Construction of a High-Density American Cranberry (Vaccinium macrocarponAit.) Composite Map Using Genotyping-by-Sequencing for Multi-pedigree Linkage Mapping

Abstract

The American cranberry (Vaccinium macrocarpon Ait.) is a recently domesticated, 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, genotyping-by-sequencing (GBS) was used to discover and genotype thousands of single nucleotide polymorphisms (SNPs) within three interrelated cranberry full-sib populations. Additional simple sequence repeat (SSR) loci were added to the SNP datasets and used to construct bin maps for the parents of the populations, which were then merged to create the first high-density cranberry composite map containing 6073 markers (5437 SNPs and 636 SSRs) on 12 linkage groups (LGs) spanning 1124 cM. Interestingly, higher rates of recombination were observed in maternal than paternal gametes. The large number of markers in common (mean of 57.3) and the high degree of observed collinearity (mean Pair-wise Spearman rank correlations >0.99) between the LGs of the parental 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, placement of centromeres on each of the 12 LGs, and anchoring of genomic scaffolds. Collectively, the results 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.

Massive phenotyping of multiple cranberry populations reveals novel QTLs for fruit anthocyanin content and other important chemical traits

“…The LOD score threshold to call significant QTL was calculated using a permutation test (1000 permutations) and a nominal significance level of 5%. We used a high-density composite map produced with 6073 markers spanning 12 linkage groups and a total length of 1130.42 cM (Schlautman et al 2017); because of the high density of the markers used here, no additional marker imputation was needed. We identified significant peaks automatically using the function big.peaks.col from the package Fragman (Covarrubias-Pazaran et al 2016b); QTLs separated from each other by more than 20 cM were considered different.…”

“…Georgi et al (2013) published the first SSRbased genetic map of American cranberry, and reported several QTLs for yield, fruit weight, titratable acidity and proanthocyanidin content. With the recent development of high-density genetic maps (Schlautman et al 2015, 2017; Covarrubias-Pazaran et al 2016a; Daverdin et al 2017), the creation of new mapping populations (Schlautman et al 2015), the development of modern massive phenotyping techniques (Houle et al 2010), and the availability of the cranberry genome (Polashock et al 2014), the identification and fine-mapping of loci governing major phytochemicals in cranberry fruit are crucial for the future breeding of cultivars with enhanced phytochemical properties for processing and consumption.…”

High-Resolution Linkage Map and QTL Analyses for Machine Harvest Traits in Autotetraploid Blueberry

“…A high-density linkage map has only been built for cranberry ( Vaccinium macrocarpon Ait.) (Schlautman et al, 2017), a diploid-relative of blueberry.…”

Pacbio sequencing reveals identical organelle genomes between American cranberry (Vaccinium macrocarponAit.) and a wild relative

“…Georgi and collaborators (2013) published the first SSR-based genetic map and reported several quantitative trait loci (QTL) for yield related traits and important phytochemicals. Subsequently, high-density genetic maps as well as more multi-trait QTL studies became available [22][23][24][25][26][27]. In addition, nuclear [28], plastid [29], and mitochondrial [30] genomes have been published recently.…”