Background: Strong artificial selection and/or natural bottle necks may limit genetic variation in domesticated
species.
Lupinus luteus, an orphan temperate crop, has suffered diversity reductions during its bitter/sweet
alkaloid domestication history, limiting breeding efforts and making molecular marker development a difficult
task. The main goal of this research was to generate new polymorphic insertion–deletion (InDel) markers to
aid yellow lupin genetics and breeding. By combining genomic reduction libraries and next generation
sequencing, several polymorphic InDel markers were developed for
L. luteus L.
Results: A total of 118 InDel in silico polymorphic markers were identified. Eighteen InDel primer sets were
evaluated in a diverse
L. luteus core collection, where amplified between 2–3 alleles per locus. Observed
heterozygosity (HO; 0.0648 to 0.5564) and polymorphic information content (PIC; 0.06 to 0.48) estimations
revealed a moderate level of genetic variation across
L. luteus accessions. In addition, ten and nine InDel loci
amplified successfully
Lupinus hispanicus
Boiss & Reut, and
Lupinus mutabilis
Sweet, respectively, two
L. luteus
close relatives. PCA analysis identified two
L. luteus clusters, most likely explained by the domestication species
history.
Conclusion: The development of InDel markers will facilitate the study of genetic diversity across
L. luteus
populations, as well as among closely related species.
