Development of Molecular Markers for Mandarin Flavors and Colors using a High-Throughput GoldenGate Assay

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 single nucleotide polymorphism (SNP) markers associated with fruit flavors, colors, as well as 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 University of Florida Citrus Research and Education Center (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 harvest 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 quantitative trait locus (QTLs) will be validated in other mandarin germplasm and segregating populations.