QTL analysis of fruit traits in watermelon

Abstract:【Objective】Watermelon is one of the important fruit vegetables in horticultural crops. Mapping QTLs of fruit traits and constructing the system of marker-assisted selection(MAS) for fruit traits were extremely important for molecular breeding in watermelon. The aim of this research is to elucidate the genetic regularity and analyze the QTLs of flesh color, β-carotene content and other fruit traits of watermelon.【Methods】The inheritance of flesh color, β-carotene content and other fruit traits were studied using 359F2 plants derived from PI186490 with white flesh and the cultivated watermelon LSW-177 with red flesh.Harvested fruits were cut longitudinally and photographed to evaluate the traits. The fruit length and fruit width were measured with a ruler. Fruit shape index was the ratio of fruit length and fruit width. Flesh firmness of edge part of fruit was measured using hardness tester and soluble solid content of both central part and edge part were measured using refractometer. Flesh color was observed using the visual method and the value of β-carotene content was measured by HPLC. 195 CAPS markers developed with the high re-sequencing data were used to construct the genetic linkage map and to analyze the QTLs.【Results】The fruit traits included flesh color, β-carotene content, fruit length, fruit width, fruit shape index, fruit flesh firmness of edge part and soluble solid content. Three kinds of flesh colors(yellow, red and white)were separated in the F2 generation with the segregation ratio of 9∶3∶4, indicating that the inheritance of the flesh color was controlled by two major genes and was fit for the recessive epistasis model. β-carotenecontent showed a skew distribution in F2 population. Fruit length, fruit width, fruit shape index, fruit flesh firmness of edge part and soluble solid content all showed a normal distribution, suggesting that they were quantative traits and were controlled by multiple genes. CAPS markers were developed by the high-throughput re-sequencing method. 420 pairs of CAPS markers were designed, among them, 247 pairs of primers gave distinct bands of the expected length and generated polymorphic bands via PCR and enzyme digestion, with a polymorphic rate of 58.8%. A CAPS-based genetic linkage map was constructed with the F2 population. The linkage map contained 195 markers and was grouped into 11 linkage groups. All the 11 linkage groups covered a total genetic distance of 2 029.8 c M, with a mean distance between markers of 10.46 c M. The largest group(chromosome 9) contained 23 markers. Chromosome 5 and chromosome 10, with the smallest number of markers, contained 14 markers respectively.Group 1(chromosome 1) had the largest genetic distance of 262.46 c M meanwhile had the largest average marker interval of 15.44 c M. Group 4 had the smallest genetic distance of 149.81 c M meanwhile had the smallest average marker interval of 8.32 c M. The order of most marker locations corresponded to the physical map. 24 loci associated with the fruit traits were detected on LG1, LG2, LG3, LG4, LG6, LG8,LG11 and explained 1.39%-70.29% of the phenotypic variation. Two main qualitative trait loci were identified for flesh color. FC4.1 associated with red flesh color was located on chromosome 4. Its genetic distance to CAPS marker WIII4-440 and Bsa HI-6 were 1.5 c M and 0.8 c M respectively. Another main QTL associated with white flesh color was located on the position between the CAPS marker WIII6-620 and WIII6-507. One main quantitative trait loci was identified for fruit shape index on LG3 with contribution rate of 69.99%; More than 10% of the phenotypic variations were explained with the β-carotene content, fruit length, fruit width, flesh firmness of edge part of fruit. The QTLs associated with two different traits were found on same region such as β-carotene content and flesh color【.Conclusion】The inheritance of flesh color was affected by two major genes and was fit for the recessive epistasis model. β-carotene content showed a skew distribution in F2 population. While other fruit traits all showed a normal distribution, suggesting that they were quantative trait and were controlled by multiple genes. An F2 genetic linkage map was constructed which contained 195 markers and was grouped into 11 linkage groups. 24 locus for the fruit traits were detected, including two main quantitative trait loci for flesh color and one main quantitative trait loci for fruit shape index. These CAPS markers linked to QTL could provide the reference data for gene location and gene cloning in watermelon.reference data for gene location and gene cloning in watermelon.