Use of genotyping-by-sequencing to determine the genetic structure in the medicinal plant chamomile, and to identify flowering time and alpha-bisabolol associated SNP-loci by genome-wide association mapping

Abstract

BackgroundChamomile (Matricaria recutita L.) has a long history of use in herbal medicine with various applications, and the flower heads contain numerous secondary metabolites which are medicinally active.In the major crop plants, next generation sequencing (NGS) approaches are intensely applied to exploit genetic resources, to develop genomic resources and to enhance breeding. Here, genotyping-by-sequencing (GBS) has been used in the non-model medicinal plant chamomile to evaluate the genetic structure of the cultivated varieties/populations, and to perform genome wide association study (GWAS) focusing on genes with large effect on flowering time and the medicinally important alpha-bisabolol content.ResultsGBS analysis allowed the identification of 6495 high-quality SNP-markers in our panel of 91 M. recutita plants from 33 origins (2–4 genotypes each) and 4 M. discoidea plants as outgroup, grown in the greenhouse in Gatersleben, Germany. M. recutita proved to be clearly distinct from the outgroup, as was demonstrated by different cluster and principal coordinate analyses using the SNP-markers. Chamomile genotypes from the same origin were mostly genetically similar. Model-based cluster analysis revealed one large group of tetraploid genotypes with low genetic differentiation including 39 plants from 14 origins. Tetraploids tended to display lower genetic diversity than diploids, probably reflecting their origin by artificial polyploidisation from only a limited set of genetic backgrounds.Analyses of flowering time demonstrated that diploids generally flowered earlier than tetraploids, and the analysis of alpha-bisabolol identified several tetraploid genotypes with a high content. GWAS identified highly significant (P < 0.01) SNPs for flowering time (9) and alpha-bisabolol (71). One sequence harbouring SNPs associated with flowering time was described to play a role in self-pollination in Arabidopsis thaliana, whereas four sequences harbouring SNPs associated with alpha-bisabolol were identified to be involved in plant biotic and abiotic stress response in various plants species.ConclusionsThe first genomic resource for future applications to enhance breeding in chamomile was created, andanalyses of diversity will facilitate the exploitation of these genetic resources. The GWAS data pave the way for future research towards the genetics underlying important traits in chamomile, the identification of marker-trait associations, and development of reliable markers for practical breeding.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3991-0) contains supplementary material, which is available to authorized users.

Aphid infestation leads to plant part‐specific changes in phloem sap chemistry, which may indicate niche construction

“…Future genomic studies using, for example, genome‐wide association mapping or transgenic overexpression lines as done, for example, by Otto et al . () and Hu et al . (), may help to understand the genetic architecture of T. vulgare in more detail and to address the induction of specific metabolic pathways.…”

“…effectors that suppress plant defences or as elicitors that are recognized by the plant and induce defensive compounds (Elzinga & Jander, 2013). Future genomic studies using, for example, genome-wide association mapping or transgenic overexpression lines as done, for example, by Otto et al (2017) and Hu et al (2018), may help to understand the genetic architecture of T. vulgare in more detail and to address the induction of specific metabolic pathways. The aphid-induced changes in the overall metabolic compositions of the phloem exudates did not differ between the chemotypes (Fig.…”

Mitochondrial relationships between various chamomile accessions

“…Five, ten or 15 individuals per accession (Table 1) were harvested in June 2017 and used for SNP screening. Main ploidy levels as declared by Das (2014), Otto et al (2017) and Faehnrich et al (2019) were assumed for the accessions and were not further verified in the present study.…”

Genome wide association study (GWAS) for morphological and yield-related traits in oil palm hybrids (Elaeis oleifera x Elaeis guineensis)

“…SNPs detected by GBS have allowed the genetic dissection of genotypic variation in complex traits in many plant species [34][35][36]. Specifically, in oil palm the GBS technique has been used for identifying candidate genes related to oil bunch [37], bunch weight [20,37], stem height [21] and oil quality traits studies [38] with the enzymes ApeKI and PstI-MspI.…”