Phenotypic characterisation and linkage mapping of domestication syndrome traits in yellow lupin (Lupinus luteus L.)

Abstract

The transformation of wild plants into domesticated crops usually modifies a common set of characters referred to as ‘domestication syndrome’ traits such as the loss of pod shattering/seed dehiscence, loss of seed dormancy, reduced anti-nutritional compounds and changes in growth habit, phenology, flower and seed colour. Understanding the genetic control of domestication syndrome traits facilitates the efficient transfer of useful traits from wild progenitors into crops through crossing and selection. Domesticated forms of yellow lupin (Lupinus luteus L.) possess many domestication syndrome traits, while their genetic control remains a mystery. This study aimed to reveal the genetic control of yellow lupin domestication traits. This involved phenotypic characterisation of those traits, defining the genomic regions controlling domestication traits on a linkage map and performing a comparative genomic analysis of yellow lupin with its better-understood relatives, narrow-leafed lupin (L. angustifolius L.) and white lupin (L. albus L.). We phenotyped an F9 recombinant inbred line (RIL) population of a wide cross between Wodjil (domesticated) × P28213 (wild). Vernalisation responsiveness, alkaloid content, flower and seed colour in yellow lupin were each found to be controlled by single loci on linkage groups YL-21, YL-06, YL-03 and YL-38, respectively. Aligning the genomes of yellow with narrow-leafed lupin and white lupin revealed well-conserved synteny between these sister species (76% and 71%, respectively). This genomic comparison revealed that one of the key domestication traits, vernalisation-responsive flowering, mapped to a region of conserved synteny with the vernalisation-responsive flowering time Ku locus of narrow-leafed lupin, which has previously been shown to be controlled by an FT homologue. In contrast, the loci controlling alkaloid content were each found at non-syntenic regions among the three species. This provides a first glimpse into the molecular control of flowering time in yellow lupin and demonstrates both the power and the limitation of synteny as a tool for gene discovery in lupins.

Pod shattering in grain legumes: emerging genetic and environment-related patterns

“…The resistance to shattering provided by invulnerabilis is sufficient for the relatively humid climates of northern Europe but does not provide strong resistance in the comparatively arid climates of the Mediterranean or western Australia (Wolko et al, 2011). Recent studies suggest that a second pod shatteringrelated allele may exist in the yellow lupin population (Iqbal et al, 2020), although this allele has not yet been mapped or described in detail. Due to the incomplete resistance to pod shattering provided by invulnerabilis, the pyramiding of multiple shattering resistance alleles is required in L. luteus.…”

Quantitative Control of Early Flowering in White Lupin (Lupinus albus L.)

“…The release of two white lupin high quality genome assemblies [ 27 , 28 ] provided an unprecedented opportunity to search for similar indels in FT homologs in this species, both by whole-genome shotgun and PCR-based approaches. Recent comparative mapping approach performed in yellow lupin, Lupinus luteus L., revealed that a major QTL for vernalization responsiveness in this species is localized in a linkage map segment syntenic to the narrow-leafed lupin genome region carrying the FTc1 gene [ 46 , 47 , 48 ]. All these observations support the conclusion on the highly conserved contribution of the FTc1 homologs into vernalization pathway in the Old World lupin clade.…”

Will Plant Genome Editing Play a Decisive Role in “Quantum-Leap” Improvements in Crop Yield to Feed an Increasing Global Human Population?

“…Examples of these traits include loss of pod shattering/seed dehiscence, loss of seed dormancy, reduced anti-nutritional compounds, changes in growth habit, phenology, flower colour, and seed colour. Understanding the genetic control of domestication syndrome traits facilitates the efficient transfer of useful traits from wild progenitors into crops through crossing and selection [ 205 , 207 ]. It has become apparent in recent years that understanding the nature of the plurality of processes underlying domestication syndrome is the key to understanding the origins of domestication.…”

“…Despite all successes, gene editing approaches to the domestication of wild plants using domestication genes [ 11 , 202 , 207 ] should not be generally considered as simple one-time events in a single gene or generation. In contrast, de novo domestication literature and examples understand domestication as co-evolutionary interactions between plants and people that are complex, would require significant institutional and infrastructural investments, and can involve many disciplines.…”