Consistent detection of QTLs for crown rust resistance in Italian ryegrass (Lolium multiflorum Lam.) across environments and phenotyping methods

Studer, Bruno; Boller, B.; Bauer, Eva; Posselt, U. K.; Widmer, Franco; Kölliker, Roland

doi:10.1007/s00122-007-0535-z

Cited by 48 publications

(47 citation statements)

References 35 publications

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“…These plants were complemented with eight parental genotypes of four different perennial ryegrass mapping populations, one parent of the p150/112 intraspecific ILGI reference population [4], and two Italian ryegrass plants which have been used to establish the Xtg-ART population characterized for bacterial wilt and crown rust resistance [57,92]. Genomic DNA was isolated from young leaves following a phenol/chloroform extraction protocol with minor modifications described in Jensen et al [2].…”

Section: Methodsmentioning

confidence: 99%

A transcriptome map of perennial ryegrass (Lolium perenne L.)

et al. 2012

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BackgroundSingle nucleotide polymorphisms (SNPs) are increasingly becoming the DNA marker system of choice due to their prevalence in the genome and their ability to be used in highly multiplexed genotyping assays. Although needed in high numbers for genome-wide marker profiles and genomics-assisted breeding, a surprisingly low number of validated SNPs are currently available for perennial ryegrass.ResultsA perennial ryegrass unigene set representing 9,399 genes was used as a reference for the assembly of 802,156 high quality reads generated by 454 transcriptome sequencing and for in silico SNP discovery. Out of more than 15,433 SNPs in 1,778 unigenes fulfilling highly stringent assembly and detection parameters, a total of 768 SNP markers were selected for GoldenGate genotyping in 184 individuals of the perennial ryegrass mapping population VrnA, a population being previously evaluated for important agronomic traits. A total of 592 (77%) of the SNPs tested were successfully called with a cluster separation above 0.9. Of these, 509 (86%) genic SNP markers segregated in the VrnA mapping population, out of which 495 were assigned to map positions. The genetic linkage map presented here comprises a total of 838 DNA markers (767 gene-derived markers) and spans 750 centi Mogan (cM) with an average marker interval distance of less than 0.9 cM. Moreover, it locates 732 expressed genes involved in a broad range of molecular functions of different biological processes in the perennial ryegrass genome.ConclusionsHere, we present an efficient approach of using next generation sequencing (NGS) data for SNP discovery, and the successful design of a 768-plex Illumina GoldenGate genotyping assay in a complex genome. The ryegrass SNPs along with the corresponding transcribed sequences represent a milestone in the establishment of genetic and genomics resources available for this species and constitute a further step towards molecular breeding strategies. Moreover, the high density genetic linkage map predominantly based on gene-associated DNA markers provides an important tool for the assignment of candidate genes to quantitative trait loci (QTL), functional genomics and the integration of genetic and physical maps in perennial ryegrass, one of the most important temperate grassland species.

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Section: Methodsmentioning

confidence: 99%

A transcriptome map of perennial ryegrass (Lolium perenne L.)

et al. 2012

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“…Two QTLs for crown rust resistance (LpPc1 and LpPc3) have been detected in LG2 of perennial ryegrass (Dumsday et al 2003, Muylle et al 2005. Moreover, another QTL for crown rust resistance has been detected in LG2 of Italian ryegrass (Studer et al 2007). A cluster of crown rust resistance loci (the Pca cluster) has been located on chromosome B in diploid oat (Yu and Wise 2000).…”

Section: Discussionmentioning

confidence: 99%

Genetic mapping of disease resistance gene analogs from the Italian ryegrass (Lolium multiflorum Lam.) genome

Miura¹,

Ding

Hirata³

et al. 2008

Breed. Sci.

