CSIRO Plant Industry, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia, QLD 4067, Australia.
BMC Genomics. 2014 Feb 24;15(1):152. doi: 10.1186/1471-2164-15-152.
Sugarcane genetic mapping has lagged behind other crops due to its complex autopolyploid genome structure. Modern sugarcane cultivars have from 110-120 chromosomes and are in general interspecific hybrids between two species with different basic chromosome numbers: Saccharum officinarum (2n = 80) with a basic chromosome number of 10 and S. spontaneum (2n = 40-128) with a basic chromosome number of 8. The first maps that were constructed utilised the single dose (SD) markers generated using RFLP, more recent maps generated using AFLP and SSRs provided at most 60% genome coverage. Diversity Array Technology (DArT) markers are high throughput allowing greater numbers of markers to be generated.
Progeny from a cross between a sugarcane variety Q165 and a S. officinarum accession IJ76-514 were used to generate 2467 SD markers. A genetic map of Q165 was generated containing 2267 markers, These markers formed 160 linkage groups (LGs) of which 147 could be placed using allelic information into the eight basic homology groups (HGs) of sugarcane. The HGs contained from 13 to 23 LGs and from 204 to 475 markers with a total map length of 9774.4 cM and an average density of one marker every 4.3 cM. Each homology group contained on average 280 markers of which 43% were DArT markers 31% AFLP, 16% SSRs and 6% SNP markers. The multi-allelic SSR and SNP markers were used to place the LGs into HGs.
The DArT array has allowed us to generate and map a larger number of markers than ever before and consequently to map a larger portion of the sugarcane genome. This larger number of markers has enabled 92% of the LGs to be placed into the 8 HGs that represent the basic chromosome number of the ancestral species, S. spontaneum. There were two HGs (HG2 and 8) that contained larger numbers of LGs verifying the alignment of two sets of S. officinarum chromosomes with one set of S. spontaneum chromosomes and explaining the difference in basic chromosome number between the two ancestral species. There was also evidence of more complex structural differences between the two ancestral species.
由于其复杂的同源多倍体基因组结构，甘蔗遗传图谱的构建一直落后于其他作物。现代甘蔗品种有 110-120 条染色体，通常是两种不同基本染色体数目的种间杂种：蔗属（2n=80），基本染色体数为 10；野蔗（2n=40-128），基本染色体数为 8。构建的第一张图谱利用 RFLP 生成的单剂量（SD）标记，最近利用 AFLP 和 SSR 生成的图谱提供了最多 60%的基因组覆盖。多样性数组技术（DArT）标记高通量允许生成更多数量的标记。
利用甘蔗品种 Q165 和 IJ76-514 的 S. officinarum 品系杂交产生的后代，生成了 2467 个 SD 标记。生成了 Q165 的遗传图谱，包含 2267 个标记，这些标记形成了 160 个连锁群（LG），其中 147 个可以利用等位基因信息放置在甘蔗的 8 个基本同源群（HG）中。HG 包含 13-23 个 LG 和 204-475 个标记，总图谱长度为 9774.4cM，平均密度为每 4.3cM 一个标记。每个同源群包含平均 280 个标记，其中 43%为 DArT 标记，31%为 AFLP，16%为 SSR，6%为 SNP 标记。多等位基因 SSR 和 SNP 标记用于将 LG 放置到 HG 中。
DArT 阵列使我们能够生成和映射比以往任何时候都多的标记，从而映射更大比例的甘蔗基因组。更多的标记使 92%的 LG 能够被放置到代表祖先物种野蔗基本染色体数的 8 个 HG 中。有两个 HG（HG2 和 8）包含更多的 LG，证实了两套 S. officinarum 染色体与一套 S. spontaneum 染色体的排列，并解释了两个祖先物种之间基本染色体数的差异。还存在两个祖先物种之间存在更复杂结构差异的证据。
