Pavy Nathalie, Lamothe Manuel, Pelgas Betty, Gagnon France, Birol Inanç, Bohlmann Joerg, Mackay John, Isabel Nathalie, Bousquet Jean
Canada Research Chair in Forest Genomics, Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada.
Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du P.E.P.S., P.O. Box 10380, Stn. Sainte-Foy, Québec, QC, G1V 4C7, Canada.
Plant J. 2017 Apr;90(1):189-203. doi: 10.1111/tpj.13478. Epub 2017 Mar 6.
Over the last decade, extensive genetic and genomic resources have been developed for the conifer white spruce (Picea glauca, Pinaceae), which has one of the largest plant genomes (20 Gbp). Draft genome sequences of white spruce and other conifers have recently been produced, but dense genetic maps are needed to comprehend genome macrostructure, delineate regions involved in quantitative traits, complement functional genomic investigations, and assist the assembly of fragmented genomic sequences. A greatly expanded P. glauca composite linkage map was generated from a set of 1976 full-sib progeny, with the positioning of 8793 expressed genes. Regions with significant low or high gene density were identified. Gene family members tended to be mapped on the same chromosomes, with tandemly arrayed genes significantly biased towards specific functional classes. The map was integrated with transcriptome data surveyed across eight tissues. In total, 69 clusters of co-expressed and co-localising genes were identified. A high level of synteny was found with pine genetic maps, which should facilitate the transfer of structural information in the Pinaceae. Although the current white spruce genome sequence remains highly fragmented, dozens of scaffolds encompassing more than one mapped gene were identified. From these, the relationship between genetic and physical distances was examined and the genome-wide recombination rate was found to be much smaller than most estimates reported for angiosperm genomes. This gene linkage map shall assist the large-scale assembly of the next-generation white spruce genome sequence and provide a reference resource for the conifer genomics community.
在过去十年中，针对针叶树白云杉（Picea glauca，松科）开发了大量的遗传和基因组资源，白云杉拥有最大的植物基因组之一（20 Gbp）。最近已产生了白云杉和其他针叶树的基因组序列草图，但需要密集的遗传图谱来理解基因组宏观结构、描绘涉及数量性状的区域、补充功能基因组研究以及协助组装片段化的基因组序列。利用一组1976个全同胞后代构建了大幅扩展的白云杉复合连锁图谱，定位了8793个表达基因。识别出了基因密度显著低或高的区域。基因家族成员倾向于定位在相同的染色体上，串联排列的基因在特定功能类别上存在显著偏差。该图谱与在八个组织中调查的转录组数据进行了整合。总共识别出69个共表达和共定位基因的簇。发现与松树遗传图谱有高度的共线性，这应有助于松科植物结构信息的转移。尽管当前白云杉基因组序列仍然高度片段化，但已识别出数十个包含多个定位基因的支架。据此，研究了遗传距离与物理距离之间的关系，发现全基因组重组率远小于报道的大多数被子植物基因组的估计值。这一基因连锁图谱将有助于下一代白云杉基因组序列的大规模组装，并为针叶树基因组学界提供参考资源。
