Genetic diversity and association analysis of Chinese chestnut (Castanea mollissima Blume) cultivars based on SSR markers

Abstract

To evaluate the genetic diversity, patterns of genetic structuring, and linkage disequilibrium (LD) of Chinese chestnut, we conducted a simple sequence repeat (SSR)-based analysis of 95 cultivars from ten provinces in China. We also conducted marker–trait association analysis with 18 important agronomic traits and 41 SSR loci. The results showed that there was a moderate level of polymorphism across all cultivars, with an average of 2.7 observed alleles per locus. The mean observed (Ho) and expected (He) heterozygosities were 0.3187 and 0.4548, respectively. Genetic structuring analysis revealed three dominant gene pools, with diverse geographic origins among the cultivars in each gene pool. Among the SSR loci used to analyze these cultivars, 9.5 % were in LD (P < 0.05). The mean r2 value for all loci was 0.0331. A general linear model (GLM) and a mixed linear model (MLM) were used for the association analysis between phenotypic traits and SSR loci. After false-positive correction, there were two loci in the GLM and one in the MLM remained significant. These results provide baseline information on the genetic diversity, genetic structuring, and kinship of these Chinese chestnut cultivars, and laid the important theoretical basis for molecular marker-assisted breeding of chestnut.