Seedless fruit in Annona squamosa L. is monogenic and conferred by INO locus deletion in multiple accessions

Understanding the genetic basis and inheritance of a trait facilitates the planning of breeding and development programs of new cultivars. In the sugar apple tree (Annona squamosa L.), the mechanism of the desirable seedless trait in the Thai seedless (Ts) and Brazilian seedless (Bs) accessions was associated with a deletion of the INNER NO OUTER (INO) locus. Genetic analysis of F1, F2 and backcross descendants of crosses of Bs to fertile wild-type varieties showed that seedlessness was recessive and monogenic. Whole genome sequencing of a third accession, Hawaiian seedless (Hs), identified a 16 kilobase deletion including INO. The finding of an identical deletion in Ts and Bs indicated a common origin among genotypes, from a single deletion event. Analysis of microsatellite markers could not preclude the possibility that all three accessions are vegetatively propagated clones. The sequence of the deletion site enabled formulation of a codominant assay for the wild-type and mutant genes that validated the INO gene deletion as the cause of seedless trait, and can be used in the selection of new seedless varieties. The study findings and obtained progenies should be useful in breeding and introgression programs of the trait into elite sugar apple lines and into other Annonas by means of interspecific crossings.