Arabinogalactan-proteins (AGPs) are complex glycoconjugates that are commonly found at the cell surface and in secretions of plants. Their location and diversity of structures have made them attractive targets as modulators of plant development but definitive proof of their direct role(s) in biological processes remains elusive. Here we overview the current state of knowledge on AGPs, identify key challenges impeding progress in the field and propose approaches using modern bioinformatic, (bio)chemical, cell biological, molecular and genetic techniques that could be applied to redress these gaps in our knowledge.

Quinolizidine alkaloids (QAs) are synthesized by the genus Lupinus as a defense against herbivores. Synthesis of QAs in lupins is species- and organ-specific. Knowledge about their biosynthesis and their corresponding pathways are still fragmentary, in part because lupins of commercial importance were mainly investigated, representing a small sample of the chemodiversity of the genus. Here, we explore the use of three Mexican lupins: Lupinus aschenbornii, Lupinus montanus, and Lupinus bilineatus as a model to study the physiology of QA biosynthesis. The corresponding QA patterns cover widely and narrowly distributed tetracyclic QAs. Quinolizidine alkaloid patterns of seeds and plantlets at different developmental stages were determined by GLC–MS and compared to identify the onset of de novo QA synthesis and to gain insight into specific and common biosynthesis trends. Onset of de novo QA biosynthesis occurred after the metabolization of seed QA during germination and was species-specific, as expected. A common QA pattern, from which the diversity of QA observed in these species is generated, was not found; however, lupanine and 3β-lupanine were found in the three specieswhile sparteine was not found in Lupinus bilineatus, suggesting that this simplest tetracyclic QA is not the precursor of more complex QAs. Similar patterns of metabolization and biosynthesis of structurally related QAs were observed, suggesting a common regulation.

The potential of secondary metabolites as systematic markers to get new insights in an intricate phylogeny of a recent evolutionary radiation is explored. A chemosystematic study of the genus Lupinus (Fabaceae) was performed, using quinolizidine (QA) and piperidine alkaloids (ammodendrine) as diagnostic characters. Seven major QA and the piperidine alkaloid ammodendrine were found to be the most frequent compounds. Two groups were supported according to their geographic origin: an Old World/Atlantic American group and a West New World group and this pattern is concordant with molecular data (here, based on an original barcode approach using the nuclear marker ITS). However, QA profiles are less informative at the species level. Despite a lack of resolution within the two groups, the alkaloid profiles agree with well supported clades based on DNA molecular characters. The combined use of chemical and barcode genetic markers represents a viable alternative for separating recent evolutionary lineages to a first approximation without having to resort to an expensive and sophisticated molecular arsenal such as next generation sequencing.

Pericon (Tagetes lucida) is an important medicinal and traditional plant used widely in ceremonies and considered as biocultural heritage. In Yautepec (Pericon Hill, in Nahuatl), Morelos, people report the extinction of this emblematic species. The extinction causes are until now not known. Nevertheless, the decline of populations may be attributable to a combination of factors, including alterations in land use, the utilisation of herbicides, habitat degradation, and overexploitation of resources. This decline could be exacerbated by the species ' inability to adapt to environmental changes. Genetic diversity is crucial to maintain the population’s adaptability in the face of diseases, environmental changes and other stressors and has an impact on population persistence. We tested the hypothesis that reduced genetic diversity in pericon populations caused the extinction of this species in Yautepec hills. The genetic diversity of six populations of Tagetes lucida were evaluated using PCR-based inter-simple sequence repeat (ISSR) markers. Ten ISSR primers produced a total of 1677 fragments with 100% polymorphism. The mean values of PIC, EMR and Rp were 0.34, 2.51 and 2.18, respectively. The results indicate that evaluated populations of Tagetes lucida have a high genetic diversity (79%), showing that the genetic factors are not the drivers of the species local extinction, and suggesting, that nongenetic factors such as overexploitation, overkill by herbicides, habitat destruction and fragmentation, the introduction of invasive species, rapid climate change, or pollution, reduce the growth rates of species and cause their populations to decline. These results show that T. lucida is a sensitive species that may require urgent conservation interventions.