Construction of Commercial Sweet Cherry Linkage Maps and QTL Analysis for Trunk Diameter

<div><p>A cross between the sweet cherry (<i>Prunus avium</i>) cultivars ‘Wanhongzhu’ and ‘Lapins’ was performed to create a mapping population suitable for the construction of a linkage map. The specific-locus amplified fragment (SLAF) sequencing technique used as a single nucleotide polymorphism (SNP) discovery platform and generated 701 informative genotypic assays; these, along with 16 microsatellites (SSRs) and the incompatibility (<i>S</i>) gene, were used to build a map which comprised 8 linkage groups (LGs) and covered a genetic distance of 849.0 cM. The mean inter-marker distance was 1.18 cM and there were few gaps > 5 cM in length. Marker collinearity was maintained with the established peach genomic sequence. The map was used to show that trunk diameter (TD) is under the control of 4 loci, mapping to 3 different LGs. Different locus influenced TD at a varying stage of the tree’s development. The high density ‘W×L’ genetic linkage map has the potential to enable high-resolution identification of QTLs of agronomically relevant traits, and accelerate sweet cherry breeding.</p></div

Collinearity between the sweet cherry high density map (LG1-8) and peach genome sequence (Scaffold1-8).

<p>In the latter, markers ‘0’ and ‘1’ refer to the two ends of each scaffold. Positions of anchored markers in each peach scaffold = physical position×3×10–6. Sequence-anchored markers are indicated by connecting lines and are shown underlined. Inter-marker distance given in cM.</p

Conservation of SSRs between the sweet cherry ‘W×L’ map, other sweet cherry maps and the peach genome sequence.

<p>Conservation of SSRs between the sweet cherry ‘W×L’ map, other sweet cherry maps and the peach genome sequence.</p

Year on year correlation for TD and ATNG.

<p>** Correlation is significant at the 0.01 level (2-tailed).</p><p>* Correlation is significant at the 0.05 level (2-tailed).</p><p>Year on year correlation for TD and ATNG.</p

LG by LG breakdown of the markers contributing to the high density ‘W×L’ linkage map.

<p>^a The ratio is No. of sig < 0.05 markers to total markers in each LG.</p><p>LG by LG breakdown of the markers contributing to the high density ‘W×L’ linkage map.</p

Collinearity between sweet cherry LGs derived the framework map (FG1-8) and the high density map (LG1-8).

<p>Sequence-anchored markers are indicated by connecting lines and are shown underlined. Inter-marker distance given in cM.</p

TD and ATNG QTL identified in the ‘W×L’ mapping population.

<p>TD and ATNG QTL identified in the ‘W×L’ mapping population.</p

LG by LG breakdown of SLAF sequences matching sequences present in the peach genome.

<p>LG by LG breakdown of SLAF sequences matching sequences present in the peach genome.</p

QTL for trunk diameter (TD) detected over the period 2012–2014 and annual trunk net growth (ATNG) in 2012 and 2014.

<p>1-LOD and 2-LOD support intervals of each QTL are marked by thick and thin bars, respectively. The partial genetic map only includes the LGs harboring relevant QTL.</p