Department of Agriculture and Food Western Australia, South Perth, Australia.
PLoS One. 2013 May 29;8(5):e64799. doi: 10.1371/journal.pone.0064799. Print 2013.
Lupin (Lupinus angustifolius L.) is the most recently domesticated crop in major agricultural cultivation. Its seeds are high in protein and dietary fibre, but low in oil and starch. Medical and dietetic studies have shown that consuming lupin-enriched food has significant health benefits. We report the draft assembly from a whole genome shotgun sequencing dataset for this legume species with 26.9x coverage of the genome, which is predicted to contain 57,807 genes. Analysis of the annotated genes with metabolic pathways provided a partial understanding of some key features of lupin, such as the amino acid profile of storage proteins in seeds. Furthermore, we applied the NGS-based RAD-sequencing technology to obtain 8,244 sequence-defined markers for anchoring the genomic sequences. A total of 4,214 scaffolds from the genome sequence assembly were aligned into the genetic map. The combination of the draft assembly and a sequence-defined genetic map made it possible to locate and study functional genes of agronomic interest. The identification of co-segregating SNP markers, scaffold sequences and gene annotation facilitated the identification of a candidate R gene associated with resistance to the major lupin disease anthracnose. We demonstrated that the combination of medium-depth genome sequencing and a high-density genetic linkage map by application of NGS technology is a cost-effective approach to generating genome sequence data and a large number of molecular markers to study the genomics, genetics and functional genes of lupin, and to apply them to molecular plant breeding. This strategy does not require prior genome knowledge, which potentiates its application to a wide range of non-model species.
羽扇豆（ Lupinus angustifolius L. ）是最近在主要农业种植中驯化的作物。它的种子富含蛋白质和膳食纤维，但脂肪和淀粉含量低。医学和饮食学研究表明，食用富含羽扇豆的食物对健康有显著益处。我们报告了该豆科植物全基因组鸟枪法测序数据集的草案组装结果，基因组覆盖率为 26.9x，预计包含 57807 个基因。对注释基因与代谢途径的分析为了解羽扇豆的一些关键特征提供了部分认识，例如种子中贮藏蛋白的氨基酸组成。此外，我们应用基于 NGS 的 RAD 测序技术获得了 8244 个序列定义的标记，用于锚定基因组序列。从基因组序列组装中总共得到 4214 个支架，这些支架被排列到遗传图谱中。草案组装和序列定义的遗传图谱的结合使得定位和研究农艺性状相关的功能基因成为可能。共分离 SNP 标记、支架序列和基因注释的鉴定有助于鉴定与羽扇豆主要病害炭疽病抗性相关的候选 R 基因。我们证明了通过应用 NGS 技术进行中深度基因组测序和高密度遗传连锁图谱的结合是一种具有成本效益的方法，可以生成基因组序列数据和大量分子标记，用于研究羽扇豆的基因组学、遗传学和功能基因，并将其应用于分子植物育种。这种策略不需要事先了解基因组知识，这使其能够广泛应用于非模式物种。
