Abstract
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.
Highlights
Wild types of narrow-leafed lupin (Lupinus angustifolius L.) were grown in classical Greek and Roman times [1]
Based on the G = Knumber/peak depth model [31], the lupin genome size was estimated at 1.153 Gb
The genome size of L. angustifolius was estimated at 1.153 Gb, and the sequencing data obtained from the whole genome shotgun approach represented a 26.9X coverage of the lupin genome
Summary
Wild types of narrow-leafed lupin (Lupinus angustifolius L.) were grown in classical Greek and Roman times [1]. These genotypes were bitter (with the seed containing approximately 1.5% alkaloids), hard-seeded (seeds were impermeable to water and remained dormant after sowing), pods shattered at maturity, and were late-flowering. The first step in modern lupin breeding began in Europe with the selection of a natural, low alkaloid mutant by von Sengbusch [2]. Domestication of this plant species was completed in the 1960’s in Western Australia. Sweet lupin has the lowest glycemic index (GI) among commonly consumed grains
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