Exploiting genotyping by sequencing to characterize the genomic structure of the American cranberry through high-density linkage mapping.
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 4849 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 4849 point map consisted of twelve linkage groups spanning 1112 cM, which anchored 2381 nuclear scaffolds accounting for ~13 Mb of the estimated 470 Mb cranberry genome. Bin mapping identified 592 and 672 unique bins in the parentals and a total of 1676 unique marker positions in the integrated map. Synteny analyses comparing the order of anchored cranberry scaffolds to their homologous positions in kiwifruit, grape, and coffee genomes provided initial evidence of homology between cranberry and closely related species.



GBS data was used to rapidly saturate the cranberry genome with markers in a pseudo-testcross population. Collinearity between the present saturated genetic map and previous cranberry SSR maps suggests that the SNP locations represent accurate marker order and chromosome structure of the cranberry genome. 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 cranberry molecular breeding through QTL mapping and genome-wide association studies (GWAS).
Department of Horticulture, University of Wisconsin, Madison, Wisconsin, USA.
Giovanny
G
Covarrubias-Pazaran
Department of Horticulture, University of Wisconsin, Madison, Wisconsin, USA.|Instituto Nacional de Investigaciones Agrícolas, Forestales y Pecuarias, Campo Experimental Pabellón, Aguascalientes, Mexico.
Luis
L
Diaz-Garcia
Department of Horticulture, University of Wisconsin, Madison, Wisconsin, USA.
Brandon
B
Schlautman
Department of Statistics, University of Wisconsin, Madison, Wisconsin, USA.
Joseph
J
Deutsch
Department of Horticulture, University of Wisconsin, Madison, Wisconsin, USA.
Walter
W
Salazar
Department of Horticulture, University of Wisconsin, Madison, Wisconsin, USA.
Miguel
M
Hernandez-Ochoa
Valley Corporation, Tomah, Wisconsin, USA.
Edward
E
Grygleski
USDA-ARS, Vegetable Crops Research Unit, University of Wisconsin, Madison, Wisconsin, USA.
Shawn
S
Steffan
Department of Horticultural Sciences, Plants for Human Health Institute, North Carolina State University, Kannapolis, North Carolina, USA.
Massimo
M
Iorizzo
USDA-ARS, Genetic Improvement of Fruits and Vegetables Laboratory, Chatsworth, New Jersey, USA.
James
J
Polashock
Blueberry and Cranberry Research and Extension Center, Rutgers University, Chatsworth, New Jersey, USA.
Nicholi
N
Vorsa
Department of Horticulture, University of Wisconsin, Madison, Wisconsin, USA. jezalapa@wisc.edu.|USDA-ARS, Vegetable Crops Research Unit, University of Wisconsin, Madison, Wisconsin, USA. jezalapa@wisc.edu.
Juan
J
Zalapa
D002874:Chromosome Mapping; D016000:Cluster Analysis; D008040:Genetic Linkage; D018745:Genome, Plant; D023281:Genomics / Q000379:methods; D005838:Genotype; D015810:Linkage Disequilibrium; D018895:Microsatellite Repeats; D020641:Polymorphism, Single Nucleotide; D026801:Synteny; D029799:Vaccinium macrocarpon / Q000235:genetics*
Genotyping by sequencing; Imputation; Linkage disequilibrium; Pseudo-testcross; Segregation distortion; Synteny; Vaccinium macrocarpon