Abstract
The assessment of genetic diversity and genetic structure of crops has a vital impact on the plant breeding program, including the characterization, use and conservation of genetic material. The genetic diversity and genetic structure of a set of 94 F3 tomato hybrids were assessed with 25 polymorphic SNP markers of quantitative trait loci (QTLs) underlying fruit size in tomatoes using Sequenom Mass ARRAY system. A total of 50 alleles were amplified and the average polymorphic information content (PIC) was 0.2220. Nei's genetic distance ranged from 0 to 0.62. Therefore, single nucleotide sequence (SNP) markers detected a significantly high degree of polymorphism in tomato hybrids. Cluster analysis using the unweighted pair group method with arithmetic mean methods (UPMA) indicated that the tomato hybrids studied are grouped into four main groups, which is to some extent consistent with the size, shape and number of locules of the tomatoes studied. Analysis of population structure with SNP markers revealed three subpopulations. Association mapping using 25 SNP markers detected 9 markers with a significant association with mean fruit weight, fruit length, fruit diameter, number of locules, and fruit shape index. The nine markers detected in this study are recommended for the tomato fruit size improvement breeding program.
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