Integration of Lupinus angustifolius L. (narrow-leafed lupin) genome maps and comparative mapping within legumes

Abstract

Narrow-leafed lupin (Lupinus angustifolius L.) has recently been considered a reference genome for the Lupinus genus. In the present work, genetic and cytogenetic maps of L. angustifolius were supplemented with 30 new molecular markers representing lupin genome regions, harboring genes involved in nitrogen fixation during the symbiotic interaction of legumes and soil bacteria (Rhizobiaceae). Our studies resulted in the precise localization of bacterial artificial chromosomes (BACs) carrying sequence variants for early nodulin 40, nodulin 26, nodulin 45, aspartate aminotransferase P2, asparagine synthetase, cytosolic glutamine synthetase, and phosphoenolpyruvate carboxylase. Together with previously mapped chromosomes, the integrated L. angustifolius map encompasses 73 chromosome markers, including 5S ribosomal DNA (rDNA) and 45S rDNA, and anchors 20 L. angustifolius linkage groups to corresponding chromosomes. Chromosomal identification using BAC fluorescence in situ hybridization identified two BAC clones as narrow-leafed lupin centromere-specific markers, which served as templates for preliminary studies of centromere composition within the genus. Bioinformatic analysis of these two BACs revealed that centromeric/pericentromeric regions of narrow-leafed lupin chromosomes consisted of simple sequence repeats ordered into tandem repeats containing the trinucleotide and pentanucleotide simple sequence repeats AGG and GATAC, structured into long arrays. Moreover, cross-genus microsynteny analysis revealed syntenic patterns of 31 single-locus BAC clones among several legume species. The gene and chromosome level findings provide evidence of ancient duplication events that must have occurred very early in the divergence of papilionoid lineages. This work provides a strong foundation for future comparative mapping among legumes and may facilitate understanding of mechanisms involved in shaping legume chromosomes.Electronic supplementary materialThe online version of this article (doi:10.1007/s10577-016-9526-8) contains supplementary material, which is available to authorized users.

Validation of Diaporthe toxica resistance markers in European Lupinus angustifolius germplasm and identification of novel resistance donors for marker-assisted selection

“…Highdensity linkage maps carrying thousands of markers, including gene-based sequence tagged sites (STS), were constructed and aligned to the draft genome sequence (Hane et al 2017;Kamphuis et al 2015;Nelson et al 2006;Yang et al 2013b). Exploitation of BAC resources for cytogenetic mapping resulted in the integration of all linkage groups with the corresponding chromosomes, as well as in the identification of several gene-rich regions (Książkiewicz et al 2013(Książkiewicz et al , 2015Leśniewska et al 2011;Przysiecka et al 2015;Wyrwa et al 2016). The release of reference transcriptomes for wild and domesticated lupin accessions constituted a platform for targeting particular genes of interest (Kamphuis et al 2015).…”

A Tale of Two Families: Whole Genome and Segmental Duplications Underlie Glutamine Synthetase and Phosphoenolpyruvate Carboxylase Diversity in Narrow-Leafed Lupin (Lupinus angustifolius L.)

“…Furthermore, BAC clones may be used as chromosome-specific cytogenetic landmarks for chromosome-scale analysis, as well as for inter-species tracking of conserved chromosome regions and profiling of their structural variation. Both approaches have been used in lupin molecular cytogenetic studies [30][31][32][33]. Indeed, BAC clones from this study (047P22, 036L23, 059J08, 067C07, and 131K15) were recently exploited in parallel research addressing lupin karyotype evolution, providing single-locus anchors for the visualization of chromosomal rearrangements across the panel of ten European and African lupin species.…”

“…Employing the BAC-based results and including those obtained in our previous studies, we provide genomic localization for all identified GS and PEPC gene variants, as well as the cytogenetic position of four GS1 and two PEPC gene copies in lupin chromosomes. The described gene variants correspond to chromosome-specific cytogenetic markers [31], as follows: GS1a1, 047P22_5; GS1a2, 087N22_2; GS1b1, 036L22_3; GS1b2, 059J08_3; PEPC2a, 067C07_2; and PEPC2b, 131K15_5_3 ( Table 1).…”

“…Two L. angustifolius nuclear genome bacterial artificial chromosome (BAC) libraries have been constructed and almost 15,000 BAC-end sequences have been obtained and annotated [28,29]. Selected BAC clones have been used as anchors for the integration of linkage groups in particular chromosomes by the molecular cytogenetic approach [30,31] and have served as material in evolutionary studies of the Lupinus genus [32,33]. Strong microsynteny in gene-rich regions between narrow-leafed lupin and other model legumes has also been observed [17,19,20,34,35].…”

“…Whole genome duplication/triplication and chromosomal rearrangements result in the multiplication of gene content within a particular genome. Gene pairs formed by duplication/triplication usually have a relatively short life span as, due to the relaxed selection constraints, some copies may be lost, others will be pseudogenized, and only a limited number will survive [31,37]. Various factors can alter the size of gene families [38][39][40][41][42][43].…”