Comparative Genomics Analyses Reveal Extensive Chromosome Colinearity and Novel Quantitative Trait Loci in Eucalyptus

Dense genetic maps, along with quantitative trait loci (QTLs) detected on such maps, are powerful tools for genomics and molecular breeding studies. In the important woody genus Eucalyptus, the recent release of E. grandis genome sequence allows for sequence-based genomic comparison and searching for positional candidate genes within QTL regions. Here, dense genetic maps were constructed for E. urophylla and E. tereticornis using genomic simple sequence repeats (SSR), expressed sequence tag (EST) derived SSR, EST-derived cleaved amplified polymorphic sequence (EST-CAPS), and diversity arrays technology (DArT) markers. The E. urophylla and E. tereticornis maps comprised 700 and 585 markers across 11 linkage groups, totaling at 1,208.2 and 1,241.4 cM in length, respectively. Extensive synteny and colinearity were observed as compared to three earlier DArT-based eucalypt maps (two maps with E. grandis × E. urophylla and one map of E. globulus) and with the E. grandis genome sequence. Fifty-three QTLs for growth (10–56 months of age) and wood density (56 months) were identified in 22 discrete regions on both maps, in which only one colocalizaiton was found between growth and wood density. Novel QTLs were revealed as compared with those previously detected on DArT-based maps for similar ages in Eucalyptus. Eleven to 585 positional candidate genes were obained for a 56-month-old QTL through aligning QTL confidence interval with the E. grandis genome. These results will assist in comparative genomics studies, targeted gene characterization, and marker-assisted selection in Eucalyptus and the related taxa.

高密度遗传图谱以及在其上定位的数量性状位点（quantitative trait loci, QTLs），是基因组学与分子育种研究的重要工具。在重要木本植物属桉属（Eucalyptus）中，近期公布的巨桉（E. grandis）基因组序列，为开展基于序列的基因组比较分析以及在QTL区域内搜寻定位候选基因提供了条件。本研究利用基因组简单序列重复（simple sequence repeats, SSR）、表达序列标签衍生SSR（expressed sequence tag derived SSR, EST-SSR）、表达序列标签衍生酶切扩增多态性序列（EST-derived cleaved amplified polymorphic sequence, EST-CAPS）以及多样性芯片技术（diversity arrays technology, DArT）标记，构建了尾叶桉（E. urophylla）与细叶桉（E. tereticornis）的高密度遗传图谱。尾叶桉与细叶桉的遗传图谱分别覆盖11个连锁群，包含700个与585个标记，总图距分别为1208.2与1241.4厘摩（cM）。通过与3份早期基于DArT标记的桉属遗传图谱（2份为巨桉×尾叶桉杂交群体图谱，1份为蓝桉（E. globulus）图谱）以及巨桉基因组序列进行比较分析，本研究观察到广泛的同线性与共线性现象。在两张图谱的22个独立区域内，共鉴定出53个与生长性状（树龄10~56个月）及木材密度（树龄56个月）相关的QTLs，其中仅发现1个生长性状与木材密度QTL的共定位位点。相较于此前基于DArT标记、针对相近树龄桉属材料定位的QTL结果，本研究发现了全新的QTL位点。通过将QTL置信区间与巨桉基因组进行序列比对，为56个月树龄的QTL位点获取了11至585个定位候选基因。上述研究结果将助力桉属及其近缘类群的比较基因组学研究、目标基因功能鉴定以及标记辅助选择育种工作。