PROCEEDINGS Open Access Association mapping for morphological and

Background: To optimize marker-assisted selection programs, knowledge of the genetic architecture of phenotypic traits is very important for breeders. Generally, most phenotypes, e.g. morphological and physiological traits, are quantitatively inherited, and thus detection of the genes underlying variation for these traits is difficult. Association mapping based on linkage disequilibrium has recently become a powerful approach to map genes or quantitative trait loci (QTL) in plants. Results: In this study, association analysis using 20 simple sequence repeat (SSR) markers was performed to detect the marker loci linked to 13 morphological traits and 10 physiological traits in a wild P. simonii population that consisted of 528 individuals sampled from 16 sites along the Yellow River in China. Based on a model controlling for both population structure (Q) and relative kinship (K), three SSR markers (GCPM_616-1 in 31.2 Mb on LG I, GCPM_4055-2 in 5.7 Mb on LG XV, and GCPM_3142 of unknown location) were identified for seven traits. GCPM_616-1 was associated with five morphological traits (R2 = 5.14-10.09%), whereas GCPM_3142 (15.03%) and GCPM_4055-2 (13.26%) were associated with one morphological trait and one physiological trait, respectively. Conclusions: The results suggest that this wild population is suitable for association mapping and the identified markers will be suitable for marker-assisted selection breeding or detection of target genes or QTL in the near future