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

• DOI: 10.1186/s12864-016-2802-3
• Publication Date: 2016-06-13T12:25:14Z
• Authors: Giovanny Covarrub...; Luis Diaz-Garcia; Brandon Schlautman; Joseph Deutsch; Walter Salazar; Miguel Hernandez-...; Edward Grygleski; Shawn Steffan; Massimo Iorizzo; James Polashock; Nicholi Vorsa; Juan Zalapa
• Keywords: Linkage Disequilibrium; Synteny; Genetic linkage

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 an excellent tool to characterize genomic structure recently domesticated (~200 years) understudied species, such as cranberry (Vaccinium macrocarpon Ait.), generating large numbers markers for studies mapping. We identified 10842 potentially mappable single nucleotide polymorphisms (SNPs) in a pseudo-testcross population wherein 5477 SNPs 211 short sequence repeats (SSRs) were used construct high density linkage map which total 4849 mapped. Recombination frequency, disequilibrium (LD), segregation distortion at level parental integrated maps characterized first time cranberry. SSR markers, backbone map, revealed collinearity previously published maps. point consisted twelve groups spanning 1112 cM, anchored 2381 nuclear scaffolds accounting ~13 Mb estimated 470 genome. Bin mapping 592 672 unique bins parentals 1676 marker positions map. Synteny analyses comparing order their homologous kiwifruit, grape, coffee genomes provided initial evidence homology closely related species. was rapidly saturate genome population. Collinearity present saturated previous suggests that SNP locations represent accurate chromosome greatly improved current coverage, allowed genome-wide investigations distortion, recombination, disequilibrium, synteny analyses. In future, can be accelerate molecular breeding through QTL association (GWAS).