A novel mutation of LTR insertion in PpCCD4 exon identified in Prunus ferganensis leads to yellow-fleshed fruits

Yellow/white-fleshed color, one of the most important traits of peach (Prunus persica (L.) Batsch.), is closely related to the mutation of the PpCCD4. Although three mutations have been identified in the PpCCD4 gene leading to yellow flesh peaches, it is still intriguing whether a new mutation mechanism exists. Here, we genotyped 335 haplotypes of the yellow-fleshed peach (Y) locus from around the world and found that a transposable element (TE) insertion in Prunus ferganensis (Kost. & Riab) Kov.& Kost, resulted in nonsense mutation in PfCCD4. We performed transient overexpression experiments on ripening fruit and confirmed that the LTR2 in the PfCCD4 exon produced a phenotype different from that of PfCCD4. By Illumina and Nanopore sequencing, we obtained genomic information of the homozygous insertion on the cultivar ‘Xinjiang Huangrou’, got the sequence and position of the variant, and further confirmed that the insertion is an LTR-type(Long terminal repeats) transposon (named LTR2), which is more ancient than the previously reported insertion, indicating that Prunus ferganensis may be one of the sources of the yellow flesh peach variation. The discovery of a new yellow-fleshed variant in Prunus ferganensis provides insight into utilizing the local germplasm resource for yellow-fleshed peach cross-breeding.