Exploiting genotyping by sequencing to characterize the genomic structure of the American cranberry through high-density linkage mapping

Authors: COVARRUBIAS-PAZARAN, GIOVANNY - University Of Wisconsin; DIAZ-GARCIA, LUIS - University Of Wisconsin; SCHLAUTMAN, BRANDON - University Of Wisconsin; DEUTSCH, JOSEPH - University Of Wisconsin; SALAZAR, WALTER - University Of Wisconsin; HERNANDEZ-OCHOA, MIGUEL - University Of Wisconsin; GRYGLESKI, EDWARD - Valley Corporation; Steffan, Shawn; IORIZZO, MASSIMO - North Carolina State University; Polashock, James; VORSA, NICHOLI - Rutgers University; Zalapa, Juan

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/27/2016
Publication Date: 6/13/2016
Publication URL: http://handle.nal.usda.gov/10113/62658
Citation: Covarrubias-Pazaran, G., Diaz-Garcia, L., Schlautman, B., Deutsch, J., Salazar, W., Hernandez-Ochoa, M., Grygleski, E., Steffan, S., Iorizzo, M., Polashock, J.J., Vorsa, N., Zalapa, J. 2016. Exploiting genotyping by sequencing to characterize the genomic structure of the American cranberry through high-density linkage mapping. Biomed Central (BMC) Genomics. 17(1):451. doi: 10.1186/s12864-016-2802-3.

Interpretive Summary: The application of genotyping by sequencing (GBS) approaches is narrowing the genetic knowledge gap between major and understudied, minor crops. GBS is an excellent tool to genetically characterize a recently domesticated (~200 years) and understudied species, such as cranberry (Vaccinium macrocarpon Ait.), by generating large numbers of molecular markers for genetic mapping. We identified 10842 potentially mappable molecular markers in a cranberry wherein 5151 were used to construct a high-density cranberry genetic map. In addition, comparative analyses of sequence order between gene coding DNA regions of cranberry with grape, coffee, and kiwifruit were performed to explore the levels of similarity between species. To date, cranberry breeding programs have relied solely on phenotypic selection because of the limited molecular resources and information available to facilitate genetic improvement using molecular tools. The present study was conducted to further molecular crop improvement strategies in cranberry to generate genomic resources to improve cranberry genetic mapping techniques. In the future, the current high-density cranberry map can be used map traits and discover genes that could be useful to accelerate breeding through the development of molecular breeding strategies that reduce the required time, labor and financial investments and provide for increased breeding efficiency.

Technical Abstract: The application of genotyping by sequencing (GBS) approaches, combined with data imputation methodologies, is narrowing the genetic knowledge gap between major and understudied, minor crops. GBS is an excellent tool to characterize the genomic structure of recently domesticated (~200 years) and understudied species, such as cranberry (Vaccinium macrocarpon Ait.), by generating large numbers of markers for genomic studies such as genetic mapping. We identified 10842 potentially mappable single nucleotide polymorphisms (SNPs) in a cranberry pseudo-testcross population wherein 5477 SNPs and 211 short sequence repeats (SSRs) were used to construct a high density linkage map in cranberry of which a total of 5154 markers were mapped. Recombination frequency, linkage disequilibrium (LD), and segregation distortion at the genomic level in the parental and integrated linkage maps were characterized for first time in cranberry. SSR markers, used as the backbone in the map, revealed high collinearity with previously published linkage maps. The 5154 point map consisted of twelve linkage groups spanning 1439 cM, which anchored 2508 nuclear scaffolds accounting for 13 Mb of the estimated 470 Mb cranberry genome. Synteny analyses comparing the order of anchored cranberry scaffolds to their homologous positions in kiwifruit, grape, and coffee genomes provided evidence that cranberry and the Ericaceae lack further whole genome duplications (WGDs) following the Ad-' WGD. GBS data was used to rapidly saturate the cranberry genome with markers in a pseudo-testcross population. Collinearity between this GBS-based genetic map and previous cranberry SSR maps suggests that the SNP locations represent accurate marker order and chromosome structure of the cranberry genome. GBS-based SNPs greatly improved current marker genome coverage, which allowed for genome-wide structure investigations such as segregation distortion, recombination, linkage disequilibrium, and synteny analyses. In the future, GBS can be used to accelerate molecular breeding through QTL mapping and genome-wide association studies (GWAS).