Genetic map building with quantitative trait loci analysis is needed to identify possible candidate genes and to predict molecular markers associated with fruit quality characteristics. The most preferred molecular markers have been used as single nucleotide polymorphisms , polymorphic insertions or deletions , or microsatellites recently. Genome-wide association studies and linkage mapping need high-throughput molecular marker assays. Although genetic mapping studies are still limited in mandarin due to the insufficiency of phenotype data and the complexity of fruit quality traits, some studies have been conducted on fruit quality traits that are important for Citrus breeding . The QTL analysis would help select parents and improve hybrids of the parents with the target gene of a favorable trait by preventing the long juvenile period of Citrus and eliminating Citrus breeding expenses . Improvements in next generation sequencing and genotyping array technologies have helped to understand the genetic basis of quantitative trait variation. SNP genotyping became the most widely used genotyping method for GWAS and QTL mapping due to being inexpensive and producing many, greenhouse vertical farming codominant SNPs. In addition, SNP genotyping can be performed with SNP arrays or produced by genotyping-by-sequencing , or whole-genome sequencing.
Fruit size is among the most crucial fruit quality traits for mandarin breeding. Generally, mandarin fruit size varies from small to medium, but tangelo and tangor hybrids have larger fruit sizes. Amparo is a small-fruited mandarin with about 40 mm diameter and 30 g weight. Moreover, Ugly has a much larger fruit size, it is a tangelo with a fruit diameter of 120 mm and a fruit weight of 580 g . Obtaining fruits in uniform fruit size is one of the essential elements for mandarin breeding. Therefore, it is important to construct a mandarin genetic map and identify markers related to fruit size. QTL identification associated with fruit size for mandarins has been conducted in several studies . In the study, Fortune , Murcott , and 116 F1 mandarin individuals derived from were analyzed for fruit quality traits by Yu et. al . It was carried out in Fortune , Murcott , and 116 F1 mandarin individuals derived from were analyzed for fruit quality traits by Yu et. al . It was carried out in January and February, with four samplings in 2012 and 2013. The map was performed by using a 1536-SNP Illumina GoldenGate assay. The constructed genetic linkage map of “FOR” consisted of 189 SNPs, while “MUR” consisted of 106 SNPs. A total of 48 QTLs related to fruit quality traits were defined in the study. 3 QTLs of them were associated with fruit weight and 3 QTLs of them were related to fruit diameter . The repeatable QTLs were determined as FW5.1 and FW8 and non-repeatable were FW4.2, FD4.2, FD5.1, and FD9.3.
FW4.2 was detected on MUR4.2 with 25.69 cM and explained % 24.60 of the phenotypic variance . QTL analysis study on fruit quality characteristics in the mandarins detected QTLs associated with fruit size. A SNP-based genetic linkage map and QTL mapping were conducted using an F1 segregating population derived from by Imai et. al . The map for “Harehime” consisted of 442 SNPs, and for “Yoshida” consisted of 332 SNPs. 4 QTLs were identified for fruit weight with 14.9-26.5 % of the phenotypic variance. FWq3 was identified spanning 15.3-31.0 cM on the Clementine genome scaffold 4. The most striking point in this study is the claim that these two QTLs can correspond since FWq3 and FW4.2 are located on the same Clementine reference genome scaffold 4 .The fruit flavor is one of the main determinants of fruit quality and consumer preference in mandarins. The ratio between sugar and acid content, which is defined as the total soluble solids: titratable acidity ratio , is significant for the taste of the fruit . Only the high sugar content and less acidity rate or less sugar and high acidity level do not affect the fruit taste positively. For this reason, fruit is required to contain a certain amount of acid content in terms of fruit taste. Fruits with a high TSS/TA ratio have a bland taste, while fruits with a low TSS/TA ratio have a sour taste. Goldenberg et. al stated that the TSS/TA ratio for mandarins that are highly desired is about 13. In addition, Citrus fruit development in relation to solids and acids. Solids gradually increase, and acids first increase and then decrease.
So meaningful comparison of varieties is only possible in relation to the date sampled. reported that tangerines, which is a popular variety in terms of their taste, are the variety of mandarin with mean of the highest sugar content , acid content , and sugar/acid ratios in Table 2. Some QTLs associated with the fruit sugar content in Citrus have been identified in some previous studies. For Soluble Sugar Content , Yu et. al detected five non-repeatable QTLs on scaffolds 2,3,4, and 8 of the Clementine reference genomes. In addition, three non-repeatable QTLs for Soluble solids content: titratable acidity were identified by Yu et. al . Moreover, they identified two non-repeatable QTLs and one repeatableQTL for TA were positioned at scaffolds 7, 8, and 9 of the Clementine reference genome. The QTLs identified for ST were positioned on the scaffold 1, 7, and 9 of the Clementine reference genome . In this study, some QTLs for TA overlapped the QTLs for ST and SSC. For example, TA9 and ST9, and TA8 and SSC8 overlapped. Imai et. al studied one of four mandarin fruit quality traits: sugar content . Only SCq1 was identified for SC on LG5 .Seedlessness is a desirable trait for Citrus breeding since the seed in the fruit may negatively affect the taste and aroma of the fruit due to effects of seeds on chemical composition . Navel orange, Satsuma mandarin, and Clementine mandarin are the most popular Citrus crops that are seedless . For Citrus fruit to be defined as seedless, it must contain no seeds, contain aborted seeds, or the number of seeds of a multi-seeded variety must be significantly reduced . Many factors play a role in mandarin seedlessness, including parthenocarpy, male and female sterility, self-incompatibility, abnormal ovules, embryo sac abortion, environmental conditions, and plant growth regulators . Seedlessness is one of the most important fruit quality characteristics in mandarin breeding