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

Abstract

BackgroundThe 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.ResultsWe 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.ConclusionsGBS 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).Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2802-3) contains supplementary material, which is available to authorized users.

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

“…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.…”

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

“…Although the present composite map anchored 1500 more nuclear scaffolds than the previous SNP linkage map, those 1500 scaffolds only represented a 1.9% increase in the total megabases of cranberry genome anchored (Covarrubias-Pazaran et al 2016). This is reflective of the sheer number of scaffolds ( i.e.…”

“…aSNP loci with >20% missing data were excluded.bSNP loci with a MAF <10% were excluded.cSNP loci with extreme segregation distortion were excluded.dGenerated in Covarrubias-Pazaran et al (2016).eGenerated in Schlautman (2015a).…”

“…The Covarrubias-Pazaran et al (2016) study increased the availability of cranberry DNA markers 10-fold and used them to construct the first high-density SNP cranberry linkage map. Therefore, to further saturate the cranberry genome with SNP markers and to test the utility of GBS to detect SNPs that are polymorphic across multiple populations, an experiment was designed to develop a cranberry composite map using GBS for multi-pedigree linkage mapping.…”

Genetic Characterization of Maximilian Sunflower for the Development of a Locally Adapted Perennial Grain Oilseed

“…Previous studies have reported that linkage decay occurs rapidly, at ?200 bp in wild Helianthus species and at 1100 bp in cultivated H. annuus lines (Liu and Burke, 2006;Mandel et al, 2011). Given the rapid linkage decay, approaches in which linkage blocks are maintained to a greater degree through consanguinity such as through family-based association mapping approaches (Guo et al, 2013) or pseudo-testcross approaches such as those used in other outcrossing species (Zhang et al, 2016;Covarrubias-Pazaran et al, 2016) may be appropriate in Maximilian sunflower. Although several wild annual Helianthus species are reported as being highly syntenic with H. annuus (Barb et al, 2014), the degree of structural chromosomal rearrangements between cultivated H. annuus and the perennial H. maximiliani is currently uncharacterized, which may influence the inference of linkage decay.…”