title: Analysis of genetic diversity and population structure in a tomato (Solanum lycopersicum L.) germplasm collection based on single nucleotide polymorphism markers.
abstract: Knowledge of genetic diversity is important to assist breeders in the selection of parental materials and in the design of breeding programs. In this study, we genotyped 348 inbred tomato lines, representing vintage and contemporary fresh-market varieties, by using 52 single nucleotide polymorphisms (SNPs); 45 of these were found to be polymorphic. The average minor allele frequency and unbiased expected heterozygosity were 0.315 and 0.356, respectively. Population structure analysis revealed that contemporary germplasm could be distinctly divided into six subpopulations representing three market classes and breeding programs (pink, green, and red). Vintage germplasm could be separated into at least two subpopulations, and more admixtures were found in vintage lines than in contemporary lines. These findings indicate that contemporary inbred lines are more diversified than vintage inbred lines. AMOVA of vintage and contemporary lines was performed. A significant difference was found (P < 0.01), which explained 17.4% of the total genetic variance. Subsequently, we constructed a core collection using 45 polymorphic SNP markers. The data showed that all alleles were captured by only 2% of lines, indicating that more alleles, as well as rare alleles, could enable more variation to be captured in the core collection. These data allow us to discard redundant inbred tomato lines and to select elite inbred lines, which will accelerate the breeding process.
authors.affiliation: College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, China.|Institute of Vegetables, Liaoning Academy of Agricultural Sciences, Shenyang Liaoning, China.
authors.forename: T
authors.initials: T
authors.lastname: Wang
authors.affiliation: Institute of Vegetables, Liaoning Academy of Agricultural Sciences, Shenyang Liaoning, China.
authors.forename: Q D
authors.initials: QD
authors.lastname: Zou
authors.affiliation: Institute of Vegetables, Liaoning Academy of Agricultural Sciences, Shenyang Liaoning, China.
authors.forename: S Y
authors.initials: SY
authors.lastname: Qi
authors.affiliation: Institute of Vegetables, Liaoning Academy of Agricultural Sciences, Shenyang Liaoning, China.
authors.forename: X F
authors.initials: XF
authors.lastname: Wang
authors.affiliation: Institute of Vegetables, Liaoning Academy of Agricultural Sciences, Shenyang Liaoning, China.
authors.forename: Y Y
authors.initials: YY
authors.lastname: Wu
authors.affiliation: Institute of Soil and Water Conservation, Liaoning Academy of Agricultural Sciences, Chaoyang, Liaoning, China.
authors.forename: N
authors.initials: N
authors.lastname: Liu
authors.affiliation: Institute of Vegetables, Liaoning Academy of Agricultural Sciences, Shenyang Liaoning, China.
authors.forename: Y M
authors.initials: YM
authors.lastname: Zhang
authors.affiliation: Institute of Vegetables, Liaoning Academy of Agricultural Sciences, Shenyang Liaoning, China.
authors.forename: Z J
authors.initials: ZJ
authors.lastname: Zhang
authors.affiliation: Institute of Vegetables, Liaoning Academy of Agricultural Sciences, Shenyang Liaoning, China haitao57@sohu.com.
authors.forename: H T
authors.initials: HT
authors.lastname: Li
mesh_terms: D005787:Gene Frequency; D017343:Genes, Plant; D056726:Genetic Association Studies; D005819:Genetic Markers; D005838:Genotype; D018551:Solanum lycopersicum / Q000235:genetics*; D000069600:Plant Breeding; D020641:Polymorphism, Single Nucleotide; D012639:Seeds / Q000235:genetics*; D017422:Sequence Analysis, DNA
chemical_list: D005819:Genetic Markers