Draft Genome Sequence, and a Sequence-Defined Genetic Linkage Map of the Legume Crop Species Lupinus angustifolius L

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.

Legume Crops Phylogeny and Genetic Diversity for Science and Breeding

“…Lupinus is the largest Genisteae genus, comprising 267 species, and appears to be monophyletic in origin (Ainouche and Bayer, 1999;Drummond et al, 2012). Chromosome numbers range between 2n = 24 to 2n = 52, and there are multiple lines of evidence showing that at least one polyploidy event has taken place since the divergence of Genisteae from other Papilionoid legumes (Wolko and Weeden, 1989;Gupta et al, 1996;Naganowska et al, 2003;Nelson et al, 2006;Parra-Gonzalez et al, 2012;Yang et al, 2013b;Kroc et al, 2014). The structural distinctiveness of Lupinus genomes from other Papilionoid genomes has been investigated by comparing genetic maps of L. angustifolius to the reference genome sequences of Medicago truncatula and Lotus japonicus Nelson et al, 2010) and by comparing the genetic map of L. albus to the genome of M. truncatula (Phan et al, 2007a).…”

“…Transcriptome sequencing has been reported for L. albus and L. luteus (Parra-Gonzalez et al, 2012;O'Rourke et al, 2013) and is underway for L. angustifolius and a range of New World lupin species. A reference genome sequence assembly for L. angustifolius is currently under construction , and a genome survey has been reported (Yang et al, 2013b). Genotyping-by-sequencing has been used to develop improved markers for anthracnose and phomopsis resistance in L. angustifolius Yang et al, 2013a).…”

Molecular Evolution and Functional Characterization of a Bifunctional Decarboxylase Involved in Lycopodium Alkaloid Biosynthesis

“…In addition, recent draft genome sequence studies on narrow-leafed lupin revealed the presence of a single LDC gene (Conant and Wolfe, 2008;Yang et al, 2013). As active copies of both ODC and LDC were not found in the same plant, divergence in the regulatory regions due to changes in the expression patterns of the LDC and ODC copies to reduce the dominant-negative effect might not have occurred during plant LDC evolution.…”

Evolution and structural diversification ofNictaba-like lectin genes in food crops with a focus on soybean (Glycine max)

“…It is the third largest family of flowering plants and includes several crops that are of high economic value as major protein sources for humans and animals. Moreover, the genome sequences of multiple members of the legume family are available, including Medicago truncatula (barrel clover), Cicer arietinum (chickpea), Lotus japonicus (Japanese trefoil), Glycine max (soybean), Cajanus cajan (pigeon pea), Phaseolus vulgaris (common bean), Vigna radiata (mung bean) and Lupinus angustifolius (lupin) (Sato et al, 2008;Schmutz et al, 2010Schmutz et al, , 2014Varshney et al, 2011Varshney et al, , 2013Young et al, 2011;Jain et al, 2013;Yang et al, 2013;Kang et al, 2014). Within the legume family, different polyploidy events have occurred.…”