数单倍型，在H. spontaneum中观察到的单倍型总数几乎是H. vulgare中检测到的两倍（分别为46个和26个）。在H. spontaneum和地方品种基因库中观察到了与H. vulgare高度不同的独特单倍型。将基于SNP的单倍型数据与EST衍生的SSR和基因组SSR进行比较，发现栽培基因库中变异性降低的趋势相似。然而，与SNP的2.1%和EST衍生的SSR的3.8%相比，栽培样本中通过基因组SSR鉴定出的独特等位基因数量要多得多（18%）。讨论了SNP和EST衍生的SSR在大麦关联作图中的潜在用途。
