Construction of a high-density genetic map for grape using specific length amplified fragment (SLAF) sequencing

<div><p>Genetic maps are important tools in plant genomics and breeding. We report a large-scale discovery of single nucleotide polymorphisms (SNPs) using the specific length amplified fragment sequencing (SLAF-seq) technique for the construction of high-density genetic maps for two elite wine grape cultivars, ‘Chardonnay’ and ‘Beibinghong’, and their 130 F₁ plants. A total of 372.53 M paired-end reads were obtained after preprocessing. The average sequencing depth was 33.81 for ‘Chardonnay’ (the female parent), 48.20 for ‘Beibinghong’ (the male parent), and 12.66 for the F₁ offspring. We detected 202,349 high-quality SLAFs of which 144,972 were polymorphic; 10,042 SNPs were used to construct a genetic map that spanned 1,969.95 cM, with an average genetic distance of 0.23 cM between adjacent markers. This genetic map contains the largest molecular marker number of the grape maps so far reported. We thus demonstrate that SLAF-seq is a promising strategy for the construction of high-density genetic maps; the map that we report here is a good potential resource for QTL mapping of genes linked to major economic and agronomic traits, map-based cloning, and marker-assisted selection of grape.</p></div

Genetic map lengths and marker distribution in 19 linkage groups of the male parent.

<p>Genetic map lengths and marker distribution in 19 linkage groups of the male parent.</p

Genetic map lengths and marker distribution in 19 linkage groups of the female parent.

<p>Genetic distance is indicated by the vertical scale in centimorgans (cM). Black lines represent mapped markers. 1–19 represent corresponding linkage groups ID.</p

Distribution of SLAFs and SNPs on chromosomes.

<p>Distribution of SLAFs and SNPs on chromosomes.</p

Genetic lengths and marker distribution in 19 linkage groups of the integrated map.

<p>Genetic lengths and marker distribution in 19 linkage groups of the integrated map.</p

Summary of SLAF-seq data for grape.

<p>Summary of SLAF-seq data for grape.</p

Number of SLAFs (A) and average sequencing depths (B) of F₁ population.

<p>The x-axis indicates the number of SLAFs (A) and the average depths (B); the y-axis indicates individual F₁ offspring.</p

The Spearman correlation coefficients between the genetic and physical positions of each linkage group on the integrated map.

<p>The Spearman correlation coefficients between the genetic and physical positions of each linkage group on the integrated map.</p

The genetic length and markers number of 19 linkage groups.

<p>The genetic length and markers number of 19 linkage groups.</p

The markers spacing and coverage of 19 linkage groups.

<p>The markers spacing and coverage of 19 linkage groups.</p