Genotyping by Sequencing in Almond: SNP Discovery, Linkage Mapping, and Marker Design

Abstract

In crop plant genetics, linkage maps provide the basis for the mapping of loci that affect important traits and for the selection of markers to be applied in crop improvement. In outcrossing species such as almond (Prunus dulcis Mill. D. A. Webb), application of a double pseudotestcross mapping approach to the F1 progeny of a biparental cross leads to the construction of a linkage map for each parent. Here, we report on the application of genotyping by sequencing to discover and map single nucleotide polymorphisms in the almond cultivars “Nonpareil” and “Lauranne.” Allele-specific marker assays were developed for 309 tag pairs. Application of these assays to 231 Nonpareil × Lauranne F1 progeny provided robust linkage maps for each parent. Analysis of phenotypic data for shell hardness demonstrated the utility of these maps for quantitative trait locus mapping. Comparison of these maps to the peach genome assembly confirmed high synteny and collinearity between the peach and almond genomes. The marker assays were applied to progeny from several other Nonpareil crosses, providing the basis for a composite linkage map of Nonpareil. Applications of the assays to a panel of almond clones and a panel of rootstocks used for almond production demonstrated the broad applicability of the markers and provide subsets of markers that could be used to discriminate among accessions. The sequence-based linkage maps and single nucleotide polymorphism assays presented here could be useful resources for the genetic analysis and genetic improvement of almond.

Construction of a highly saturated linkage map in Japanese plum (Prunus salicina L.) using GBS for SNP marker calling

“…ApeKI was selected from a panel of restriction enzymes because it is able to produce hundreds of thousands of fragments between 150 and 500bp. Several studies of the genomes of Prunus species have used this criterion successfully to select the restriction enzyme for GBS [21; 28; 31; 37; 38]. GBS sequencing libraries were prepared by ligating the digested DNA to nucleotide adapters (barcodes), followed by standard PCR.…”

Mutation of a bHLH transcription factor allowed almond domestication

“…The final assembly constitutes 4078 scaffolds, of which 2572 are organized in eight pseudomolecules, with a final N50 of 21.8 Mb (where N50 is the minimum contig length needed to cover 50% of the genome) and a L90 of 306 (where L90 is the smallest number of contigs whose length sum makes up 90% of genome size) (table S1). A high level of collinearity between the almond genomic assembly and the recently reported single-nucleotide polymorphism (SNP)/ short sequence repeat (SSR) genetic linkage maps (25)(26)(27) was demonstrated ( fig. S1).…”

“…The long PacBio reads were used to perform the genome assembly, whereas the Illumina reads were used to perform gap filling and scaffolding. The scaffolds obtained were organized in pseudomolecules using the P. persica reference genome, as the genomes across the Prunus genus are essentially collinear (23)(24)(25). The final assembly constitutes 4078 scaffolds, of which 2572 are organized in eight pseudomolecules, with a final N50 of 21.8 Mb (where N50 is the minimum contig length needed to cover 50% of the genome) and a L90 of 306 (where L90 is the smallest number of contigs whose length sum makes up 90% of genome size) (table S1).…”

Genome-wide SNP identification in Prunus rootstocks germplasm collections using Genotyping-by-Sequencing: phylogenetic analysis, distribution of SNPs and prediction of their effect on gene function

“…In Prunus species, single-digest GBS has been used for identification of a high number of SNPs for linkage maps construction [32][33][34][35] and analysis of population genetic structure [36][37][38] . The use of double-digest GBS in Prunus has not been reported as far as the authors know.…”