A high-density genetic map and QTL mapping of leaf traits and glucosinolates in Barbarea vulgaris

Abstract

Background: Barbarea vulgaris is a wild cruciferous plant and include two distinct types: the G- and P-types named after their glabrous and pubescent leaves, respectively. The types differ significantly in resistance to a range of insects and diseases as well as glucosinolates and other chemical defenses. A high-density linkage map was needed for further progress to be made in the molecular research of this plant.

Results: We performed restriction site-associated DNA sequencing (RAD-Seq) on an F₂ population generated from G- and P-type B. vulgaris. A total of 1545 SNP markers were mapped and ordered in eight linkage groups, which represents the highest density linkage map to date for the crucifer tribe Cardamineae. A total of 722 previously published genome contigs (50.2 Mb, 30% of the total length) can be anchored to this high density genetic map, an improvement compared to a previously published map (431 anchored contigs, 38.7 Mb, 23% of the assembly genome). Most of these (572 contigs, 31.2 Mb) were newly anchored to the map, representing a significant improvement. On the basis of the present high-density genetic map, 37 QTL were detected for eleven traits, each QTL explaining 2.9-71.3% of the phenotype variation. QTL of glucosinolates, leaf size and color traits were in most cases overlapping, possibly implying a functional connection.

Conclusions: This high-density linkage map and the QTL obtained in this study will be useful for further understanding of the genetic of the B. vulgaris and molecular basis of these traits, many of which are shared in the related crop watercress.

Keywords: Barbarea vulgaris; Genetic linkage map; Glucosinolates; Leaf traits; QTL; Restriction site-associated DNA sequencing (RAD-Seq).

Fig. 1

The high-density genetic map of Barbarea vulgaris. Map distances based on Kosambi map units (CM) are shown on the left margin and the marker names are shown on the right margin of each linkage group

Fig. 2

Anchoring of sequenced contigs of G-type Barbarea vulgaris to the eight linkage groups and correspondence with a previously published high density linkage map. The present and previously published linkage groups are shown to the left and right, respectively. Map distances based on Kosambi map units (CM) are shown on the left margin and marker names and anchored contigs are shown on the right margin of each linkage group for the present linkage maps, while map distances are shown on the right margin and anchored contigs are shown on the left margin for the previous linkage maps. Markers that harbor the same sequenced contig are connected by a straight line between the present and previous maps

Fig. 3

The QTL positions on the high density map of the F₂ population. QTL names refer to Table 4

Fig. 4

Glucosinolates in Barbarea vulgaris leaves as detected in this investigation, with suggested biosynthetic relationships. a. General glucosinolate structure, using gluconasturtiin (NAS, 2-phenylethylglucosinolate) as example. b. Biosynthetic relationships of phenylalanine-derived glucosinolates. The general glucosinolate biosynthesis leads to NAS, which is hydroxylated in either of two stereochemical configurations, yielding either BAR (glucobarbarin, (2S)-2-hydroxy-2-phenylethylGSL) or EBAR (epiglucobarbarin, (2R)-2-hydroxy-2-phenylethylglucosinolate). This hydroxylation was previously anticipated to be carried out by either of two gene products, SHO and RHO. Results of this work suggest involvement of several complementing gene products, provisionally named with suffixes a and b. A further glucosinolate in the P-type is p-hydroxy EBAR (p-hydroxyepiglucobarbarin or (2R)-2-hydroxy-2-(4-hydroxyphenyl)ethylglucosinolate. c. Biosynthetic relationships of tryptophan-derived glucosinolates. The general indole glucosinolate biosynthesis leads to IM (glucobrassicin, indol-3-ylmethylglucosinolate). A homolog of A. thaliana CYP81F is expected to lead to the 4-hydroxy derivative 4hIM [38], which is probably taken to the 4-methoxy derivative 4mIM by a homolog of A. thaliana IGMT [60]. In all structures except the upper complete structure, the constant glucosinolate backbone is indicated as GSL