Genomic Analysis Of Two Early Clementine Varieties, Derived From Spontaneous and Induced Mutations, Reveals a Common 2MB Deletion On Chromosome 3

In the frame of the Citruseq project the complete genome of Arrufatina and Nero, two self-incompatible Citrus clementinavarieties directly derived from Clemenules, have been sequenced. Arrufatina is a sport mutation that appeared spontaneously in the field while Nero is a mutation obtained by irradiation. Both are early commercial varieties and exhibit similar physiological behaviour and agronomical traits, although Nero, in addition, shows male and female sterility. Sequencing of both genomes at coverage higher than 50x was performed with Illumina. The published haploid clementine genome (phytozome.org) was used as the genome of reference and the SNPs present in each variety were identified after comparison with the parental diploid Clementine genome.

Estimations of loss of heterozygosity in the derived varieties were used to reveal putative deletions. In both varieties, the comparative algorithm used predicted that most of the lost SNPs accumulated in a specific region on chromosome 3, spanning around 2 Mb. Although this observation suggested that this region was in hemizygous dosage, further molecular characterization unequivocally identified two different haplotypes showing dissimilar allelic frequency. This region is under study in order to investigate the effect of the deleted genes on fruit earliness.