A microsatellite map of white clover

Abstract

The white clover ( Trifolium repens) nuclear genome (n = 2x = 16) is an important yet under-characterised genetic environment. We have developed simple sequence repeat (SSR) genetic markers for the white clover genome by mining an expressed sequence tag (EST) database and by isolation from enriched genomic libraries. A total of 2,086 EST-derived SSRs (EST-SSRs) were identified among 26,480 database accessions. Evaluation of 792 EST-SSR primer pairs resulted in 566 usable EST-SSRs. Of these, 335 polymorphic EST-SSRs, used in concert with 30 genomic SSRs, detected 493 loci in the white clover genome using 92 F1 progeny from a pair cross between two highly heterozygous genotypes--364/7 and 6525/5. Map length, as estimated using the joinmap algorithm, was 1,144 cM and spanned all 16 homologues. The R (red leaf) locus was mapped to linkage group B1 and is tightly linked to the microsatellite locus prs318c. The eight homoeologous pairs of linkage groups within the white clover genome were identified using 96 homoeologous loci. Segregation distortion was detected in four areas (groups A1, D1, D2 and H2). Marker locus density varied among and within linkage groups. This is the first time EST-SSRs have been used to build a whole-genome functional map and to describe subgenome organisation in an allopolyploid species, and T. repens is the only Trifolieae species to date to be mapped exclusively with SSRs. This gene-based microsatellite map will enable the resolution of quantitative traits into Mendelian characters, the characterisation of syntenic relationships with other genomes and acceleration of white clover improvement programmes.

Evidence on the Molecular Basis of the Ac/ac Adaptive Cyanogenesis Polymorphism in White Clover (Trifolium repens L.)

“…Here we have identified the gene that is likely to underlie the Ac/ac cyanogenic glucoside polymorphism; we have found that, like Li/li, this component of the cyanogenesis polymorphism apparently arises through a gene presence/absence polymorphism. With recent advances in the development of genetic and genomic tools for white clover (e.g., Barrett et al 2004;Cogan et al 2007), this species may prove a useful resource for further studies on the molecular genetics of adaptation.…”

“…It is a perennial and an insectpollinated, obligate outcrosser; plants also spread vegetatively by stolons. Chromosome number and genetic map data indicate that white clover is an allotetraploid (e.g., Barrett et al 2004). While Ac and Li have not been mapped, both cyanogenesis genes are believed to be present in only one of the two parental genomes (e.g., Williams and Williamson 2001); this suggests that the species originated through the hybridization of a cyanogenic and an acyanogenic Trifolium species (Williams and Williamson 2001;Badr et al 2002).…”

Development of Genomic Resources in the Species of Trifolium L. and Its Application in Forage Legume Breeding

“…The location of the SI locus was described by Casey et al [14] and utilised a characterised BAC library for white clover with partial BAC end sequencing reported by Febrer et al [14]. Genetic maps in white clover have been reported by several groups [12,[15][16][17]. They were all based on a mixture of SSR and AFLP markers [12], or exclusively SSR markers.…”

Development of mapping populations for genetic analysis in yams (Dioscorea rotundata Poir. and Dioscorea alata L.)

“…In choosing the crossing parents, it is recommended that, they should be different in the traits of interest in order to facilitate linkage mapping and segregation analysis (Young, 1994). However, when using mapping populations based on highly heterozygous parents, differences in the trait of interest between the parents is not essential, because many of the genes underpinning the trait still segregate in the population (Barrett et al, 2004). There are several methods for generating a mapping population, but the choice depends on the pollination pattern of the plant species.…”

“…One advantage of the former breeding method is that, it minimizes the risk of inbreeding depression and segregation distortion in the mapping population, both of which can significantly reduce the power and utility of a genome map (Faville et al, 2003). The successful use of a double heterozygous (or double-pseudotestcross) strategy in open pollinated species has been reported in linkage mapping for perennial ryegrass (Faville et al, 2004), white clover (Barrett et al, 2004) Eucalyptus (Grattapaglia and Sederoff, 1994) and asparagus (Lewis and Sink, 1996).…”