Nucleotide polymorphism and copy number variant detection using exome capture and next generation sequencing in the polyploid grass Panicum virgatum

Switchgrass (Panicum virgatum) is a polyploid, outcrossing grass species native to North America and has recently been recognized as a potential biofuel feedstock crop. Significant phenotypic variation including ploidy is present across the two primary ecotypes of switchgrass, referred to as upland and lowland switchgrass. The tetraploid switchgrass genome is approximately 1400 Mbp, split between two subgenomes, with significant repetitive sequence content limiting the efficiency of re-sequencing approaches for determining genome diversity. To characterize genetic diversity in upland and lowland switchgrass as a first step in linking genotype to phenotype, we designed an exome capture probe set based on transcript assemblies that represent ~50 Mb of annotated switchgrass exome sequences. We then evaluated and optimized the probe set using solid phase comparative genome hybridization and liquid phase exome capture followed by next generation sequencing. Using the optimized probe set, we ...柳枝稷（Switchgrass，*Panicum virgatum*）是原产于北美洲的多倍体异花授粉草本植物，近年来被认定为极具潜力的生物燃料原料作物。该物种的两个主要生态型——高地柳枝稷与低地柳枝稷间，存在包括倍性在内的显著表型变异。四倍体柳枝稷的基因组大小约为1400 Mbp，分为两个亚基因组，其较高的重复序列含量限制了重测序（re-sequencing）方法在解析基因组多样性时的应用效率。为表征高地与低地柳枝稷的遗传多样性，并作为连接基因型与表型关系的初步研究步骤，我们基于覆盖约50 Mb注释后外显子组序列的转录组组装结果，设计了一套外显子组捕获探针组（exome capture probe set）。随后我们通过固相比较基因组杂交（solid phase comparative genome hybridization）与液相外显子组捕获（liquid phase exome capture）结合下一代测序（next generation sequencing）的实验方案，对该探针组进行了评估与优化。利用该优化后的探针组，我们……