Fig 1.
Main steps of the novel RAD-seq protocol.
1–2) sample genomic DNA is digested. The resulting digested DNA fragments are ligated to a P1 adaptor, that presents a biotin group and a 4 bp overhang complementary to BamHI recognition site. 3-4-5) Biotinilated fragments are random sheared to a target size of 300–200 bp, captured using streptavidin beads and ligated to standard barcoded adaptors for 5500 SOLiD Fragment libraries. 6) RAD-seq libraries are amplified and purified before sequencing.
Fig 2.
Summary of SOLiD sequencing errors at the starting sequence.
Reads per sample with no colors errors (green); Reads per sample with one color error (yellow); discarded reads per sample due to color errors higher than one (red). The black dotted line indicates the average number of reads per sample.
Table 1.
Number of reads and sequence produced by each filtering step during reads treatment.
Fig 3.
number of alignments per sample.
High quality (MapQ > 10) alignments per sample are shown in green, low quality (MapQ < 10) alignments in yellow and unaligned and multiple aligned reads in red.
Table 2.
Number of identified BamHI recognition sites.
Fig 4.
A) SNP density across the 12X grapevine reference genome PN40024. Each block represents a bin of 500kb. The bar “Un” shows SNPs found on unassembled genomic sequences. B) summary of SNPs annotation according to the grape gene annotation v2.1.
Fig 5.
Minor allele frequency (MAF) distribution within cultivated (yellow) and wild (blue) grapevine populations, taking into account all nuclear SNP loci identified through the novel RAD-seq assay.
Fig 6.
The decay of LD in sativa and sylvestris populations.
Each point represents the median r2 value in sequential bins of 10kb against physical position.
Table 3.
Indices of genetic diversity evaluated in cultivated and wild accessions separately.