Abstract:

Association analysis is a procedure for detecting QTLs as well as their alleles based on linkage disequilibrium. The genotyping data of 16 SSR and 10 SCoT markers on 99 Chrysanthemum morifolium cultivars were used to detect associations with 10 phenotypic traits by using GLM and MLM methods. The Shannon’s index of the population ranged from 1.46–2.52. Genetic structure analysis showed that the selected cultivars were composed of 5 subpopulations. There were 8 SSR loci associated with 7 phenotypic characters（P < 0.01），among which 3 traits of propagative organ（inflorescence diameter，inflorescence height，ligulate flower width）were associated with 5 loci，while 4 traits of vegetation organ（petiole length，leaf blade length，stipule size，lamina magnitude）were associated with 4 loci by using GLM models. The ratio of explanation on the phenotype of individual locus ranged from 0.06–0.40. Inflorescence diameter was significantly associated with three SCoT loci by using GLM models. Four phenotypic characters were associated with 3 SSR loci based on MLM models. These markers（JH42，JH81 and JH86）detected by MLM method can be found according to GLM method similarly. Howerver，the ratio of explanation obtained by MLM method was slightly lower than by GLM method.

Key words: Chrysanthemum morifolium, SSR marker, SCoT marker, population structure, association analysis