Candidate Domestication-Related Genes Revealed by Expression Quantitative Trait Loci Mapping of Narrow-Leafed Lupin (Lupinus angustifolius L.)

Abstract

The last century has witnessed rapid domestication of the narrow-leafed lupin (Lupinus angustifolius L.) as a grain legume crop, exploiting discovered alleles conferring low-alkaloid content (iucundus), vernalization independence (Ku and Julius), and reduced pod shattering (lentus and tardus). In this study, a L. angustifolius mapping population was subjected to massive analysis of cDNA ends (MACE). The MACE yielded 4185 single nucleotide polymorphism (SNP) markers for linkage map improvement and 30,595 transcriptomic profiles for expression quantitative trait loci (eQTL) mapping. The eQTL highlighted a high number of cis- and trans-regulated alkaloid biosynthesis genes with gene expression orchestrated by a regulatory agent localized at iucundus locus, supporting the concept that ETHYLENE RESPONSIVE TRANSCRIPTION FACTOR RAP2-7 may control low-alkaloid phenotype. The analysis of Ku shed light on the vernalization response via FLOWERING LOCUS T and FD regulon in L. angustifolius, providing transcriptomic evidence for the contribution of several genes acting in C-repeat binding factor (CBF) cold responsiveness and in UDP-glycosyltransferases pathways. Research on lentus selected a DUF1218 domain protein as a candidate gene controlling the orientation of the sclerified endocarp and a homolog of DETOXIFICATION14 for purplish hue of young pods. An ABCG transporter was identified as a hypothetical contributor to sclerenchyma fortification underlying tardus phenotype.

Alkaloids of narrow-leaved lupine as a factor determining alternative ways of the crop’s utilization and breeding

“…The identified alkaloid biosynthesis genes were mapped, but only one transcriptomic factor from the RAP2 family of factors regulating secondary metabolism was closely linked with the iuc gene (Kroc et al, 2019). Investigating the mapping populations with the technique of massive analysis for cDNA ends (MACE) confirmed the idea that the ETHYLENE-RESPONSIVE TRANSCRIPTION RAC2-7 gene factor could control the low-alkaloid phenotype in narrow-leaved lupine (Plewiński et al, 2019).…”

A Tale of Two Families: Whole Genome and Segmental Duplications Underlie Glutamine Synthetase and Phosphoenolpyruvate Carboxylase Diversity in Narrow-Leafed Lupin (Lupinus angustifolius L.)

“…Moreover, the type of duplication contributes to the further evolutionary fate, demonstrated by different gene expression patterns and the methylation status of duplicates [84]. A recent expression quantitative trait loci mapping study of an L. angustifolius recombinant inbred line population (83A:476 x P27255) provided leaf transcriptomic profiles for 30,595 genes, including all GS and PEPC homologs present in the genome, except GS2a2 unannotated hitherto [85]. Gene expression values corresponding to GS and PEPC homologs were extracted from the Supplementary Materials, Table 6, of Plewiński et al study [85] and are presented here in Table 4 for direct reference.…”

“…A recent expression quantitative trait loci mapping study of an L. angustifolius recombinant inbred line population (83A:476 x P27255) provided leaf transcriptomic profiles for 30,595 genes, including all GS and PEPC homologs present in the genome, except GS2a2 unannotated hitherto [85]. Gene expression values corresponding to GS and PEPC homologs were extracted from the Supplementary Materials, Table 6, of Plewiński et al study [85] and are presented here in Table 4 for direct reference. Indeed, that survey highlighted significant differences in leaf expression levels between particular gene duplicates, namely between GS1a1 and GS1a2 or GS1a3 (43.1 ± 16.4 vs. 13.8 ± 5.2 and 11.5 ± 5.0, respectively); GS1b1 and GS1b2 (0.3 ± 0.3 vs. 2.6 ± 1.2, respectively); GS1c1 and GS1c2 (0.1 ± 0.2 vs. 187.5 ± 52.4, respectively); PEPC1a, PEPC1b, and PEPC1c (17.0 ± 4.0 vs. 0.5 ± 0.5 vs. 65.0 ± 8.7, respectively); and PEPC3a and PEPC3b (10.5 ± 2.5 vs. 51.0 ± 11.2, respectively) [85].…”

“…Gene expression values corresponding to GS and PEPC homologs were extracted from the Supplementary Materials, Table 6, of Plewiński et al study [85] and are presented here in Table 4 for direct reference. Indeed, that survey highlighted significant differences in leaf expression levels between particular gene duplicates, namely between GS1a1 and GS1a2 or GS1a3 (43.1 ± 16.4 vs. 13.8 ± 5.2 and 11.5 ± 5.0, respectively); GS1b1 and GS1b2 (0.3 ± 0.3 vs. 2.6 ± 1.2, respectively); GS1c1 and GS1c2 (0.1 ± 0.2 vs. 187.5 ± 52.4, respectively); PEPC1a, PEPC1b, and PEPC1c (17.0 ± 4.0 vs. 0.5 ± 0.5 vs. 65.0 ± 8.7, respectively); and PEPC3a and PEPC3b (10.5 ± 2.5 vs. 51.0 ± 11.2, respectively) [85]. The observed differences in the gene expression of L. angustifolius GS and PEPC paralogs support the previously mentioned hypothesis on the expected sub-functionalization of WGD-derived duplicates.…”

“…Normalized leaf expression level of GS and PEPC genes in a L. angustifolius recombinant inbred line (RIL) mapping population (83A:476 x P27255)[85].…”