A lemon segregating population shed light on the origin of ‘Interdonato’ and on the regulation of spinescence

Thorns are sharp pointed structures characterizing the plant architecture of many Citrus species, especially in the juvenility phase, suggesting their involvement as a defence structure against herbivores. They mainly occur in the axil of the leaf and represent an undesired trait due to the direct damages of leaves and fruits, with consequence on pathogen infections and fruit marketability, and hampering the manual harvesting of the fruits. Taking advantage from the availability of a lemon segregating population ('Interdonato' × 'Femminello Siracusano 2Kr', 120 accessions) showing a wide variability in several morphological traits including spinescence a marker-trait association study was conducted to identify genetic region(s) underlying the trait. To this extent, thorns length and frequency (thorns number per stem) were monitored in one-year-old stems for three consecutive years to take into adequate consideration the variable of plant age. The phenotypic evaluation revealed a mean value for thorn length ranking from 0 to 31.84 mm, while frequency varied from 0 to 100%. Genotyping was performed through a target sequencing approach called single-primer enrichment technology (SPET), leading to the identification of 30,008 robust SNPs. Interestingly, the genetic comparison of the two parental lines revealed extended windows of homozygosity in 'Interdonato' compared to the reference lemon genome in linkage groups 3, 4, and 8. The availability of a segregating population and the design of SSR markers in the identified regions did not highlight the occurrence of deletions suggesting the origin of 'Interdonato' as a cross between lemon and citron. QTL analysis on the average length of thorn led to the identification of a QTL region (max LOD=4.53) located in LG 9 spanning from 54 to 59 cM. Three QTL regions were instead detected for the frequency of thorns in LG 1 (max LOD=4.9, from 65 to 70 cM), LG6 (max LOD=4.8, from 70 to 75 cM) and LG 9 (max LOD=4.3, from 50 to 53 cM). The identification of markers in close linkage with spinescence represents a valuable tool for the set-up of marker-assisted selection plans and for shading light on the genetic regulation of the trait.