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Title: Construction of a high-density American cranberry (Vaccinium macrocarpon Ait.) composite map using genotyping-by-sequencing for multi-pedigree linkage mapping

Author
item SCHLAUTMAN, BRANDON - University Of Wisconsin
item COVARRUBIAS-PAZARAN, GIOVANNY - University Of Wisconsin
item DIAZ-GARCIA, LUIS - University Of Wisconsin
item IORIZZO, MASSIMO - North Carolina State University
item Polashock, James
item GRYGLESKI, EDWARD - Valley Corporation
item VORSA, NICHOLI - Rutgers University
item Zalapa, Juan

Submitted to: Genes, Genomes, and Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/3/2017
Publication Date: 4/1/2017
Publication URL: https://handle.nal.usda.gov/10113/6472179
Citation: Schlautman, B., Covarrubias-Pazaran, G., Diaz-Garcia, L., Iorizzo, M., Polashock, J., Grygleski, E., Vorsa, N., Zalapa, J. 2017. Construction of a high-density American cranberry (Vaccinium macrocarpon Ait.) composite map using genotyping-by-sequencing for multi-pedigree linkage mapping. Genes, Genomes, and Genomics. 7(4):1177-1189. doi: 10.1534/g3.116.037556.

Interpretive Summary: Cranberry is a recently domesticated, but economically important, fruit crop with limited molecular resources. New genetic resources could accelerate genetic gain in cranberry through characterization of its genetic features and by enabling molecular-assisted breeding. To increase the availability of cranberry genomic resources, the genotyping-by-sequencing (GBS) approach was used to simultaneously discover and genotype thousands of single nucleotide polymorphisms (SNPs) within three inter-related cranberry populations, whose pedigrees trace to seven wild cranberry selections that represent the genetic base of the commercial cranberry industry. Additional, simple sequence repeat (SSR) markers were added to the SNP datasets and genetic maps constructed for the three populations, which were merged to create the first high-density cranberry composite map containing 6073 markers (5437 SNPs and 636 SSRs) in 12 chromosomes. Collectively, the results presented represent an important contribution to the current understanding of cranberry genetic structure and to the availability of molecular tools for future genetic research and breeding efforts in cranberry.

Technical Abstract: The American cranberry (Vaccinium macrocarpon Ait.) is a recently domesticated, but economically important, fruit crop with limited molecular resources. New genetic resources could accelerate genetic gain in cranberry through characterization of its genomic structure and by enabling molecular-assisted breeding strategies. To increase the availability of cranberry genomic resources, the genotyping-by-sequencing (GBS) approach was used to simultaneously discover and genotype thousands of single nucleotide polymorphisms (SNPs) within three inter-related cranberry full-sib populations, whose pedigrees trace to seven wild cranberry selections that represent the genetic base of the commercial cranberry industry. Additional SSR loci were added to the SNP datasets and bin maps were constructed for the parents of the three populations, which were merged to create the first high-density cranberry composite map containing 6073 markers (5437 SNPs and 636 SSRs) in 12 linkage groups (LGs) spanning 1124 cM. The large number of markers in common (i.e. an average of 57.3) and high degree of observed collinearity (i.e. mean Pair-wise Spearman Rank Correlations > 0.99) between the LGs of the parental component maps demonstrates the utility of GBS in cranberry for identifying polymorphic SNP loci that are transferable between pedigrees and populations in future trait-association studies. Furthermore, the high-density of markers anchored within the component maps allowed identification of segregation distortion regions (SDRs), placement of centromeres on each of the 12 LGs, and anchoring of genomic scaffolds. Collectively, the results presented represent an important contribution to the current understanding of cranberry genomic structure and to the availability of molecular tools for future genetic research and breeding efforts in cranberry.