A microsatellite map of white clover

Area of Science:

• Genetics
• Genomics
• Plant Breeding

Background:

• The white clover (Trifolium repens) nuclear genome is crucial for agriculture but remains genetically underexplored.
• Developing genetic markers is essential for understanding its complex genetic architecture.

Purpose of the Study:

• To develop and utilize simple sequence repeat (SSR) genetic markers for constructing a comprehensive genetic map of the white clover genome.
• To identify subgenome organization and map specific loci within the allopolyploid white clover.

Main Methods:

• Mining expressed sequence tag (EST) databases and genomic libraries to identify SSRs.
• Utilizing 92 F1 progeny from a cross between two heterozygous genotypes for marker analysis.
• Employing the joinmap algorithm for map length estimation and linkage group identification.

Main Results:

• Identified 2,086 EST-derived SSRs (EST-SSRs), with 566 usable and 335 polymorphic markers.
• Constructed a 1,144 cM whole-genome map spanning all 16 homologues, detecting 493 loci.
• Mapped the R (red leaf) locus to linkage group B1 and identified eight homoeologous pairs of linkage groups.

Conclusions:

• This study presents the first whole-genome functional map for an allopolyploid species using EST-SSRs.
• The developed map facilitates the resolution of quantitative traits and accelerates white clover improvement programs.
• Trifolium repens is the first species in the Trifolieae tribe to be mapped exclusively using SSRs.