A high-density consensus linkage map of white lupin highlights synteny with narrow-leafed lupin and provides markers tagging key agronomic traits

Abstract

White lupin (Lupinus albus L.) is a valuable source of seed protein, carbohydrates and oil, but requires genetic improvement to attain its agronomic potential. This study aimed to (i) develop a new high-density consensus linkage map based on new, transcriptome-anchored markers; (ii) map four important agronomic traits, namely, vernalization requirement, seed alkaloid content, and resistance to anthracnose and Phomopsis stem blight; and, (iii) define regions of synteny between the L. albus and narrow-leafed lupin (L. angustifolius L.) genomes. Mapping of white lupin quantitative trait loci (QTLs) revealed polygenic control of vernalization responsiveness and anthracnose resistance, as well as a single locus regulating seed alkaloid content. We found high sequence collinearity between white and narrow-leafed lupin genomes. Interestingly, the white lupin QTLs did not correspond to previously mapped narrow-leafed lupin loci conferring vernalization independence, anthracnose resistance, low alkaloids and Phomopsis stem blight resistance, highlighting different genetic control of these traits. Our suite of allele-sequenced and PCR validated markers tagging these QTLs is immediately applicable for marker-assisted selection in white lupin breeding. The consensus map constitutes a platform for synteny-based gene cloning approaches and can support the forthcoming white lupin genome sequencing efforts.

High-quality genome sequence of white lupin provides insight into soil exploration and seed quality

“…The production of 94 Gb of very long reads along with a depth of 208× (119 Gb) of Illumina 150 bp paired-end sequences for the assembly polishing and with the addition of Bionano optical map technology allowed a genome assembly of 451 Mb. The contig sequences obtained by a meta assembly strategy based on CANU 15 and FALCON 16 were scaffolded in a first step using a Bionano optical map and in a second step using a high density genetic map 17 . The chromosome-level assembly (termed Lalb, Table 1, Supplementary Fig.…”

“…6d, e, Supplementary Data 15). Instead, we identified a list of candidate genes on Chr18 as associated to the pauper QTL that is responsible for the sweet trait of modern WL accessions, including AMIGA 17,46 (Supplementary Note 9). This region of 958 kb contains 66 genes amongst which several strong candidates encoding for protein with enzymatic activity such as cinnamoyl-CoA reductase and acyltransferases ( Supplementary Data 16).…”

The genome evolution and low-phosphorus adaptation in white lupin

“…A Hi-C library was constructed and generated~100-fold coverage of Hi-C linkage data (100 bp paired-end reads). We then linked the contigs into scaffolds based on the Hi-C data 16 with the help of a previously published linkage map 17 ( Supplementary Fig. 2).…”

White lupin (Lupinus albus) variation for adaptation to severe drought stress

“…Selection for specific adaptation is advisable when targeting severely drought‐prone environments on the one hand and moisture‐favourable environments on the other. Early onset of flowering, which proved controlled by two complementary dominant genes in Adhikari, Buirchell, Yan, and Sweetingham () while showing a polygenic control with respect to vernalization requirement (Książkiewicz et al., ), is a key adaptive trait for drought escape, but variation for intrinsic drought tolerance can be exploited as well within a given phenological class. Selection for wide adaptation is not precluded on the basis of our results and may be justified when targeting less unfavourable or climatically variable regions or, in some cases, because of the limited cultivation and economic importance of the crop.…”

“…In conclusion, this study, whose plant material encompassed much greater diversity of origin than that in earlier studies, indicated the presence of substantial variation in white lupin for drought tolerance and specific adaptation to either drought-stressed or favourable growing conditions. Also, it identified different promising parent material depending on the target environments and the adaptation showing a polygenic control with respect to vernalization requirement (Książkiewicz et al, 2017), is a key adaptive trait for drought escape, but variation for intrinsic drought tolerance can be exploited as well within a given phenological class. Selection for wide adaptation is not precluded on the basis of our results and may be justified when targeting less unfavourable or climatically variable regions or, in some cases, because of the limited cultivation and economic importance of the crop.…”