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

Volatile aromatics 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). Given long seedling juvenility, large tree size, and associated costs in citrus breeding, trait-associated marker development and marker-assisted selection could potentially lead to a more expeditious and economical approach to these challenges. 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 an 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 SNPs sequences were blasted and aligned to the Clementine genome, and most genome sequences showed high identities between these mandarin hybrids and Clementine. 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 42 QTLs were identified, with 18 of them being stable over samplings and mapped as major QTLs. Multiple QTLs in a genome region on linkage group 4 were detected for flavedo color space value L, a, b, a/b, and juice color space value a, a/b through samplings. Carotenoid biosynthetic pathway genes pds1 and ccd4 were found within this genome region. Identification of QTLs for flavors is in process. QTLs are being validated in other mandarins. Several candidate genes are being under analysis.