Teagasc, Agriculture and Food Development Authority, Kinsealy Research Centre, Malahide Road, Dublin, D17, Ireland.
Biotechnol Biofuels. 2013 Aug 7;6(1):114. doi: 10.1186/1754-6834-6-114.
Little is known about the levels of variation in lignin or other wood related genes in Salix, a genus that is being increasingly used for biomass and biofuel production. The lignin biosynthesis pathway is well characterized in a number of species, including the model tree Populus. We aimed to transfer the genomic resources already available in Populus to its sister genus Salix to assess levels of variation within genes involved in wood formation.
Amplification trials for 27 gene regions were undertaken in 40 Salix taxa. Twelve of these regions were sequenced. Alignment searches of the resulting sequences against reference databases, combined with phylogenetic analyses, showed the close similarity of these Salix sequences to Populus, confirming homology of the primer regions and indicating a high level of conservation within the wood formation genes. However, all sequences were found to vary considerably among Salix species, mainly as SNPs with a smaller number of insertions-deletions. Between 25 and 176 SNPs per kbp per gene region (in predicted exons) were discovered within Salix.
The variation found is sizeable but not unexpected as it is based on interspecific and not intraspecific comparison; it is comparable to interspecific variation in Populus. The characterisation of genetic variation is a key process in pre-breeding and for the conservation and exploitation of genetic resources in Salix. This study characterises the variation in several lignocellulose gene markers for such purposes.
柳树属（Salix）的木质素或其他与木材相关的基因变异水平知之甚少，而该属正越来越多地被用于生物量和生物燃料生产。木质素生物合成途径在许多物种中都得到了很好的描述，包括模式树种杨树（Populus）。我们旨在将杨树中已有的基因组资源转移到其姐妹属柳树属，以评估参与木材形成的基因内的变异水平。
在 40 种柳树中进行了 27 个基因区域的扩增试验。其中 12 个区域进行了测序。对所得序列与参考数据库的比对搜索，结合系统发育分析，表明这些柳树序列与杨树非常相似，证实了引物区域的同源性，并表明木材形成基因具有高度的保守性。然而，所有序列在柳树种间差异很大，主要表现为 SNP，少数为插入-缺失。每个基因区域（预测外显子）内每个 kbp 有 25 到 176 个 SNP。
发现的变异是相当大的，但并不出人意料，因为它是基于种间而不是种内比较的；与杨树的种间变异相当。遗传变异的特征是柳树的预育种以及遗传资源的保护和利用的关键过程。本研究为这些目的对几个木质素纤维素基因标记的遗传变异进行了特征描述。
