Construction of a High-Density Genetic Map of Acca sellowiana (Berg.) Burret, an Outcrossing Species, Based on Two Connected Mapping Populations

Abstract

Acca sellowiana, known as feijoa or pineapple guava, is a diploid, (2n = 2x = 22) outcrossing fruit tree species native to Uruguay and Brazil. The species stands out for its highly aromatic fruits, with nutraceutical and therapeutic value. Despite its promising agronomical value, genetic studies on this species are limited. Linkage genetic maps are valuable tools for genetic and genomic studies, and constitute essential tools in breeding programs to support the development of molecular breeding strategies. A high-density composite genetic linkage map of A. sellowiana was constructed using two genetically connected populations: H5 (TCO × BR, N = 160) and H6 (TCO × DP, N = 184). Genotyping by sequencing (GBS) approach was successfully applied for developing single nucleotide polymorphism (SNP) markers. A total of 4,921 SNP markers were identified using the reference genome of the closely related species Eucalyptus grandis, whereas other 4,656 SNPs were discovered using a de novo pipeline. The individual H5 and H6 maps comprised 1,236 and 1,302 markers distributed over the expected 11 linkage groups, respectively. These two maps spanned a map length of 1,593 and 1,572 cM, with an average inter-marker distance of 1.29 and 1.21 cM, respectively. A large proportion of markers were common to both maps and showed a high degree of collinearity. The composite map consisted of 1,897 SNPs markers with a total map length of 1,314 cM and an average inter-marker distance of 0.69. A novel approach for the construction of composite maps where the meiosis information of individuals of two connected populations is captured in a single estimator is described. A high-density, accurate composite map based on a consensus ordering of markers provides a valuable contribution for future genetic research and breeding efforts in A. sellowiana. A novel mapping approach based on an estimation of multipopulation recombination fraction described here may be applied in the construction of dense composite genetic maps for any other outcrossing diploid species.

Keywords: Acca sellowiana; Myrtaceae; composite genetic map; feijoa; genotyping by sequencing; multiparent family; pineapple guava.

Figure 1

Density distribution of Discovery-identified Acca sellowiana single nucleotide polymorphisms (SNPs) across the Eucalyptus grandis chromosomes. The SNP density was estimated in a 1 Mb window. The y-axis indicates the physical position in Mb. Of the 43,377 Discovery-identified SNPs, 41,815 were distributed across the E. grandis chromosomes and showed in the graphic. The remaining 1525, identified in sequence scaffolds, are not displayed.

Figure 2

Origin and types of marker configuration for GBS-SNP markers identified for H5 and H6 populations. (A) Venn diagram showing common and unique single nucleotide polymorphisms (SNPs) between H5 and H6 populations identified by Discovery (D) and UNEAK (U) pipelines. (B) Distribution of five joint types of marker configurations for common markers between H5 and H6 populations. The joint marker configuration types considered the marker types in H5 and H6 populations simultaneously.

Figure 3

Genetic linkage map of Acca sellowiana. The composite linkage map (in the middle) integrated the information of the single population H5 (on the left) and H6 (on the right) maps. Map distances (cM) are indicated at the left side of the figure. Single nucleotide polymorphisms (SNP) markers common between linkage groups (LGs) of the three genetic maps are connected with lines.