The first genetic map for yellow lupin enables genetic dissection of adaptation traits in an orphan grain legume crop

Iqbal, Muhammad Munir; Huynh, Mark D.; Udall, Joshua A.; Kilian, Andrzej; Adhikari, Kedar; Berger, Jens; Erskine, William; Nelson, Matthew N.

doi:10.1186/s12863-019-0767-3

Cited by 16 publications

(22 citation statements)

References 65 publications

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“…Efforts to improve the genomic resources of L. luteus are underway. The first genetic map for L. luteus has been recently released (Iqbal et al, 2019). A high-quality reference genome will help to implement MAS and identify loci responsible for the low-alkaloid content in L. luteus.…”

Section: Defense-related Traitsmentioning

confidence: 99%

The Effects of Domestication on Secondary Metabolite Composition in Legumes

Contador

et al. 2020

Front. Genet.

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Legumes are rich in secondary metabolites, such as polyphenols, alkaloids, and saponins, which are important defense compounds to protect the plant against herbivores and pathogens, and act as signaling molecules between the plant and its biotic environment. Legume-sourced secondary metabolites are well known for their potential benefits to human health as pharmaceuticals and nutraceuticals. During domestication, the color, smell, and taste of crop plants have been the focus of artificial selection by breeders. Since these agronomic traits are regulated by secondary metabolites, the basis behind the genomic evolution was the selection of the secondary metabolite composition. In this review, we will discuss the classification, occurrence, and health benefits of secondary metabolites in legumes. The differences in their profiles between wild legumes and their cultivated counterparts will be investigated to trace the possible effects of domestication on secondary metabolite compositions, and the advantages and drawbacks of such modifications. The changes in secondary metabolite contents will also be discussed at the genetic level to examine the genes responsible for determining the secondary metabolite composition that might have been lost due to domestication. Understanding these genes would enable breeding programs and metabolic engineering to produce legume varieties with favorable secondary metabolite profiles for facilitating adaptations to a changing climate, promoting beneficial interactions with biotic factors, and enhancing health-beneficial secondary metabolite contents for human consumption.

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Section: Defense-related Traitsmentioning

confidence: 99%

The Effects of Domestication on Secondary Metabolite Composition in Legumes

Contador

et al. 2020

Front. Genet.

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“…Much less advanced researches on identifying QTL and creating genetic maps are reported in genus Lupinus. Recently, the first map has been generated for yellow lupine [22], previously for white lupine [48] and two for narrow-leafed lupine [11,17]. In recent years we have observed significant interest in recognizing of the genomes of these species.…”

Section: Discussionmentioning

confidence: 99%

“…The DArTseq technique has been available at DArT PL since 2012. Despite such a short presence on the market, it has already been used for genotyping of several species [11,[18][19][20][21][22] In our study, which started in early 2000, we focused on generating a new, recombinant inbred line population for narrow-leafed lupin. Our goal was to develop a population, which would show a wide variety of phenological, morphological and agronomical traits.…”

Section: Introductionmentioning

confidence: 99%

Preliminary Genetic Map of a New Recombinant Inbred Line Population for Narrow-leafed Lupin (Lupinus angustifolius L.)

Kozak¹,

Galek²,

Zalewski³

et al. 2019

Agronomy

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Genetic maps are an essential tool for investigating molecular markers’ linkage with traits of agronomic importance. Breeders put a lot of emphasis on this type of markers, which are used in breeding programs implementation and speed up the process of a new variety development. In this paper, we construct a new, high-density linkage genetic map for Polish material on narrow-leafed lupin. The mapping population originated from crossing the Polish variety ‘Emir’ and the Belarusian breeding line ‘LAE-1’. A new map was constructed based on DArTseq markers—a new type of marker generated with the next-generation sequencing (NGS) technique. The map was built with 4602 markers, which are divided into 20 linkage groups, corresponding with the number of gametic chromosomes in narrow-leafed lupin. On the new map there are 1174 unique loci. The total length of all linkage group is 3042 cM. This map was compared to the reference genome of narrow-leafed lupin and the CDS sequence for model legume species: emphMedicago truncatula, emphLotus japonicus and Glycine max. Analysis revealed the presence of the DArTseq marker common for all investigated species. We were able to map 38 new, unplaced scaffolds on the new genetic map of narrow-leafed lupin. The high-density genetic map we received can be used for quantitative trait locus (QTL) mapping, genome-wide association study analysis and assembly of the reference genome for the whole genome sequencing (WGS) method

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“…The vernalisation response was moderate in domesticated parent Wodjil (accelerating Fig. 4 The locations of genomic regions controlling vernalisation response, flower colour, alkaloid content and seed colour on a yellow lupin linkage map reported by Iqbal et al (2019). Arrows indicate the location of domestication traits Table 3 Summary of significant (P < 0.001) quantitative trait loci (QTL) positions controlling vernalisation response, total effect, additive effect, P value and LOD or − log (10) scores…”

Section: Vernalisation Response In Yellow Lupinmentioning

confidence: 99%

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

et al. 2020

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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.

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The first genetic map for yellow lupin enables genetic dissection of adaptation traits in an orphan grain legume crop

Cited by 16 publications

References 65 publications

The Effects of Domestication on Secondary Metabolite Composition in Legumes

The Effects of Domestication on Secondary Metabolite Composition in Legumes

Preliminary Genetic Map of a New Recombinant Inbred Line Population for Narrow-leafed Lupin (Lupinus angustifolius L.)

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

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