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Abstract：
BACKGROUND: Molecular marker technologies are undergoing a transition from largely serial assays measuring DNA fragment sizes to hybridization-based technologies with high multiplexing levels. Diversity Arrays Technology (DArT) is a hybridization-based technology that is increasingly being adopted by barley researchers. There is a need to integrate the information generated by DArT with previous data produced with gel-based marker technologies. The goal of this study was to build a high-density consensus linkage map from the combined datasets of ten populations, most of which were simultaneously typed with DArT and Simple Sequence Repeat (SSR), Restriction Enzyme Fragment Polymorphism (RFLP) and/or Sequence Tagged Site (STS) markers.
RESULTS: The consensus map, built using a combination of JoinMap 3.0 software and several purpose-built perl scripts, comprised 2,935 loci (2,085 DArT, 850 other loci) and spanned 1,161 cM. It contained a total of 1,629 \'bins\' (unique loci), with an average inter-bin distance of 0.7 +/- 1.0 cM (median = 0.3 cM). More than 98% of the map could be covered with a single DArT assay. The arrangement of loci was very similar to, and almost as optimal as, the arrangement of loci in component maps built for individual populations. The locus order of a synthetic map derived from merging the component maps without considering the segregation data was only slightly inferior. The distribution of loci along chromosomes indicated centromeric suppression of recombination in all chromosomes except 5H. DArT markers appeared to have a moderate tendency toward hypomethylated, gene-rich regions in distal chromosome areas. On the average, 14 +/- 9 DArT loci were identified within 5 cM on either side of SSR, RFLP or STS loci previously identified as linked to agricultural traits.
CONCLUSIONS: Our barley consensus map provides a framework for transferring genetic information between different marker systems and for deploying DArT markers in molecular breeding schemes. The study also highlights the need for improved software for building consensus maps from high-density segregation data of multiple populations.
RESULTS: The consensus map, built using a combination of JoinMap 3.0 software and several purpose-built perl scripts, comprised 2,935 loci (2,085 DArT, 850 other loci) and spanned 1,161 cM. It contained a total of 1,629 \'bins\' (unique loci), with an average inter-bin distance of 0.7 +/- 1.0 cM (median = 0.3 cM). More than 98% of the map could be covered with a single DArT assay. The arrangement of loci was very similar to, and almost as optimal as, the arrangement of loci in component maps built for individual populations. The locus order of a synthetic map derived from merging the component maps without considering the segregation data was only slightly inferior. The distribution of loci along chromosomes indicated centromeric suppression of recombination in all chromosomes except 5H. DArT markers appeared to have a moderate tendency toward hypomethylated, gene-rich regions in distal chromosome areas. On the average, 14 +/- 9 DArT loci were identified within 5 cM on either side of SSR, RFLP or STS loci previously identified as linked to agricultural traits.
CONCLUSIONS: Our barley consensus map provides a framework for transferring genetic information between different marker systems and for deploying DArT markers in molecular breeding schemes. The study also highlights the need for improved software for building consensus maps from high-density segregation data of multiple populations.
摘要：
背景：分子标记技术正在经历从测量DNA片段大小的大量连续测定到具有高多重水平的基于杂交的技术的转变。多样性阵列技术（DArT）是一种基于杂交的技术，越来越多地被大麦研究人员采用。需要将由DArT产生的信息与用基于凝胶的标记技术产生的先前数据相结合。本研究的目标是从十个种群的组合数据集构建一个高密度的共识连锁图，其中大多数是用DArT和简单序列重复(SSR)同时键入的，限制性酶片段多态性(RFLP)和/或序列标记位点(STS)标记。
结果：共识图，使用JoinMap3.0软件和几个专门构建的perl脚本的组合构建，包含2,935个基因座（2,085DArT，850个其他基因座），跨度为1,161cM。它总共包含1,629个“垃圾箱”(独特的基因座)，平均箱间距离为0.7+/-1.0cM(中位数=0.3cM)。超过98%的图谱可以用单个DArT测定覆盖。基因座的排列非常相似，几乎和最佳一样，为单个种群构建的成分图中的基因座排列。通过合并分量图而不考虑分离数据得出的合成图的轨迹顺序仅稍差。沿染色体的基因座分布表明，除5H外，所有染色体中重组的着丝粒抑制。DArT标记似乎有适度的低甲基化趋势，远端染色体区域的基因丰富区域。平均而言,在SSR的任一侧的5cM内鉴定出14+/-9个DArT基因座，RFLP或STS基因座先前鉴定为与农业性状相关。
结论：我们的大麦共识图谱为在不同标记系统之间转移遗传信息和在分子育种方案中部署DArT标记提供了一个框架。该研究还强调了需要改进的软件来从多个种群的高密度隔离数据中构建共识图。
结果：共识图，使用JoinMap3.0软件和几个专门构建的perl脚本的组合构建，包含2,935个基因座（2,085DArT，850个其他基因座），跨度为1,161cM。它总共包含1,629个“垃圾箱”(独特的基因座)，平均箱间距离为0.7+/-1.0cM(中位数=0.3cM)。超过98%的图谱可以用单个DArT测定覆盖。基因座的排列非常相似，几乎和最佳一样，为单个种群构建的成分图中的基因座排列。通过合并分量图而不考虑分离数据得出的合成图的轨迹顺序仅稍差。沿染色体的基因座分布表明，除5H外，所有染色体中重组的着丝粒抑制。DArT标记似乎有适度的低甲基化趋势，远端染色体区域的基因丰富区域。平均而言,在SSR的任一侧的5cM内鉴定出14+/-9个DArT基因座，RFLP或STS基因座先前鉴定为与农业性状相关。
结论：我们的大麦共识图谱为在不同标记系统之间转移遗传信息和在分子育种方案中部署DArT标记提供了一个框架。该研究还强调了需要改进的软件来从多个种群的高密度隔离数据中构建共识图。
