first genetic map of the American cranberry: exploration of synteny conservation and quantitative trait loci

• Published in: Theoretical and applied genetics 2013-03, Vol.126 (3), p.673-692
• Main Authors: Georgi, Laura, Johnson-Cicalese, Jennifer, Honig, Josh, Das, Sushma Parankush, Rajah, Veeran D, Bhattacharya, Debashish, Bassil, Nahla, Rowland, Lisa J, Polashock, James, Vorsa, Nicholi
• Format: Article
• Language: English
• Subjects: Agriculture; Arabidopsis - genetics; Arabidopsis thaliana; Biochemistry; Biomedical and Life Sciences; biosynthesis; Biotechnology; Blueberry Plants - genetics; Chromosome Mapping; Chromosomes, Plant - genetics; Cranberries; cultivars; Databases, Genetic; DNA Primers - genetics; DNA, Plant - genetics; flavonoids; fruit yield; Gene expression; Genes; Genetic aspects; Genetic Linkage; Genetic Markers; Genomes; Genotype; Germplasm; grapes; Life Sciences; linkage groups; loci; Microsatellite Repeats; Original Paper; pathogens; Phenotype; Physiological aspects; Plant Biochemistry; Plant Breeding/Biotechnology; Plant Genetics and Genomics; pleiotropy; Quantitative Trait Loci; Sequence Analysis, DNA; Synteny; titratable acidity; Vaccinium macrocarpon; Vaccinium macrocarpon - genetics; Vitaceae; Vitis - genetics; Vitis vinifera
• ISSN: 0040-5752; 1432-2242
• DOI: 10.1007/s00122-012-2010-8

The first genetic map of cranberry (Vaccinium macrocarpon) has been constructed, comprising 14 linkage groups totaling 879.9 cM with an estimated coverage of 82.2 %. This map, based on four mapping populations segregating for field fruit-rot resistance, contains 136 distinct loci. Mapped markers include blueberry-derived simple sequence repeat (SSR) and cranberry-derived sequence-characterized amplified region markers previously used for fingerprinting cranberry cultivars. In addition, SSR markers were developed near cranberry sequences resembling genes involved in flavonoid biosynthesis or defense against necrotrophic pathogens, or conserved orthologous set (COS) sequences. The cranberry SSRs were developed from next-generation cranberry genomic sequence assemblies; thus, the positions of these SSRs on the genomic map provide information about the genomic location of the sequence scaffold from which they were derived. The use of SSR markers near COS and other functional sequences, plus 33 SSR markers from blueberry, facilitates comparisons of this map with maps of other plant species. Regions of the cranberry map were identified that showed conservation of synteny with Vitis vinifera and Arabidopsis thaliana. Positioned on this map are quantitative trait loci (QTL) for field fruit-rot resistance (FFRR), fruit weight, titratable acidity, and sound fruit yield (SFY). The SFY QTL is adjacent to one of the fruit weight QTL and may reflect pleiotropy. Two of the FFRR QTL are in regions of conserved synteny with grape and span defense gene markers, and the third FFRR QTL spans a flavonoid biosynthetic gene.