The highest LOD score of the QTL for fruit weight on scaffold 8 of the Clementine reference genome was 2.91 in this study. Imani et. al reported that 5 QTLs for fruit weight on the scaffolds 3, 4, and 7 of the Clementine reference genome range phenotypic variance from 14.9 % to 26.5%. Among these QTLs, the LOD score was 3.68. Fruit diameter is a trait responsible for fruit size as well. Yu et. al identified 3 QTLs associated with fruit diameters 4, 5, and 9. The highest LOD score was 2.9 among 3 QTLs. In our study, although we study 32 fruit quality traits, we did not identify any QTLs for fruit size. In addition, Imai et. al 2017 claimed that FW4.2 and FWq3 might correspond on scaffold 4 of the Clementine genome due to their same position. However, we did not detect any QTLs for fruit size and in the same position.The sugar content and acidity of the fruit are responsible for fruit quality. Yu et. al 2016 reported that the QTLs identified for SSC on the scaffolds 2, 3, 4, and 8 of the Clementine genome. Among these QTLs, the highest LOD score was 2.92. A QTL was detected for SSC on scaffold 5 of the Clementine genome, with the highest LOD score of 2.80 by Imani et. al 2017. For TA, Yu et. al identified QTLs on scaffolds 7, 8, and 9 on the Clementine reference genome. The highest LOD score was reported as 2.99. In our study, hydroponic vertical garden although we could not identify any QTLs for sugar content, we detected QTLs associated with TA, acid content, and pH.
We have seen that in the distributions of TA, AC, and pH, the offspring are highly transgressive with many individuals beyond the range of the parents. These features are highly correlated with each other . As a result of mapping for these features, QTLs in Kiyomi were on scaffold 2, while for Amoa 8 they were in scaffold 5 of the Clementine reference genome. The QTLs detected in our study did not correspond to the QTLs detected in previous reference studies on TA. In our study about fruit acidity, 3 more QTLs were detected. These were associated with AC and pH. The QTL was positioned on scaffold 5 for pH in Amoa 8 and the QTLs were located on scaffolds 2 in Kiyomi and 5 of the Clementine genome for AC in Amoa 8.Sugiyama et. al detected 3 QTLs for all total carotenoids. They were located on scaffolds 6 and 7 of the Clementine reference genome. Asins et. al measured flavedo color and fruit juice color for fruit color properties by using a chromatic circle. They identified 4 QTLs for fruit color in the parent Fortune and 4 QTLs for fruit color and 3 QTLs for juice color in the parent Chandler. Yu et. al measured flavedo color and fruit juice color for fruit color properties . Flavedo color and juice color were measured with a colorimeter. QTLs were identified for fruit color. The QTLs for fruit color with the highest significant levels were all found in the Murcott parent. Among these 8 QTLs, all except for 1 QTL are on scaffold 4 of the Clementine genome.
In our study, 10 fruit skin colors were measured. PCA analysis of these was performed and instead of 10 color features, PC1and PC2 were used for color traits for QTL mapping. None of the QTL mapping results gave a significant peak for fruit color traits. Therefore, we could not detect any QTL for fruit skin color in our study. For the flesh color, one QTL was determined for FC, which was measured by associating it with the red color of the fruit on Kiyomi but not on Amoa 8.The QTLs were discovered only for a small subset of traits in our study. It can be thought that one of the main reasons is related to the effect of population size on QTLdetection. In previous studies, 201 full sibs , 116 F1 hybrids , and 110 F1 hybrids were used as population. In our study, 100 individuals were used but 96 individuals were evaluated. A typical QTL population consists of 100 to 300 individuals. Large effected QTLs in a smaller population can be identified but the QTLs of smaller effect can be identified in a larger population . We may not have detected QTL for color traits because of the way that color was determined. Each pixel was assigned one color. The color traits were detected by the software. There may have been an error in the separation between pixels by the software. For example, green and moro red colors had highly positive correlations . This might explain this situation. In addition, the RUBY gene regulates anthocyanins accumulation in Citrus. Under cold conditions, this gene is upregulated, and the anthocyanins levels increase in fruits. The fruit color feature is highly dependent on the environmental conditions and changes accordingly. Thus, it makes it difficult to detect genetic control of the color traits.
