Construction of a High-Density American Cranberry (Vaccinium macrocarpon Ait.) 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.

Keywords: Vaccinium; centromere region; genetic map; simple sequence repeat; single nucleotide polymorphism.

Figure 1

Description of the pedigrees of the three mapping populations (green), CNJ02, CNJ04, and GRYG, derived from crosses between five interrelated cranberry parental genotypes (blue), CNJ97-105 (Mullica Queen), NJS98-23 (Crimson Queen), Stevens, [BGx(BLxNL)]95, and GH1x35. All pedigrees trace to “The Big Seven” native cranberry selections (red), which have played important roles in cranberry production and breeding history. The pedigree contains five first generation removed from the wild genotypes resulting from crosses between two native selections (orange), and additional later generation genotypes (blue).

Figure 2

Line graphs representing the distribution of the number of recombination bins, estimated using the multiple spanning tree algorithm implemented in ASMap (Wu et al. 2008; Taylor and Butler 2015), in each linkage group (LG) of the six parental component bin maps constructed for three cranberry full-sib populations: GRYG {i.e., [BGx(BLxNL)]95 × GH1x35}, CNJ02 (i.e., MQ × CQ), and CNJ04 (i.e., MQ × ST). The GRYG population (red) included 352 progeny; the CNJ02 population (blue) included 168 progeny, and the CNJ04 population (green) included 67 progeny.

Figure 3

Comparisons of the LGs of the parental linkage maps for the (A) GRYG {[BGx(BLxNL)]95 × GH1x35}, (B) CNJ02 (Mullica Queen × Crimson Queen), and (C) CNJ04 (Mullica Queen × Stevens) full-sib cranberry mapping populations. LGs from the maternal maps are on the left side of each circular ideogram while the paternal LGs are on the right. Links are drawn between common markers in the LGs of the two parental maps in each population. Scatterplots of the position (centimorgans) of the common markers in the paternal map plotted on the x-axis and position in the maternal map plotted on the y-axis display collinearity of marker order. Bars display phased genotype data which show position (centimorgans) of phase changes (the gametic recombination) which occurred in both parents for a random subset of 60 progeny from each population. Outer ring displays the position (centimorgans) of markers in the parental maps colored by the χ² P-value obtained from the tests for distortion from expected Mendelian segregation ratios. Marker colors range from dark green for markers not showing distortion (χ² P > 0.1) to dark red for markers showing highly significant segregation distortion (χ² P < 0.0005).

Figure 4

Plots of recombination frequency (RF_M) estimated from phased genotype data by starting at the terminal markers at the beginning (red points) and end (blue points) of each linkage and recording the proportion of offspring with an observed recombination (i.e., change of phase) in the interval between the terminal marker (m₀) and each subsequent marker (m_n) for the 12 cranberry LGs. Centromere spans (gray regions) were placed on the 12 LGs of the cranberry parental component bin maps constructed for the parents of the CNJ04 population, Mullica Queen (a) and Stevens (b); the CNJ02 population, Mullica Queen (c) and Crimson Queen (d); and the GRYG population, [BGx(BLxNL)]95 (e) and GH1x35 (f) using the method developed in Limborg et al. (2016). Centromeric spans in the LGs were defined as the range (centimorgans) extending from the intersection (dark lines) of the recombination frequency (RF_M) estimates made from both ends of the LG outwards until reaching the first marker with an RF_M = 0.45 in both directions. (g) Marker density in the cranberry composite map is shown to explore the relationship between marker density and centromere position.