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ARS Home » Southeast Area » Byron, Georgia » Fruit and Tree Nut Research » Research » Publications at this Location » Publication #330622

Research Project: Breeding Stone Fruit Adapted to the Production Environment of the Southeastern United States

Location: Fruit and Tree Nut Research

Title: Fine QTL mapping of mandarin (Citrus reticulata) fruit characters using high-throughput SNP markers

item YU, YUAN - University Of Florida
item Chen, Chunxian
item GMITTER JR., FRED - University Of Florida

Submitted to: Tree Genetics and Genomes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/1/2016
Publication Date: 7/18/2016
Citation: Yu, Y., Chen, C., Gmitter Jr., F.G. 2016. Fine QTL mapping of mandarin (Citrus reticulata) fruit characters using high-throughput SNP markers. Tree Genetics and Genomes. 12:17.

Interpretive Summary: Tree fruit cultivar improvement is hindered due to lack of genetic information and molecular markers on important fruit quality characters. Development of molecular markers linked to certain traits will hasten conventional breeding through marker-assisted selection. High-density genome maps for mandarin cultivars were constructed. Quantitative trait loci (QTLs), along with candidate genes, were identified for flesh and juice colors and other fruit characters. Some QTLs were validated. These flanking single nucleotide polymorphism markers were useful to identify new genes for these fruit characters and to accelerate selection of cultivars of desired fruit quality for the industry and consumer.

Technical Abstract: Seedlessness, flavor, and color are top priorities for mandarin (Citrus reticulata Blanco) cultivar improvement. Given long juvenility, large tree size, and high breeding cost, marker-assisted selection (MAS) may be an expeditious and economical approach to these challenges. The objectives of this study were to construct high-density mandarin genetic maps and to identify single nucleotide polymorphism (SNP) markers associated with fruit quality traits. Two parental genetic maps were constructed from an F1 population derived from ‘Fortune’ x ‘Murcott’, two mandarin cultivars with distinct fruit characters, using a 1536-SNP Illumina GoldenGate assay. The map for ‘Fortune’ (FOR) consisted of 189 SNPs spanning 681.07 cM and for ‘Murcott’ (MUR) consisted of 106 SNPs spanning 395.25 cM. Alignment of the SNP sequences to the Clementine (C. clementina) genome showed highly conserved synteny between the genetic maps and the genome. A total of 48 fruit quality quantitative trait loci (QTLs) were identified, and ten of them stable over two or more samplings were considered as major QTLs. Multiple QTLs for flavedo color space values L, a, b, a/b, and juice color space values a, a/b, were detected in a single genomic region on linkage group 4. Two carotenoid biosynthetic pathway genes, pds1 and ccd4, were found within this QTL interval. Several SNPs were potentially useful in MAS for these fruit characteristics. QTLs were validated in 13 citrus selections, which may be useful in further validation and tentative MAS in mandarin fruit quality improvement.