The reason for defining QTLs for Moro red and red features can be explained in this way. Although there were not a lot of distorted markers on Chromosome 6, a QTL colocalizing with RUBY was not identified on Amoa 8. Although Amoa 8 is a tangor with intense red internal color and there were not a lot of distorted markers on Chromosome 6 , RUBY did not underlie any color QTL. There could be several possible reasons. ex. RUBY may not be the only gene that controls anthocyanins accumulation in this population. We may not be able to detect RUBY has a QTL because there are no markers in linkage with RUBY. Anotherpossibility is that the sequence surrounding the RUBY mutation does not vary within the population, so it would not be detected as a QTL. Another reason could be related to fruit maturity. The fruits were harvested based on the maturity time of the parents and sent for analysis. Anthocyanin accumulation from offspring that do not have the same maturity period as their parents may not have been fully realized in hybrids. Color formation in immature fruits may not have occurred sufficiently. The Citrus fruit maturity can be calculated according to the Australian Citrus Standard ) x 16.5) . Since acidity and sugar rate determine fruit maturity, The high acid concentration in immature fruits may have prevented the coloration of fruits.Crinkle-leaf and deep suture are very important disorders of sweet cherry because they are so widespread and have such a damaging effect on vegetative growth and fruit yield. Both disorders have been reported throughout cherry producing regions of California, the Pacific Northwest, Utah, and British Columbia. Although there is no complete accounting of the economic impact associated with affected trees in California, these two disorders together probably cost sweet cherry fruit and nursery tree growers more money each year than any other disease or disorder. Over the past decade or more incidence of crinkle-leaf has fluctuated widely, seemingly independent of rainfall rates. One cherry orchard in particular had an abundance of crinkle-leaf one year but was virtually free of the disorder the next year, following a winter of normal precipitation. Boron nutrition may have been a factor in the transient nature of crinkle-leaf in this orchard: C. G. Woodbridge has reported results that support this interpretation, and boron-deficient trees are often known to be poor-bearing. Woodbridge showed that cherry trees with narrowed leaves and irregular leaf margins produced normal leaves on new growth after boron applications. Water inputs from rain or irrigation may alter the availability of soil-bound boron, making more of it available for uptake by trees.Cherry crinkle-leaf is neither contagious nor transmissible by normal methods of virus transmission, yet it is easily propagated through standard horticultural practices. It is thought to arise from bud mutations and may occur spontaneously on previously unaffected tree branches. Even though crinkle-leaf cannot be transmitted, buds taken from affected trees and used for propagation can perpetuate the disorder in subsequent generations of trees. Conversely, unaffected buds grafted onto crinkle leaf–affected branches produce normal growth. Even though field observations of crinkle-leaf might suggest that the disorder can spread, increases seen in orchards appear to result from the development of symptoms from spontaneous mutations.The ‘Bing’ and ‘Black Tartarian’ cultivars are most widely affected by crinkle-leaf. More crinkle-leaf is generally observed in hotter growing areas; the disorder is more prevalent in California than in Washington or Oregon. ‘Lambert’ and ‘Royal Ann’ cultivars do not regularly exhibit symptoms of crinkle-leaf.
Crinkle-leaf has also been reported on Prunus domestica cv. ‘Italian Prune.’ In cherry, the disorder may affect only a single branch or spur of a tree, or it may affect the whole tree. Trees with the disorder may not exhibit symptoms for several years after planting.Fruit is an important source of human healthy diet which can provide vitamins, minerals, vertical vegetable tower and a wide range of bio-active compounds, including antioxidant carotenoids and various polyphenols . The quality and nutrition of fresh fruits are gradually formed during ripening. Studying the molecular mechanism of fruit ripening is an important way to understand the formation of fruit quality. Fruit ripening is a complex biological process to form delicious and nutritious fruits for attracting animals to eat and spread seeds . Some general ripening-associated changes take place among some fruit species, including the cell wall degradation for fruit softening, alteration of the composition and levels of secondary metabolites, such as pigments, flavors, and aromas during fruit ripening . These changes are influenced by multiple genetic and biochemical pathways that are regulated by several critical transcription factors .The tomato is the main horticultural crops and it is hot popular food for consumers. Tomato is considered as an ideal model material for studying fleshy fruit ripening . In climacteric fruits, including tomatoes, increased ethylene production is required for the onset of ripening . During fruit development and ripening, the biosynthesis and signal transduction of ethylene are both regulated by several TFs, including RIPENING INHIBITOR , COLORLESS NON-RIPENING , NONRIPENING , TOMATO AGAMOUS-LIKE1 , NOR-like1, and APETALA2a . TDR4/FUL1 and its homolog MBP7/FUL2 are MADS-box family TFs with high sequence similarity to Arabidopsis FRUITFULL. In contrast to the above-mentioned TFs, TDR4/FUL1 and MBP7/FUL2 do not regulate ethylene biosynthesis but affect fruit ripening in an ethylene-independent manner . A previous study revealed that TDR4/FUL1 mRNA and protein accumulate during ripening in tomato fruit, while MBP7/FUL2 mRNA and protein accumulate during the pre-ripening stage and throughout ripening process . RNAi-silencing of each of the FUL homologs independently results in very mild changes to tomato fruit pigmentation, while the silencing of both genes results in an orange ripe fruit with highly reduced levels of lycopene, suggesting that FUL1/TDR4 and FUL2/MBP7 possess redundant functions in fruit ripening . The expression of genes involved in cell wall modification, cuticle production, volatile production, and glutamate accumulation was also altered in TDR4 silencing tomato fruit . Chromatin immuno precipitation coupled with microarray analysis revealed that FUL homologs take part in many biological processes through the regulation of ripening-related gene expression, both in cooperation with and independent of RIN . In order to further study the effect of TDR4 on tomato quality metabolism, we utilized virus-induced gene silencing to silence TDR4 in tomato fruit. Analysis of transcripts and metabolites of TDR4-silened fruit indicated that it was involved in the metabolism of several amino acids and biosynthesis of secondary metabolites, altering fruit nutrient levels and flavor. The result shows that TDR4 regulates the nutrient levels and quality of tomato fruit.Tomato plants were planted in commercial tomato-cultivated soil and grown under standard glasshouse conditions of 16-h day length and 25◦C, with a night temperature of 18◦C with 75% relative humidity. Flowers were tagged at 1 day post-anthesis . Ten plants are for control and 10 plants were used to silence TDR4 gene; each plant was no less than 15 fruits.Amino acids are primary metabolites that contribute to the flavor and nutritional value of tomato fruits. In TDR4-silenced fruit, levels of three amino acids were significantly reduced,including L-tyrosine , L-phenylalanine , and Lglutamic acid . KEGG pathway analysis revealed that the metabolic pathway of aromatic amino acids, such as phenylalanine and tyrosine, biosynthesis, and glutamate metabolism were also altered in TDR4-silenced fruits compared to control fruit , indicating that TDR4 gene plays a role in the accumulation of certain amino acids during tomato fruit ripening, which contributes to flavor formation of tomato fruit.