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

item GEORGI, LAURA - Rutgers University
item JOHNSON-CICALESE, JENNIFER - Rutgers University
item HONIG, JOSH - Rutgers University
item DAS, SUSHMA - Rutgers University
item RAJAH, VEERAN - Rutgers University
item BHATTACHARYA, DEBASHISH - Rutgers University
item Bassil, Nahla
item Rowland, Lisa
item Polashock, James
item VORSA, NICHOLI - Rutgers University

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/18/2012
Publication Date: 1/3/2013
Citation: Georgi, L., Johnson-Cicalese, J., Honig, J., Das, S.P., Rajah, V.D., Bhattacharya, D., Bassil, N.V., Rowland, L.J., Polashock, J.J., Vorsa, N. 2013. The first genetic map of the American cranberry: exploration of synteny conservation and quantitative trait loci. Theoretical and Applied Genetics. 126:673-692.

Interpretive Summary: Breeding of woody perennials, such as American cranberry, takes many years since the cycle from seed to selection of superior plants is long. The selection period can be shortened if desired traits can be identified in seedlings using genetic markers. As a first step in this process, we have determined the locations of 136 genetic markers on the chromosomes of the American cranberry. The markers were selected for their close proximity to genes involved in the biosynthesis of fruit compounds important for human health and genes involved in defense against certain pathogens. We were also able to determine the location of markers associated with other desired traits such as fruit rot resistance, fruit weight, fruit acidity, and fruit yield. These markers form the foundation of future work wherein the genetic markers can be used to select seedlings with desired horticultural or biochemical traits. The results of this work will be used by other research scientists involved in breeding cranberry or related species, such as blueberry. Results will also be used by other researchers to study the genetic and biochemical bases for traits such as disease resistance.

Technical Abstract: The first genetic map of cranberry 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 simple sequence repeat (SSR) and cranberry sequence-characterized amplified region (SCAR) 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 grape 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. The sound fruit yield 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