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

Abstract

Background Yellow lupin ( Lupinus luteus L.) is a promising grain legume for productive and sustainable crop rotations. It has the advantages of high tolerance to soil acidity and excellent seed quality, but its current yield potential is poor, especially in low rainfall environments. Key adaptation traits such as phenology and enhanced stress tolerance are often complex and controlled by several genes. Genomic-enabled technologies may help to improve our basic understanding of these traits and to provide selective markers in breeding. However, in yellow lupin there are very limited genomic resources to support research and no published information is available on the genetic control of adaptation traits. Results We aimed to address these deficiencies by developing the first linkage map for yellow lupin and conducting quantitative trait locus (QTL) analysis of yield under well-watered (WW) and water-deficit (WT) conditions. Two next-generation sequencing marker approaches - genotyping-by-sequencing (GBS) and Diversity Array Technology (DArT) sequencing - were employed to genotype a recombinant inbred line (RIL) population developed from a bi-parental cross between wild and domesticated parents. A total of 2,458 filtered single nucleotide polymorphism (SNP) and presence / absence variation (PAV) markers were used to develop a genetic map comprising 40 linkage groups, the first reported for this species. A number of significant QTLs controlling total biomass and 100-seed weight under two water (WW and WD) regimes were found on linkage groups YL-03, YL-09 and YL-26 that together explained 9 and 28% of total phenotypic variability. QTLs associated with length of the reproductive phase and time to flower were found on YL-01, YL-21, YL-35 and YL-40 that together explained a total of 12 and 44% of total phenotypic variation. Conclusion These genomic resources and the QTL information offer significant potential for use in marker-assisted selection in yellow lupin. Electronic supplementary material The online version of this article (10.1186/s12863-019-0767-3) contains supplementary material, which is available to authorized users.

The Effects of Domestication on Secondary Metabolite Composition in Legumes

“…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.…”

Genetic and comparative mapping of Lupinus luteus L. highlight syntenic regions with major orthologous genes controlling anthracnose resistance and flowering time

“…In addition, the deficiency of information on which molecular and genetic is enormous compared to many other crops. Even though some work has been undertaken on these aspects [22][23][24] , there are still many gaps which need to be filled to help the species improvement.…”

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

“…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.…”

“…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.…”