Department of Biology, University of Florida, Gainesville, 32611, USA.
Mol Ecol. 2010 Mar;19 Suppl 1:132-46. doi: 10.1111/j.1365-294X.2009.04469.x.
Tragopogon miscellus (Asteraceae) is an evolutionary model for the study of natural allopolyploidy, but until now has been under-resourced as a genetic model. Using 454 and Illumina expressed sequence tag sequencing of the parental diploid species of T. miscellus, we identified 7782 single nucleotide polymorphisms that differ between the two progenitor genomes present in this allotetraploid. Validation of a sample of 98 of these SNPs in genomic DNA using Sequenom MassARRAY iPlex genotyping confirmed 92 SNP markers at the genomic level that were diagnostic for the two parental genomes. In a transcriptome profile of 2989 SNPs in a single T. miscellus leaf, using Illumina sequencing, 69% of SNPs showed approximately equal expression of both homeologs (duplicate homologous genes derived from different parents), 22% showed apparent differential expression and 8.5% showed apparent silencing of one homeolog in T. miscellus. The majority of cases of homeolog silencing involved the T. dubius SNP homeolog (164/254; 65%) rather than the T. pratensis homeolog (90/254). Sequenom analysis of genomic DNA showed that in a sample of 27 of the homeologs showing apparent silencing, 23 (85%) were because of genomic homeolog loss. These methods could be applied to any organism, allowing efficient and cost-effective generation of genetic markers.
小甘菊（菊科）是研究自然异源多倍体的进化模式生物，但作为遗传模式生物，其资源却相对匮乏。本研究利用 454 和 Illumina 测序技术对小甘菊的双亲二倍体进行表达序列标签测序，共鉴定出 7782 个在该异源四倍体中存在于两个亲本组之间的单核苷酸多态性（SNP）。通过 Sequenom MassARRAY iPlex 基因分型对这些 SNP 中的 98 个进行了验证，证实了在基因组水平上有 92 个 SNP 标记可以对两个亲本组进行诊断。在对单个小甘菊叶片中 2989 个 SNP 的转录组分析中，利用 Illumina 测序，69%的 SNP 显示两个同源基因（来自不同亲本的重复同源基因）的表达大致相等，22%的 SNP 显示明显的差异表达，8.5%的 SNP 显示小甘菊中一个同源基因的明显沉默。同源基因沉默的大多数情况涉及到 T. dubius SNP 同源基因（164/254；65%），而不是 T. pratensis 同源基因（90/254）。对基因组 DNA 的 Sequenom 分析表明，在 27 个表现出明显沉默的同源基因中，有 23 个（85%）是由于基因组同源基因丢失所致。这些方法可以应用于任何生物体，从而有效地、经济地产生遗传标记。
