Genetic Diversity Assessment of Upland Cotton Variety Resources in China Based on Phenotype Traits and Molecular Markers

Evaluating germplasm resources comprehensively and accurately is of great significance to their efficient utilization. To comprehensively characterize the genetic relationships among upland cotton (Gossypium hirsutum L.) varieties, the genetic diversity of 172 upland cotton varieties in China was assessed using 18 phenotype traits and 154 polymorphic simple sequence repeat molecular markers. According to the variation analysis of phenotype traits, the variation coefficient, which reflects the level of phenotypic genetic diversity, varied widely among traits. The analysis of marker polymorphism showed that the average allele number, gene diversity index, and polymorphism information content were 2.62, 0.3985 and 0.3343, respectively, indicating a relatively low level of genetic diversity. All varieties grouped into five clusters (I-V) based on phenotypic data. Among the five clusters, clusters III and IV further grouped into four (III-1, III-2, III-3, and III-4) and two subclusters (IV-1 and IV-2), respectively. Cluster I and subclusters III-1, III-3, III-4, and IV-1 displayed prominent values in some of the 18 traits. Then, all varieties grouped into nine clusters (A-I) based on molecular marker data. Clusters C, D, E, F, H, and I displayed prominent values in some of the 18 traits. Clustering based on phenotype traits and/or molecular markers was largely congruent with varietal pedigree information, but the clustering of varieties was independent of the varietal ecological sources. Results in this study suggest that varieties with prominent complementary traits in different phenotypeand/or marker-based clusters can be selected as parents in breeding.