2018 ASHS Annual Conference

Reduced Representation Sequencing approaches such as Genotyping by Sequencing have been widely applied in major crops such as maize and soybean and are now being used in horticultural crops like berries and fruit trees. As the original and largest producer of blueberry, the United States maintains the most diverse blueberry germplasm resources. We previously developed a diploid blueberry F₁ interspecific population for genetic linkage map construction by crossing the parent F₁#10 (Vaccinium darrowii Fla4B × Vaccinium corymbosum W85-20) with the parent W85-23 (Vaccinium corymbosum). Employing a Capture-Seq technology developed by RAPiD Genomics, with emphasis on probe design in predicted gene regions, 117 F₁ progeny, two parents, and two grandparents of this population were sequenced, yielding 138.64 Gbp raw sequenced reads with a depth per locus of ~13.23x. A total of 143,313 raw SNPs referenced to 95% of publicly available blueberry genome scaffolds were called and filtered to arrive at an approximately 80k high quality SNP set. We then developed a parental-dependent sliding window approach to further genotype this population, deduced bin markers from sliding windows along each reference scaffold, and used the markers for linkage map construction. Twelve blueberry linkage groups were constructed using OneMap (an R package) resulting in the highest density map reported to date in blueberry. We also scored many horticulturally significant traits in this population including important fruit quality traits such as fruit color, firmness, flavor, and weight over multiple years. Correlation among these traits was calculated using Spearman’s rho function. An R/qtl package was used to associate these traits to our fine map and identify corresponding regions with high LOD scores. In summary, we report here the first Capture-Seq based blueberry linkage map of our diploid population with a saturated marker density. This map is being used to identify QTL for important traits and will facilitate ongoing efforts to develop a chromosome level blueberry genome assembly.