Genome mapping of white clover (Trifolium repens L.) and comparative analysis within the Trifolieae using cross-species SSR markers

Abstract

Allotetraploid white clover (Trifolium repens L.), a cool-season perennial legume used extensively as forage for livestock, is an important target for marker-assisted breeding. A genetic linkage map of white clover was constructed using simple sequence repeat (SSR) markers based on sequences from several Trifolieae species, including white clover, red clover (T. pratense L.), Medicago truncatula (Gaertn.) and soybean (Glycine max L.). An F 1 population consisting of 179 individuals, from a cross between two highly heterozygous genotypes, GA43 and Southern Regional Virus Resistant, was used for genetic mapping. A total of 1,571 SSR markers were screened for ampliWcation and polymorphism using DNA from two parents and 14 F 1 s of the mapping population. The map consists of 415 loci ampliWed from 343 SSR primer pairs, including 83 from white clover, 181 from red clover, 77 from M. truncatula, and two from soybean. Linkage groups for all eight homoeologous chromosome pairs of allotetraploid white clover were detected. Map length was estimated at 1,877 cM with 87% genome coverage. Map density was approximately 5 cM per locus. Segregation distortion was detected in six segments of the genome (homoeologous groups A1, A2, B1, B2, C1, and D1). A comparison of map locations of markers originating from white clover, red clover, and alfalfa (M. sativa L.) revealed putative macro-colinearity between the three Trifolieae species. This map can be used to link quantitative trait loci with SSR markers, and accelerate the improvement of white clover by marker-assisted selection and breeding.

Applied Genetics and Genomics in Alfalfa Breeding

“…Currently, simple sequence repeat (SSR) markers are widely used for QTL analysis in alfalfa, most of which were derived from Medicago truncatula [52]. The SSR markers have facilitated genetic studies of alfalfa, including genetic map construction [53][54][55], comparative mapping [53,56], population structure analysis [11] and QTL identification [37,57]. However, the number of SSR markers is insufficient for the needs of fine mapping and genome-wide association studies.…”

“…In addition to these disease resistances, QTL for nitrogen nutrition [84], flowering time [85] and aerial morphological characteristics [86] have been identified. A high level of synteny has been found between alfalfa and related species, including M. truncatula [53,56,87,88], a close relative whose genome has been sequenced [89].…”

Genomic and transcriptomic approaches towards the genetic improvement of an underutilised crops: The case of Bambara groundnut

“…Sequence data derived from medicago truncatula, soybean, cowpea and common bean can be used to develop cross-species simple sequence repeat (SSR) markers. For example, Medicago truncatula based SSRs provided genetic markers for linkage mapping in alfalfa (Medicago sativa) (Sledge et al, 2005) and more distantly related crop legumes (Gutierrez et al, 2005;Zhang et al, 2007). This approach can be applied in bambara groundnut, where a closely related legume crop sequence data, such as common bean, mung bean or soybean can help in identifying molecular markers for the traits of interest.…”

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.…”