New evidence of ancestral polyploidy in the Genistoid legume Lupinus angustifolius L. (narrow-leafed lupin)

Abstract

This is the first clear evidence of duplication and/or triplication of large chromosomal regions in a genome of a Genistoid legume, the most basal clade of Papilionoid legumes. Lupinus angustifolius L. (narrow-leafed lupin) is the most widely cultivated species of Genistoid legume, grown for its high-protein grain. As a member of this most basal clade of Papilionoid legumes, L. angustifolius serves as a useful model for exploring legume genome evolution. Here, we report an improved reference genetic map of L. angustifolius comprising 1207 loci, including 299 newly developed Diversity Arrays Technology markers and 54 new gene-based PCR markers. A comparison between the L. angustifolius and Medicago truncatula genomes was performed using 394 sequence-tagged site markers acting as bridging points between the two genomes. The improved L. angustifolius genetic map, the updated M. truncatula genome assembly and the increased number of bridging points between the genomes together substantially enhanced the resolution of synteny and chromosomal colinearity between these genomes compared to previous reports. While a high degree of syntenic fragmentation was observed that was consistent with the large evolutionary distance between the L. angustifolius and M. truncatula genomes, there were striking examples of conserved colinearity of loci between these genomes. Compelling evidence was found of large-scale duplication and/or triplication in the L. angustifolius genome, consistent with one or more ancestral polyploidy events.

The western Mediterranean region provided the founder population of domesticated narrow-leafed lupin

“…DArTseq reads were aligned with the Tanjil reference genome using the nucmer aligner (Delcher et al 1999), setting the minimum cluster length (-c) to 25 bp and ≤ 3 matches. The latter threshold was selected to take account of the remnants of whole-genome triplication in the genome of narrow-leafed lupin (Hane et al 2017; Kroc et al 2014). Then, the positions of SNPs relative to the Tanjil reference genome were determined from SNP positions on the DArTseq reads and the reads’ match position on the reference, summarised in variant call format (VCF) relative to the lupin reference genome (Hane et al 2017).…”

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).…”

Grain Legumes

“…Narrow-leafed lupin, as the most popular lupin crop, is characterized with rich molecular achievements including draft genome sequence (Yang et al 2013b) and well-saturated genetic maps (Nelson et al 2006(Nelson et al , 2010Kroc et al 2014;Yang et al 2013b). In that species, the microsatellite-anchored fragment length polymorphism (MFLP) technique plays a pivotal role in selection marker development (Yang et al 2001).…”