Development of a high-density cranberry SSR linkage map for comparative genetic analysis and trait detection

Authors: SCHLAUTMAN, BRANDON - University Of Wisconsin; COVARRUBIAS-PAZARAN, GIOVANNY - University Of Wisconsin; DIAZ-GARCIA, LUIS - University Of Wisconsin; JOHNSON-CICALESE, JENNIFER - Rutgers University; IORRIZO, MASSIMO - North Carolina State University; RODRIGUEZ-BONILLA, LORRAINE - University Of Wisconsin; BOUGIE, TIERNEY - University Of Wisconsin; BOUGIE, TIFANNY - University Of Wisconsin; Wiesman, Eric; Steffan, Shawn; Polashock, James; VORSA, NICHOLI - Rutgers University; Zalapa, Juan

Submitted to: Molecular Breeding
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/30/2015
Publication Date: 8/14/2015
Publication URL: http://handle.nal.usda.gov/10113/61588
Citation: Schlautman, B., Covarrubias-Pazaran, G., Diaz-Garcia, L.A., Johnson-Cicalese, J., Iorrizo, M., Rodriguez-Bonilla, L., Bougie, T., Bougie, T., Wiesman, E., Steffan, S., Polashock, J., Vorsa, N., Zalapa, J. 2015. Development of a high-density cranberry SSR linkage map for comparative genetic analysis and trait detection. Molecular Breeding. 35(8):177. doi: 10.1007/s11032-015-0367-5.

Interpretive Summary: The domestication and commercialization of cranberry began in the mid-1800s. However, cranberry has undergone relatively little genetic improvement compared to other commercial fruit crops due to its recent domestication and limited private and public breeding programs. The cranberry industry currently relies on asexual propagation of a small number of clonal cultivars which are native selections or 1st, 2nd, or 3rd generation hybrids of those native selections. Moreover, to date, cranberry breeding programs have relied solely on phenotypic selection because of the limited molecular resources and information available to facilitate genetic improvement. The present study was conducted to further molecular crop improvement strategies in cranberry by applying recently generated genomic resources to improve cranberry genetic mapping techniques. Specifically, 541 previously published genetic markers were mapped in a bi-parental full-sib population derived from a cross of CNJ97-105 (Mullica Queen®) by NJS98-23 (Crimson Queen®) to construct an improved high density cranberry genetic linkage map. To determine whether sufficient marker saturation was achieved for investigating the genetic basis of quantitative traits in cranberry, trait mapping was conducted for total yield, yield stability, and mean fruit weight based on field data from the same segregating progeny. In addition, comparative analyses of sequence order between gene coding DNA regions of cranberry with grape, tomato, and kiwifruit was performed to explore the levels of similarity between the species. This study is the first step towards the development of cranberry marker-assisted selection (MAS) strategies that reduce the required time, labor and financial investments and provide for increased breeding efficiency. MAS is especially critical for cranberry because of its long juvenility period, expensive and intensive management techniques, lengthy phenotyping phase (6-8 years) required for selection for important horticultural traits, e.g., yield, and because dedication of field space for robust experimental designs in cranberry are limiting and financially impractical. MAS could also be useful for developing strategies for trait introgression between cranberry and other economically important Vaccinium species such as blueberry, lingonberry, V. oxycoccos, and bilberry through interspecific hybridization.

Technical Abstract: Since its domestication 200 years ago, breeding of the American Cranberry (Vaccinium macrocarpon) has relied on phenotypic selection because applicable resources for molecular improvement strategies such as marker-assisted selection (MAS) remain limited. To enable MAS in cranberry, the first high density SSR linkage map with 541 markers representing all 12 cranberry chromosomes was constructed for the CNJ02-1 progeny from a cross of elite cultivars, CNJ97-105-4 and NJ98-23. The population was phenotyped for a three-year period for total yield (TY), mean fruit weight (MFW), and biennial bearing index (BBI) and data were analyzed using mixed models and best linear unbiased predictors (BLUPs). Significant differences between genotypes were observed for all traits. Quantitative trait loci (QTL) analyses using BLUPs identified 4 MFW QTLs on three linkage groups (LGs), 3 TY QTLs on 3 LGs, and 1 BBI QTL which co-localized with a TY QTL. Local BLAST of a cranberry nuclear genome assembly identified homologous sequences for the mapped SSRs which were then anchored to 12 pseudo-chromosomes using the linkage map information. Analyses comparing coding regions (CDS) anchored in the cranberry linkage map with grape, kiwifruit, and tomato genomes were performed. Moderate micro-synteny between the cranberry and kiwifruit genomes was detected, although none of the regions overlapped with the QTLs identified in this study. The linkage map, QTLs, and elite genotypic constitutions identified herein may be applied in subsequent cranberry MAS programs for the development of new cultivars, and potential marker transferability should allow for comparative genomic studies within economically important Vaccinium species.