Association Analysis Of Phenotypic Traits With Scot Molecular Markers In Chtysanthemum × Morifolium Ramat.

Chrysanthemum × morifolium Ramat. are flowering plants of genus chrysanthemum in the Asteraceae family. Adored by the Chinese people, Chrysanthemums have an extremely complicated genetic background due to centuries of mutation, natural hybridization, and artificial selection, making breeding programs difficult. Based on linkage disequilibrium, association analysis is used to detect gene loci or marker loci that have specific functions and are closely correlated with phenotypic variations. The results may be of value to molecular-marker assisted selection. In this study, phenotypic traits of 59 representative chrysanthemum cultivars were combined with SCoT markers in an association analysis to search for molecular marker loci correlated with quantitative traits. The main results are as follows:(1) Phenotypic variation coefficient analysis showed that all phenotypic traits were interspecifically more variable than intraspecifically, exhibiting great potential for classifying Chrysanthemums. R cluster analysis showed that, other than plant height, flower diameter, and petal length-to-width ratio, all phenotypic traits were closely correlated with each other. Principal component analysis found that cultivars were mainly differentiated by petal length-to-width ratio, petal length, leaf width, leaf length, leaf length-to-petiole length ratio, plant height, and petiole posture, indicating the necessity of including leaf traits in morphological classification.(2) From an initial set of 36 SCoT primers, ten primers yielding clear and stable products were selected to process the 59 Chrysanthemum cultivars, generating 243 amplification bands, of which 240 were polymorphic. The percentage of polymorphism loci was 97.76%. Polymorphism Information Content(PIC) ranged between 0.85 and 0.96, with an average value of 0.9267. SCoT markers thus appeared to effectively reflect the genetic diversity of Chrysanthemum cultivars.(3) UPGMA clustering analysis of the SCoT markers showed, other than 9 chrysanthemum cultivars, the remaining 51 chrysanthemum cultivars were categorized into 4 groups which differed from traditional groupings based on petal morphology. Population structure analysis assigned the 59 chrysanthemum cultivars into 3 interpenetrating groups, deviating once again from traditional classification. The 3 groups nonetheless were somewhat morphologically distinct, and their germplasm permeated obviously each other.(4) Association analysis detected 23 SCoT marker loci corresponding to 7 phenotypic traits(P < 0.01). Of these loci, 18 were associated with flower characteristics such as petal length, petal width, and petal length-to-width ratio, and 9 were correlated with leaf traits including petiole length, leaf length, stipule size, and leaf length-to-width ratio. Each locus explained between 0.0094 and 0.2181 of the observed phenotypic variance.