and is important for obtaining seedless fruits. Thus, QTLs responsible for this trait are required to select for it more effectively. Five genomic regions were detected for seed number by using 201 full-sib population, which were crossed reciprocally between Fortune and Chandler . Four QTLs associated with seed numbers were detected in 2014 and 2015. The QTL SN11 was identified on the linkage group Gr9b on locus CTUCH7 with 8.8 %, moreover the other QTLs on the Clementine linkage groups with 8.4, 10.7, and 11.3 % of the explained phenotypic variance, respectively. Yu et. al detected non-repeatable QTLs associated with seed number. These QTLs on scaffolds 3 and 9 of the Clementine reference genome explained phenotypic variance with 21.32% and 19.59 %, respectively .Fruit color is one of the most influential fruit quality attributes of Citrus features because the first thing that affects consumer preference is the appearance and color of the fruit . Citrus peels consist of the pigmented peripheral epicarp or flavedo and albedo .The part responsible for the fruit peel color is the flavedo of the fruit . The color of mandarin peels is usually greenish-yellow, yellow, yellow-orange, orange, and reddish. Fruit pulp color is as important as a fruit quality feature as peel color. Color pigments are responsible for the color of fruit flesh and skin. These pigments are carotenoids and flavonoids. In general, mandarins have a yellow to orange hue. Carotenoids are the primary pigments for yellow to orange colors.There are three main cultivar groups in terms of including carotenoids in Citrus. The first group is the carotenoid-poor group. There are pomelos, lemons and limes, nft vertical farming and grapefruits in this group. The other group is the violaxanthin-abundant group, which includes oranges. The third is the cryptoxanthin-abundant group, primarily containing mandarins . Lycopene, which is responsible for the pink color, is also a carotene and is found in grapefruit such as ‘Star RUBY’ and navel orange such as ‘Cara Cara.’ Anthocyanins are a subgroup of flavonoids that give blue, purple, and red colors to the fruit. Anthocyanins are phenolic compounds responsible for the red color of Citrus fruits such as blood oranges . In addition, with the increase in the popularity of red-colored fruits, mandarin hybrids with red flesh have been introduced to the global market.
These red-fleshed mandarin hybrids are rich in anthocyanins, and examples include ‘Sun Red,’ ‘Early Sicily,’ and ‘Sweet Sicily’ varieties released in Italy . There are some significant genes in the carotenoid biosynthesis pathway in Citrus. They are PSY, PDS, LCYB1, LCYB2, CHY, CHYB, and CCD. The gene responsible for anthocyanin biosynthesis in Citrus is the RUBY gene which encodes an MYB transcription factor. MYB transcription factor regulates anthocyanin biosynthesis with a basic helix-loop-helix transcription factor and a WD40 repeat protein. The expression of the RUBY gene depends on environmental conditions. This gene is upregulated under cold temperatures, causing anthocyanin accumulation in the fruit .Previous QTL studies on fruit color were based on detecting QTLs associated with carotene content in Citrus fruits. Papers reporting QTLs associated with anthocyanin content in Citrus have not yet been published. created a population derived from the female parent ‘Okitsu-46’ and the male parent ‘Nou-5’ . For QTL mapping, EST-based CAPS markers were used to generate linkage maps from 51 progenies and their parents. Their extracts were prepared to measure by HPLC the carotenoid content. According to the results, the A255 map was generated with 345 markers and covered 660cM. In contrast, the G434 map was constructed with 254 markers covering 642 cM. It was cited that there was transgressive segregation for total and each carotenoid contents in progenies. Transgressive segregation arises from the distribution of alleles between parents. It leads to the form of extreme phenotypes in segregated populations compared to the parental phenotypes. QTLs for fruit pericarp and 35 QTLs for pulp were identified. Each QTL for flavonoids in fruit pericarp was explained by phenotypic variance from 30.2 to 71.8%. At the same time, each QTL for flavonoids in fruit pericarp was explained by phenotypic variance from 26.7 to 63.0%. The QTLs for flavonoids were on Chr3, Chr7, and Chr9.Since it is directly related to the external appearance, the rind or peel thickness is a vital fruit quality feature. The peel or rind of the fruit has flavedo and albedo sections and it is reported that mandarins have thinner albedo thickness among other Citrus varieties in general. For example, the albedo thickness of sweet oranges varies from 5 mm to 10 mm. Grapefruits have an albedo thickness of more than 10 mm. Lemons have ±5 mm, and mandarins have an albedo thickness of less than 3 mm on average. Asins et. al performed a QTL analysis associated with rind thickness. A total of QTLs for rind thickness was on the Clementine linkage group, with phenotypic variation explained by each QTL ranging from 9.0 to 21.3% . The juice volume is an essential trait for inner fruit quality. Pulp segments filled with many vehicles are called juice sacs in the Citrus flavedo part. Juice sacs include sugars, organic acids, vitamins, and polyphenolic plant compounds. Juice volume is considered an important criterion, especially for the fruit juice industry . 2 QTLs for juice volume were detected on Clementine linkage groups by Asins et. al . The QTL JV_11 on Cl3 explained 7.4% of phenotypic variance, and JV_11 on Cl4b explained 10.8% of phenotypic variance. In addition, 7 QTLs were identified for juice content . The paper reported that JC was calculated as a percentage of JV and fruit weight . All QTLs related to juice volume and content are defined only on the Clementine map . Yu et. al identified only one QTL associated with juice percentage . JP was calculated by using juice volume and fruit weight. The QTL JP7.2 was on MUR 7.2 with a 2.78 LOD score . In this study, the parents of the mandarin hybrids differ in several fruit traits related to size, seediness, sugar content, and acidity. We sought to achieve a better understanding of the genetic basis of variation in fruit characteristics, including fruit quality and rind color in an outcross F1 population of mandarin hybrids.