Fig 1.
The distributions of phenotypes in the diversity panel of 457 red raspberry accessions studied in this investigation.
Distributions of phenotypes for (A) plant vigour, (B) leaf colour, (C) fruit size, and thorn density (D).
Table 1.
The number of sequenced SNPs retained at each stage of the filtering process in 457 R. idaeus selections.
Fig 2.
A heatmap showing the distribution of 5,639 biallelic SNP markers in 1 Mbp windows across the seven chromosomes of the ‘Malling Jewel’ raspberry reference genome sequence.
Fig 3.
A plot of the genetic vs. physical positions of the SNP markers mapped in the Paris×486 mapping population.
Markers in blue are those mapped to the ‘Paris’ (A) map whilst those in red are those mapped to the ‘486’ (B) map.
Table 2.
The significant QTLs identified in the Paris×486 mapping population, along with the most closely associated SNP markers, their physical position on the ‘Malling Jewel’ genome sequence, their corresponding genetic position and the LOD and percentage of observed variance explained by each QTL.
Fig 4.
Genetic linkage map and QTL summary for fruit size, leaf colour, plant vigour and thorn density derived from the raspberry Paris×486 mapping population.
QTL are represented by bars (1-LOD interval) and extended lines (2-LOD interval). Colours served to distinguish between QTL for different traits: red – fruit size; blue – leaf colour; green – plant vigour; black – thorn density. A. represents the linkage map of the female ‘Paris’ parent, whilst B. represents the male ‘S0486’ parent. Linkage groups are to scale and represented in cM according to the scale bars to the left of each linkage map.
Fig 5.
Manhattan plots of markers significantly associated with fruit size, leaf colour, and thorn density in the red raspberry diversity panel used in this investigation, constructed against the ‘Malling Jewel’ reference genome sequence using BLINK implemented in GAPIT showing marker-trait associations exceeding the − log10(p) genome-wide threshold of ~7.5 (red dashed line).
The suggestive threshold of -log10(p) ~ 5 is also indicated with the blue dotted line.