Staton Margaret, Zhebentyayeva Tetyana, Olukolu Bode, Fang Guang Chen, Nelson Dana, Carlson John E, Abbott Albert G
Department of Entomology and Plant Pathology, University of Tennessee Institute of Agriculture, Knoxville, TN, USA.
Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA.
BMC Genomics. 2015 Oct 5;16:744. doi: 10.1186/s12864-015-1942-1.
Chinese chestnut (Castanea mollissima) has emerged as a model species for the Fagaceae family with extensive genomic resources including a physical map, a dense genetic map and quantitative trait loci (QTLs) for chestnut blight resistance. These resources enable comparative genomics analyses relative to model plants. We assessed the degree of conservation between the chestnut genome and other well annotated and assembled plant genomic sequences, focusing on the QTL regions of most interest to the chestnut breeding community.
The integrated physical and genetic map of Chinese chestnut has been improved to now include 858 shared sequence-based markers. The utility of the integrated map has also been improved through the addition of 42,970 BAC (bacterial artificial chromosome) end sequences spanning over 26 million bases of the estimated 800 Mb chestnut genome. Synteny between chestnut and ten model plant species was conducted on a macro-syntenic scale using sequences from both individual probes and BAC end sequences across the chestnut physical map. Blocks of synteny with chestnut were found in all ten reference species, with the percent of the chestnut physical map that could be aligned ranging from 10 to 39 %. The integrated genetic and physical map was utilized to identify BACs that spanned the three previously identified QTL regions conferring blight resistance. The clones were pooled and sequenced, yielding 396 sequence scaffolds covering 13.9 Mbp. Comparative genomic analysis on a microsytenic scale, using the QTL-associated genomic sequence, identified synteny from chestnut to other plant genomes ranging from 5.4 to 12.9 % of the genome sequences aligning.
On both the macro- and micro-synteny levels, the peach, grape and poplar genomes were found to be the most structurally conserved with chestnut. Interestingly, these results did not strictly follow the expectation that decreased phylogenetic distance would correspond to increased levels of genome preservation, but rather suggest the additional influence of life-history traits on preservation of synteny. The regions of synteny that were detected provide an important tool for defining and cataloging genes in the QTL regions for advancing chestnut blight resistance research.
中国板栗（Castanea mollissima）已成为壳斗科的模式物种，拥有丰富的基因组资源，包括物理图谱、高密度遗传图谱以及抗栗疫病的数量性状位点（QTL）。这些资源使得与模式植物进行比较基因组学分析成为可能。我们评估了板栗基因组与其他注释完善且组装好的植物基因组序列之间的保守程度，重点关注板栗育种群体最感兴趣的QTL区域。
中国板栗的综合物理图谱和遗传图谱得到了改进，目前包含858个基于共享序列的标记。通过添加42,970个细菌人工染色体（BAC）末端序列，综合图谱的实用性也得到了提高，这些序列跨越了估计800 Mb板栗基因组中超过2600万个碱基。利用来自单个探针的序列以及跨越板栗物理图谱的BAC末端序列，在宏观共线性尺度上对板栗与十种模式植物物种进行了共线性分析。在所有十种参考物种中都发现了与板栗的共线性块，可比对的板栗物理图谱百分比范围为10%至39%。利用综合遗传图谱和物理图谱来鉴定跨越先前确定的三个赋予抗疫病能力的QTL区域的BAC。将这些克隆汇集并测序，产生了396个序列支架，覆盖1390万碱基对。使用与QTL相关的基因组序列在微观共线性尺度上进行比较基因组分析，确定从板栗到其他植物基因组的共线性范围为比对的基因组序列的5.4%至12.9%。
在宏观和微观共线性水平上，发现桃、葡萄和杨树的基因组与板栗在结构上最为保守。有趣的是，这些结果并未严格遵循系统发育距离减小会对应基因组保存水平提高的预期，而是表明生活史特征对共线性保存有额外影响。检测到的共线性区域为在QTL区域定义和编目基因提供了重要工具，以推进栗疫病抗性研究。
