Development of Molecular Markers for Fresh Mandarin Flavors and Colors Using a High-Throughput Goldengate Assay

Volatiles and carotenoids are the two major interrelated chemical components that determine citrus fruit flavors and colors. Improvement in seedlessness, flavor and color ranks high among the prioritized breeding goals for mandarin (Citrus reticulata Blanco). The objectives of this project were to construct high-density mandarin genetic maps and to identify SNP markers associated with fruit flavors, colors, and other fruit quality traits, using a recently developed Illumina GoldenGate assay containing 1,536 BAC end sequence-associated SNPs and a population of 116 ‘Fortune’ x ‘Murcott’ F₁ hybrids generated in the UF-CREC breeding program. These fruit quality traits, including fruit size and weight, seed number, juice percentage, flavedo and juice colors, sugar and acids, and juice flavors, were investigated in 2011 and 2012 season. The integrated mandarin genetic map consisted of 752 SNPs on 380 marker sites, spanning 1306 cM on nine linkage groups. The coverage of the integrated genetic map on the Clementine genome varied among nine scaffolds from 82% of scaffold 2 to 98.8% of scaffold 4. A total of 93 QTLs were identified using composite interval mapping for all traits; of these, 58 QTLs were detected for color traits. A major QTL for flavedo color L, a, b, a/b, and juice color a, a/b,  was identified on linkage group 4; pds1 and nced4, encoding phytoene desaturation and nine-cis-epoxycarotenoid dioxygenase 4 respectively, were found within this QTL interval. Identification of QTLs for flavors is in process. The molecular markers or QTLs will be validated in other mandarin germplasm and segregating populations.