Modified three – way crosses involving advanced interspecific tomato hybrids (F12) and commercially cultivated tomato varieties namely Supersteak (S), Beef (Florida) (BF) and Plumb (Rio grande) (PR) were made to generate F1 hybrids. The F1 hybrids were crossed to both the pollen and seed parents to produce the backcrosses and were also allowed to random mate to produce the F2 and F3 populations. The parents, F1s, F2s, F3s and backcrosses were evaluated under rainfed conditions. Floral trait analysis and genomic analysis using Single Nucleotide Polymorphisms (SNPs) markers of the quantitative trait loci (QTL) underlying fruit size in tomato were also performed. The Analysis of Variance (ANOVA) on agronomic, yield, floral and fruit traits showed significant differences (P = 0.05) among the tomato genotypes. The cross, S x (W x R) was the most promising three – way hybrid that can be exploited for increased fruit size and yield in the humid tropics. Mean fruit weight had significant and positive correlation with all the floral traits with the exception of flower and style lengths. The number of locules per fruit had the highest correlation value (r = 0.984**) with fruit size. Path coefficient analysis revealed that number of locules per fruit had the highest positive direct effect (p = 0.8086) on fruit size. This was closely followed by ovary diameter (p = 0.7942) and stigma diameter (p = 0.7685). On the other hand, style length had the highest negative direct effect (p = -0.9147) on fruit size. The fruit shape index showed significant positive correlation with the ovary shape index (r = 0.835**) and seed shape index (r = 0.718**). However, fruit shape index was negatively and significantly correlated with ovary diameter (r = -0.601*), fruit diameter (r = -0.576*) and seed diameter (r = -0.519*). The structure analysis revealed that the tomato genotypes studied had three sub-populations. The association mapping using 25 SNPs markers detected 9 markers with significant association with mean fruit weight, fruit length, fruit diameter, number of locules per fruit and fruit shape index. The SNP marker, Solyc11-17 exhibited significant association with both fruit diameter , number of locules per fruit and fruit shape index. The variation in fruit diameter explained by the marker, Solyc11-17 was higher than the variations in number of locule and fruit shape index (141.5%, 23% and 18.3%) respectively. All the 9 markers detected are recommended for fruit size improvement breeding programe in tomato.
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