A high-density consensus map of barley to compare the distribution of QTLs for partial resistance to Puccinia hordei and of defence gene homologues

Abstract

A consensus map of barley was constructed based on three reference doubled haploid (DH) populations and three recombinant inbred line (RIL) populations. Several sets of microsatellites were used as bridge markers in the integration of those populations previously genotyped with RFLP or with AFLP markers. Another set of 61 genic microsatellites was mapped for the Wrst time using a newly developed Xuorescent labelling strategy, referred to as A/T labelling. The Wnal map contains 3,258 markers spanning 1,081 centiMorgans (cM) with an average distance between two adjacent loci of 0.33 cM. This is the highest density of markers reported for a barley genetic map to date. The consensus map was divided into 210 BINs of about 5 cM each in which were placed 19 quantitative trait loci (QTL) contributing to the partial resistance to barley leaf rust (Puccinia hordei Otth) in Wve of the integrated populations. Each parental barley combination segregated for diVerent sets of QTLs, with only few QTLs shared by any pair of cultivars. Defence gene homologues (DGH) were identiWed by tBlastx homology to known genes involved in the defence of plants against microbial pathogens. Sixty-three DGHs were located into the 210 BINs in order to identify candidate genes responsible for the QTL eVects. Eight BINs were cooccupied by a QTL and DGH(s). The positional candidates identiWed are receptor-like kinase, WIR1 homologues and several defence response genes like peroxidases, superoxide dismutase and thaumatin.

A high density barley microsatellite consensus map with 775 SSR loci

“…The segregation data of 968 marker loci mapped in L · V and of 450 marker loci mapped in Su · V were obtained from Marcel et al (2007). Those data sets predominantly consisted of AFLP markers, but also included 138 and 24 microsatellite loci, respectively (Table 1).…”

“…In such a way, an integrated map of 3,610 markers was obtained from which the coordinates of 775 unique microsatellite loci were extracted. In the final microsatellite integrated map of barley the position of BIN markers, as defined by Marcel et al (2007), are given as reference. Mostly, the same BIN-defining markers and numbers as defined by Kleinhofs and Graner (2001) were maintained.…”

“…A skeleton map with common markers was constructed using JoinMap Ò 3.0 and used to fit the markers from the six individual maps. The BIN markers, as defined by Marcel et al (2007) are in bold. The loci preceded by an asterisk are BIN markers, which are not microsatellites.…”

“…Therefore, they represent a functional class of molecular markers (Andersen and Lü bberstedt 2003). The functional SSR markers include earlier published genic SSR markers (Saghai Maroof et al 1994;Becker and Heun 1995;Pillen et al 2000) and recently developed EST-derived SSR markers (Thiel et al 2003;Rostoks et al 2005;Varshney et al 2006a;Marcel et al 2007). In total, 44% of the SSR marker loci (339) placed on the consensus map are genic/functional-SSR loci.…”

“…Availability of the primer sequences for a total of 580 SSR loci, approximately 75% of all loci integrated in the consensus map, at one place should accelerate the use of SSR markers in barley breeding activities. The primer sequences for 172 SSR loci (170 loci mapped in Varshney et al 2006a andMarcel et al 2007; two unpublished loci) have been made available in public domain for the first time. Primer sequences for the remaining 194 SSR loci can be obtained from Andreas Graner (for GBM loci) and Marion Rö der (for GBMS loci), as per Material Transfer Agreement (MTA) basis.…”