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Genomic DNA sequences homologous to the nucleotide binding site (NBS)-leucine-rich repeat (LRR) genes were mapped for Italian ryegrass (Lolium multiflorum Lam.) by using previously published disease resistance gene analogs (RGAs). The RGAs were cloned by means of a nested polymerase chain reaction (PCR) approach with degenerate primers designed from conserved regions of the NBS domain of plant disease resistance genes (R-genes), and primer pairs for specific sequence-tagged sites (STS) were subsequently designed for efficient generation of the RGA fragments. To map the RGA clones on the Italian ryegrass genetic map, an F 1 mapping family was used for the detection of restriction-site polymorphisms of the RGA fragments. Out of 50 RGA fragments, 11 detected genetic polymorphism in the F 1 family. Polymorphic marker loci data were used for linkage analysis with JoinMap version 3.0. The linkage analysis revealed that 10 of the 11 RGAs were mapped in seven linkage groups constructed with amplified fragment length polymorphism (AFLP), simple sequence repeat (SSR) , and expressed sequence tag (EST)-derived cleaved amplified polymorphic sequence (CAPS) markers. This information will be useful for the development of new genetic markers linked to genes associated with disease resistance.

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“…This is supported by the strong correlations of crown rust disease scores of a set of Italian ryegrass cultivars among sites of the EUCAR-PIA multisite rust evaluation trial (Boller et al 2003;Schubiger et al 2006). Studer et al (2007) also found crown rust resistance of individual genotypes used for a QTL mapping study to be detected consistently over a number of environments. The Italian ryegrass populations described here varied significantly for crown rust resistance, providing opportunities for selection.…”

Section: Disease Resistance Needs Improvementmentioning

confidence: 92%

Ecotypes of Italian ryegrass from Swiss permanent grassland outperform current recommended cultivars

et al. 2009

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Italian ryegrass (Lolium multiflorum Lam. ssp. italicum Volkart ex Schinz et Keller) thrives well in permanent grassland in mild and moist regions of Switzerland. Ecotypes of Italian ryegrass from Swiss permanent meadows have often been used successfully as the base material of breeding programmes. However, their agronomic performance per se has never been studied in detail. Therefore, field trials were conducted to assess the potential of this semi-natural genetic resource for use in breeding. Twenty ecotype populations were collected in different geographical regions in 2003 and seed was increased. Plot trials with 20 ecotype populations were conducted 2005-2007 at three locations, supplemented by row trials at two additional locations, and including four currently recommended cultivars as controls. Average performance in terms of yield, vigour and resistance to snow mould of ecotypes was superior to the cultivars. Depending on the characteristic, between three and 16 of the 20 ecotypes performed significantly better than the cultivars mean. However, resistance against crown rust of all ecotypes was significantly poorer than that of the cultivars. Correlation and regression analysis showed that more eastern and more northern collecting sites harboured better performing ecotypes. However, the most consistent site related factor favouring performance of the ecotypes in terms of yield, vigour, snow mould and Xanthomonas resistance was a low abundance of species which are typical of Arrhenatheretum type meadows. Data from the plot trials were related to results obtained with spaced plants at a single site, either in a seedling nursery or in the greenhouse. Resistance against crown rust was extremely well predicted by spaced plant observations. Xanthomonas resistance observed after artificial inoculation in the greenhouse was also significantly, but less closely correlated with field observations. An early date of ear emergence as observed on spaced plants was associated with high annual yield in the plot trials. It is concluded that in intensively managed habitats, natural selection has resulted in ecotype populations of Italian ryegrass which are highly promising for use in breeding. Individual plant selection for resistance can be expected to efficiently reduce their high susceptibility to crown rust.

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Consistent detection of QTLs for crown rust resistance in Italian ryegrass (Lolium multiflorum Lam.) across environments and phenotyping methods

Cited by 48 publications

References 35 publications

A transcriptome map of perennial ryegrass (Lolium perenne L.)

A transcriptome map of perennial ryegrass (Lolium perenne L.)

Genetic mapping of disease resistance gene analogs from the Italian ryegrass (Lolium multiflorum Lam.) genome

Ecotypes of Italian ryegrass from Swiss permanent grassland outperform current recommended cultivars

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