A framework linkage map of perennial ryegrass based on SSR markers

Abstract

A moderate-density linkage map for Lolium perenne L. has been constructed based on 376 simple sequence repeat (SSR) markers. Approximately one third (124) of the SSR markers were developed from GeneThresher libraries that preferentially select genomic DNA clones from the gene-rich unmethylated portion of the genome. The remaining SSR marker loci were generated from either SSR-enriched genomic libraries (247) or ESTs (5). Forty-five percent of the GeneThresher SSRs were associated with an expressed gene. Unlike EST-derived SSR markers, GeneThresher SSRs were often associated with genes expressed at a low level, such as transcription factors. The map constructed here fulfills 2 definitions of a "framework map". Firstly, it is composed of codominant markers to ensure map transferability either within or among species. Secondly, it was constructed to achieve a level of statistical confidence in the support-for-order of marker loci. The map consists of 81 framework SSR markers spread over 7 linkage groups, the same as the haploid chromosome number. Most of the remaining 295 SSR markers have been placed into their most likely interval on the framework map. Nine RFLP markers and 1 SSR marker from another map constructed using the same pedigree were also incorporated to extend genome coverage at the terminal ends of 5 linkage groups. The final map provides a robust framework with which to conduct investigations into the genetic architecture of trait variation in this commercially important grass species.

Expressed sequence tag-derived microsatellite markers of perennial ryegrass (Lolium perenne L.)

“…Although EST-derived microsatellite markers are reported to yield lower levels of intraspecific polymorphisms compared to SSRs developed from non-coding genomic regions (Saha et al 2006), the number of 143 SSR markers, which were polymorphic in VrnA, was high (47% of the 306 primer pairs amplifying in VrnA, 19% of 744 ESTs used for primer design). This is comparable to previous findings in ryegrasses, where similar proportions (21-31%, depending on the library source) of SSRs for which primers had been tested, were polymorphic and could be mapped in a specific population (Faville et al 2004;Gill et al 2006;Hirata et al 2006).…”

“…The percentage of ESTs with significant gene annotations (40%) is comparable to results found in previous studies, where 47% of mapped EST-SSRs were functionally annotated with BLASTN hits (E \ 1 -10 ) to other plant species (Faville et al 2004). GeneThresher 1 -derived SSRs revealed 45% to be highly similar (E \ 1 -7 ) to genes expressed in other species (Gill et al 2006). Moreover, the enhanced transferability to other pedigrees and species (almost 80% for Festuca-Lolium species; Saha et al 2004) makes them useful for alignment of linkage maps and for studying interspecific synteny.…”

“…In perennial ryegrass, a major component of permanent pastures and meadows of temperate regions worldwide, SSR markers are mainly involved in cultivar identification and comparison (Kubik et al 2001;Roldán-Ruiz et al 2001), genetic diversity studies (Jensen et al 2007), genetic linkage mapping and trait dissection in order to implement marker assisted breeding strategies (Yamada et al 2005). Although several studies report on the development of SSR markers in perennial ryegrass (Faville et al 2004;Gill et al 2006;Jensen et al 2007;Jones et al 2001;Kubik et al 2001;Lauvergeat et al 2005), the number of publicly available microsatellite markers is still limited and has to be increased in order to ensure a reasonable genome coverage required for linkage mapping and trait dissection in Lolium species. Since isolation and characterisation of SSR loci from genomic libraries is labour-intensive and costly (Squirrell et al 2003), extended genome and cDNA sequencing projects have been exploited for in silico gene discovery and marker development.…”

Comparative Analyses Between Lolium/Festuca Introgression Lines and Rice Reveal the Major Fraction of Functionally Annotated Gene Models Is Located in Recombination-Poor/Very Recombination-Poor Regions of the Genome

“…3. Access to a GeneThresher database (Gill et al 2006) in which 25,000 sequences have already been aligned to the rice genome allowed the selection of a sequence from a putative gene on a BAC/PAC clone of interest and primers were then designed from within that sequence. ½Gene Thresher sequences used had all previously been aligned to a BAC/PAC clone on rice linkage group 1.…”

Genetic mapping and annotation of genomic microsatellites isolated from globe artichoke

“…Some clustering of SSRs has been observed around the putative centromeric region of LG1, -2, -3 and -10, a pattern which is not unusual (Arens et al 1995;Bhattramakki et al 2000;Gill Jones et al 2002;McCouch et al 2002;Ramsay et al 2000). The addition of new markers has allowed the filling of some of the gaps in the base maps, especially on LGs 4, 8 and 14; and the addition of a second bridge marker to LG9.…”