| Tomato(Solanum lycopersicum L.) is one of the most economically important vegetable crops in the world. The quality-related traits are always hotspots of tomato breeding. Weak light is a major limiting factor for tomato production, and plant breeding is the most effective way to improve weak light tolerance and reduce the yield loss. The discovery of molecular markers associated with tomato quality and weak light tolerance will greatly promote variety improvement and germplasm innovation in tomato.In the present study, association mapping population including 191 tomato inbred lines was selected from 348 tomato lines. Genetic diversity, population structure, and linkage disequilibrium (LD) were analyzed based on three types of molecular marker (SNPs, InDels, and SSRs). Finally, association analysis between genotypes and tomato quality and weak light tolerance related traits was performed, and the molecular markers associated with the target traits were detected. The main results were as follows:1. In this study,348 inbred tomato lines were genotyped through 52 single-nucleotide polymorphisms (SNPs), among which 45 were informative for subsequent analysis. Genetic diversity analysis found that average expected heterozygosity and PIC were 0.395 and 0.309, respectively. Among the six subpopulations, Cherry tomato had the highest genetic variation, Chinese tomato came second. Population structure and clustering analysis revealed that 348 tomato lines could be divided into three main groups, corresponding to cherry, European tomato, and Chinese tomato. Chinese tomato could be further separated into three subgroups represented pink, non-ripening, and red tomato. Subsequently,191 lines were selected based on the genetic distance from 348 tomato lines. Finally, a core collection was constructed, and the data showed that only a small number of accessions (2%) were needed to retain all SNP alleles as well as the whole allelic diversity.2. In this study,191 tomato inbred lines were genotyped using 273 molecular markers, 238 markers (103SNPs,113InDels, and 22SSRs) showed polymorphism. Three types of molecular markers were different in distribution of allele frequency, InDels and SSRs had more low frequency alleles. Genetic diversity and population structure analysis showed that SNPs could detected more genetic variation and subpopulations within cultivated tomatoes, this indicated SNPs are more efficient in distinguishing closely related tomato lines. Population stucture analysis based on 238 markers subdivided 191 tomato lines into four or six subpopulation. LD analysis indicated that LD decays over 3-5cM when InDel and all markers was used, while it happened within 10?15 cM when SNP was used.3. In this study, fruit quality-related traits of 191 tomato lines were assessed in two years, the selected traits included fruit weight, fruit diameter, fruit shape, locule number, sugar content, and fruit firmness. Six fruit quality-related traits were significant difference among individuals, and all traits were not significant difference among different years except sugar content. Association mapping for the six traits with mixed linear model,115 significant associated markers were detected. There were 10 for fruit weight,16 markers for fruit diameter,38 for fruit shape,11 for locule number,17 for sugar content, and 23 for fruit firmness. The explanation rate of phenotypic variation ranged from 0.8% to 14.8%, SSR45 explained the highest phenotypic variation for fruit firmness.4. A total of 191 tomato lines were evaluated for weak light tolerance under both well light and weak light environments. The selected criteria included plant height, stem diameter, chlorophyll content, fruit weight, rate of fruit set, and five relative weak light tolerance indexes. Five traits were significant different among two light treats, fruit weight, stem diameter, chlorophyll content, and the rate of fruit set fell by an average of 33.02%?24.10%? 26.50%, and 39.02%, on the contrary, plant height, on average, increased by 28.87%. The correlations of five relatively weak light tolerance indexes were poor, which suggested that the five indexes were controlled by different genetic composition. The results of mapping showed that 73 significant associations were detected. There were 20 associations for plant height, concluding 14 for fruit weight,13 for stem diameter,18 for rate of fruit set, and 8 for chlorophyll content. Finally, five weak light tolerance index for correlation analysis suggested that 48 significant associations were detected. There were 8 associations for weak light tolerance index of fruit weight,10 for weak light tolerance index of plant height,15 for weak light tolerance index of stem diameter,5 for weak light tolerance index of rate of fruit set, and 10 for weak light tolerance index of chlorophyll content, phenotypic variation rates were between 2.1% and 8.7%. |
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