Department of Biology, Life Sciences Centre, Dalhousie University, Halifax, Canada.
BMC Genomics. 2010 Sep 24;11:515. doi: 10.1186/1471-2164-11-515.
Genetic maps provide an important genomic resource for understanding genome organization and evolution, comparative genomics, mapping genes and quantitative trait loci, and associating genomic segments with phenotypic traits. Spruce (Picea) genomics work is quite challenging, mainly because of extremely large size and highly repetitive nature of its genome, unsequenced and poorly understood genome, and the general lack of advanced-generation pedigrees. Our goal was to construct a high-density genetic linkage map of black spruce (Picea mariana, 2n = 24), which is a predominant, transcontinental species of the North American boreal and temperate forests, with high ecological and economic importance.
We have developed a near-saturated and complete genetic linkage map of black spruce using a three-generation outbred pedigree and amplified fragment length polymorphism (AFLP), selectively amplified microsatellite polymorphic loci (SAMPL), expressed sequence tag polymorphism (ESTP), and microsatellite (mostly cDNA based) markers. Maternal, paternal, and consensus genetic linkage maps were constructed. The maternal, paternal, and consensus maps in our study consistently coalesced into 12 linkage groups, corresponding to the haploid chromosome number (1n = 1x = 12) of 12 in the genus Picea. The maternal map had 816 and the paternal map 743 markers distributed over 12 linkage groups each. The consensus map consisted of 1,111 markers distributed over 12 linkage groups, and covered almost the entire (> 97%) black spruce genome. The mapped markers included 809 AFLPs, 255 SAMPL, 42 microsatellites, and 5 ESTPs. Total estimated length of the genetic map was 1,770 cM, with an average of one marker every 1.6 cM. The maternal, paternal and consensus genetic maps aligned almost perfectly.
We have constructed the first high density to near-saturated genetic linkage map of black spruce, with greater than 97% genome coverage. Also, this is the first genetic map based on a three-generation outbred pedigree in the genus Picea. The genome length in P. mariana is likely to be about 1,800 cM. The genetic maps developed in our study can serve as a reference map for various genomics studies and applications in Picea and Pinaceae.
遗传图谱为理解基因组组织和进化、比较基因组学、基因和数量性状位点作图以及将基因组片段与表型特征相关联提供了重要的基因组资源。云杉（Picea）基因组学工作极具挑战性，主要是因为其基因组的大小极其庞大且高度重复，基因组未测序且理解不足，以及普遍缺乏高级世代系谱。我们的目标是构建黑云杉（Picea mariana，2n = 24）的高密度遗传连锁图谱，黑云杉是北美北方和温带森林中主要的、跨大陆的物种，具有很高的生态和经济重要性。
我们使用三世代杂交家系和扩增片段长度多态性（AFLP）、选择性扩增微卫星多态性位点（SAMPL）、表达序列标签多态性（ESTP）和微卫星（主要基于 cDNA）标记，开发了黑云杉的近饱和和完整遗传连锁图谱。构建了母系、父系和共识遗传连锁图谱。本研究中的母系、父系和共识遗传图谱一致凝聚为 12 个连锁群，与 12 个倍性（1n = 1x = 12）的属 Picea 的单倍体染色体数相对应。母系图谱和父系图谱各有 816 个和 743 个标记分布在 12 个连锁群中。共识图谱由 1111 个标记组成，分布在 12 个连锁群中，覆盖了黑云杉基因组的近 97%。图谱标记包括 809 个 AFLP、255 个 SAMPL、42 个微卫星和 5 个 ESTP。遗传图谱的总估计长度为 1770cM，平均每个标记 1.6cM。母系、父系和共识遗传图谱几乎完全吻合。
我们构建了第一个黑云杉高密度至近饱和遗传连锁图谱，基因组覆盖率大于 97%。此外，这是云杉属中第一个基于三世代杂交家系的遗传图谱。P. mariana 的基因组长度可能约为 1800cM。我们研究中开发的遗传图谱可以作为 Picea 和松科基因组学研究和应用的参考图谱。
