Ogutcen Ezgi, Ramsay Larissa, von Wettberg Eric Bishop, Bett Kirstin E
Department of Plant Sciences University of Saskatchewan 51 Campus Drive Saskatoon Saskatchewan S7N 5A8 Canada.
Department of Plant and Soil Science University of Vermont 63 Carrigan Drive Burlington Vermont 05405 USA.
Appl Plant Sci. 2018 Jul 16;6(7):e01165. doi: 10.1002/aps3.1165. eCollection 2018 Jun.
Lentil is an important legume crop with reduced genetic diversity caused by domestication bottlenecks. Due to its large and complex genome, tools for reduced representation sequencing are needed. We developed an exome capture array for use in various genetic diversity studies.
Based on the CDC Redberry draft genome, we developed an exome capture array using multiple sources of transcript resources. The probes were designed to target not only the cultivated lentil, but also wild species. We assessed the utility of the developed method by applying the generated data set to population structure and phylogenetic analyses.
The data set includes 16 wild lentils and 22 cultivar accessions of lentil. Alignment rates were over 90%, and the genic regions were well represented in the capture array. After stringent filtering, 6.5 million high-quality variants were called, and the data set was used to assess the interspecific relationships within the genus .
The developed exome capture array provides large amounts of genomic data to be used in many downstream analyses. The method will have useful applications in marker-assisted breeding programs aiming to improve the quality of cultivated lentil.
小扁豆是一种重要的豆类作物，由于驯化瓶颈导致遗传多样性降低。由于其基因组庞大且复杂，需要用于简化基因组测序的工具。我们开发了一种外显子捕获阵列，用于各种遗传多样性研究。
基于CDC红莓草图基因组，我们利用多种转录本资源开发了一种外显子捕获阵列。探针不仅针对栽培小扁豆设计，也针对野生种。我们通过将生成的数据集应用于群体结构和系统发育分析来评估所开发方法的实用性。
该数据集包括16个野生小扁豆和22个小扁豆栽培品种。比对率超过90%，基因区域在捕获阵列中得到了很好的体现。经过严格筛选，共鉴定出650万个高质量变异，该数据集用于评估该属内的种间关系。
所开发的外显子捕获阵列提供了大量可用于许多下游分析的基因组数据。该方法将在旨在提高栽培小扁豆品质的标记辅助育种计划中具有有用的应用。
