Quantitative Trait Locus Analysis of Morphogenetic and Developmental Traits in an SSR and AFLP-Based Genetic Map of White Clover (\u3cem\u3eTrifolium Repens\u3c/em\u3e L.)

Molecular marker-assisted plant breeding is a key target for the temperate legume pasture crop white clover (Trifolium repens L.). The first genetic linkage map of white clover has been constructed using self-fertile mutants to derive an intercross based fourth and fifth generation inbred parental genotypes (F2[I.4R x I.5J]). The framework map was constructed using simple sequence repeat (TRSSR) and amplified fragment length polymorphism (AFLP) markers. Eighteen linkage groups (LG) corresponding to the anticipated 16 chromosomes of white clover (2n = 4x = 32), with a total map length of 825 cM were derived from a total of 135 markers (78 TRSSR loci and 57 AFLP loci). The F2(I.4R x I.5J) family has been subjected to intensive phenotypic analysis for a range of morphogenetic and developmental traits over several years at IGER, Aberystwyth, Wales and East Craigs, near Edinburgh, Scotland. The resulting phenotypic data were analysed independently to identify QTL (quantitative trait loci) for the various traits, using single marker regression (SMR), interval mapping (IM) and composite interval mapping (CIM) techniques. Multiple coincident QTL regions were identified from the different years and different sites for the same or related traits. The data were reanalysed using a meta-analysis across years and sites and Best Linear Unbiased Estimates (BLUEs) were derived for the plant spread, petiole length, leaf width, leaf length, leaf area, internode length, plant height and flowering date traits. A total of 24 QTLs were identified on 10 of the linkage groups. Three regions on LGs 2, 7 and 12 all demonstrated overlapping QTLs for multiple traits (Figure 1). A meta-analysis approach can quickly identify regions of the genome that control the trait in a robust predictable manner across multiple spatial and temporal replication for rapid targeted genetic enhancement via marker-assisted breeding. This first genetic dissection of agronomic traits in white clover provides the basis for comparative trait-mapping studies and the enhanced development and implementation of marker-assisted breeding strategies