White lupin (Lupinus albus L.) is a legume plant rich in seed protein and appreciated in crop rotation due to improvement of soil structure and fertility. Primitive white lupin accessions are late flowering unless subjected to cold period during seed germination. It is an undesirable trait in spring-based agriculture. Moreover, white lupin is very susceptible to anthracnose, and the only known resistant lines are late-flowering landraces from Ethiopia. Tracking of early flowering during white lupin breeding has been challenging for many years due to the lack of knowledge on underlying genes and limited molecular resources. To address this issue, we performed genomic and genetic analysis of white lupin germplasm differing by time to flowering, including mapping population derived from Kiev Mutant (early flowering, anthracnose susceptible) and P27174 (late flowering, anthracnose resistant). Thirty six flowering induction pathway genes were subjected to molecular marker development and linkage mapping. Markers representing 24 homologs were localized in 17 linkage groups. Four quantitative trait loci (QTLs) of flowering time, consistent across field and greenhouse experiments, were localized in three linkage groups. Three QTLs absolutely co-localized with GIGANTEA, FLOWERING LOCUS T, and SEPALLATA 3 gene–based markers whereas one neighbored the FRIGIDA 3 marker by 3.6 cM. Analysis of narrow-leafed lupin genome regions highly syntenic to these QTLs highlighted these homologs as candidate genes for early flowering. Molecular markers developed in the present study should have facilitated the issue of tracking late-flowering alleles in further white lupin breeding approaches involving primitive Ethiopian germplasm.

Insight into plant genomes at the cytomolecular level provides useful information about their karyotype structure, enabling inferences about taxonomic relationships and evolutionary origins. The Old World lupins demonstrate a high level of genomic diversification involving variation in chromosome numbers (2n=32-52), basic chromosome numbers (x=5-7, 9, 13) and in nuclear genome size (2C DNA=0.97-2.68 pg). Lupins comprise both crop and wild species and provide an intriguing system to study karyotype evolution. In order to investigate lupin chromosome structure, heterologous FISH was used. Sixteen BACs that had been generated as chromosome markers for the reference species, Lupinus angustifolius, were used to identify chromosomes in the wild species and explore karyotype variation. While all ‘single-locus’ in L. angustifolius, in the wild lupins these clones proved to be ‘single-locus’, ‘single-locus’ with additional signals, ‘repetitive’ or had no detectable BAC-FISH signal. The diverse distribution of the clones in the targeted genomes suggests a complex evolution history, which possibly involved multiple chromosomal changes such as fusions/fissions and repetitive sequence amplification. Twelve BACs were sequenced and we found numerous transposable elements including DNA transposons as well as LTR and non-LTR retrotransposons with varying quantity and composition among the different lupin species. However, at this preliminary stage, no correlation was observed between the pattern of BAC-FISH signals and the repeat content in particular BACs. Here, we describe the first BAC-based chromosome-specific markers for the wild species: L. cosentinii, L. cryptanthus, L. pilosus, L. micranthus and one New World lupin, L. multiflorus. These BACs could constitute the basis for an assignment of the chromosomal and genetic maps of other lupins, e.g. L. albus and L. luteus. Moreover, we identified karyotype variation that helps illustrate the relationships between the lupins and the extensive cytological diversity within this group. In this study we premise that lupin genomes underwent at least two rounds of fusion and fission events resulting in the reduction in chromosome number from 2n=52 through 2n=40 to 2n=32, followed by chromosome number increment to 2n=42.

White lupin (Lupinus albus L.) is a pulse annual plant cultivated from the tropics to temperate regions for its high-protein grain as well as a cover crop or green manure. Wild populations are typically late flowering and have high vernalization requirements. Nevertheless, some early flowering and thermoneutral accessions were found in the Mediterranean basin. Recently, quantitative trait loci (QTLs) explaining flowering time variance were identified in bi-parental population mapping, however, phenotypic and genotypic diversity in the world collection has not been addressed yet. In this study, a diverse set of white lupin accessions (n = 160) was phenotyped for time to flowering in a controlled environment and genotyped with PCR-based markers (n = 50) tagging major QTLs and selected homologs of photoperiod and vernalization pathway genes. This survey highlighted quantitative control of flowering time in white lupin, providing statistically significant associations for all major QTLs and numerous regulatory genes, including white lupin homologs of CONSTANS, FLOWERING LOCUS T, FY, MOTHER OF FT AND TFL1, PHYTOCHROME INTERACTING FACTOR 4, SKI-INTERACTING PROTEIN 1, and VERNALIZATION INDEPENDENCE 3. This revealed the complexity of flowering control in white lupin, dispersed among numerous loci localized on several chromosomes, provided economic justification for future genome-wide association studies or genomic selection rather than relying on simple marker-assisted selection.

White lupin (Lupinus albus L.) is a high-protein grain legume crop, grown since ancient Greece and Rome. Despite long domestication history, its cultivation remains limited, partly because of susceptibility to anthracnose. Only some late-flowering, bitter, low-yielding landraces from Ethiopian mountains displayed resistance to this devastating disease. The resistance is controlled by various genes, thereby complicating the breeding efforts. The objective of this study was developing tools for molecular tracking of Ethiopian resistance genes based on genotyping-by-sequencing (GBS) data, envisaging linkage mapping and genomic selection approaches. Twenty GBS markers from two major quantitative trait loci (QTLs), antr04_1/antr05_1 and antr04_2/antr05_2, were converted to PCR-based markers using assigned transcriptome sequences. Newly developed markers improved mapping resolution around both anthracnose resistance loci, providing more precise QTL estimation. PCR-based screening of diversified domesticated and primitive germplasm revealed the high specificity of two markers for the antr04_1/antr05_1 locus (TP222136 and TP47110) and one for the antr04_2/antr05_2 locus (TP338761), highlighted by simple matching coefficients of 0.96 and 0.89, respectively. Moreover, a genomic selection approach based on GBS data of a recombinant inbred line mapping population was assessed, providing an average predictive ability of 0.56. These tools can be used for preselection of candidate white lupin germplasm for anthracnose resistance assays.

White lupin (Lupinus albus L.) is an ancient grain legume that is still undergoing improvement of domestication traits, including vernalization-responsiveness, providing frost tolerance and preventing winter flowering in autumn-sowing agriculture, and vernalization-independence, conferring drought escape by rapid flowering in spring-sowing. A recent genome-wide association study highlighted several loci significantly associated with the most contrasting phenotypes, including deletions in the promoter of the FLOWERING LOCUS T homolog, LalbFTc1, and some DArT-seq/silicoDArT loci. The present study aimed to develop and validate a versatile PCR marker array enabling molecular selection of spring- and winter-type white lupin ecotypes. Candidate DArT-seq and silicoDArT loci were transformed into cleaved amplified polymorphic sequence (CAPS) or derived CAPS markers. Developed markers, together with those previously published for LalbFTc1 INDELs and quantitative trait loci from linkage maps, were implemented for screening of white lupin germplasm panel subjected to 2-year phenotyping of phenology traits. Three DArT-seq, two silicoDArT and seven LalbFTc1 INDEL markers were positively validated, constituting a convenient PCR-based marker assay for rapid and accurate reselection of white lupin germplasm towards early flowering and thermoneutrality or late flowering and vernalization-responsiveness, as well as for tracking high genetic and phenotypic diversity within white lupin landraces, revealed in the present study.