Pangenome Analyses of Pyrus Unravel the Mechanism of Ethylene-Dependent and Ethylene-Independent Fruit Formation

Fleshy fruits are classified as ethylene dependent or ethylene independent according to the ethylene production rate at the onset of ripening. However, the mechanism regulating ethylene production in fruits is unclear. Pears ( Pyrus spp.) contain both types of fruits. Analyses of 5 Pyrus genomes and 109 resequenced pear accessions revealed an important chromosomal locus closely associated with ethylene-producing phenotype. This locus was closely linked to a novel long noncoding RNA (lncRNA). Interestingly, the expression of this lncRNA showed an opposite pattern to ethylene production. Fruits overexpressing this lncRNA displayed extremely low ethylene production and a late ripening phenotype, which was observed for both tomatoes and pears. Therefore, this lncRNA was termed Ethylene Inhibiting Factor ( EIF ). Variable deletions of 3.8 kb and 1.1 kb regions altered EIF expression and enabled the categorization of pears into six genotypes. The huge number of transposable elements (TEs) were observed and they probably drove fragment rearrangement, generating the EIF , which repressed the ethylene production, resulting in ethylene-independent pear fruit. These findings provide new insights into the molecular basis of ethylene-producing phenotype in Maloideae fruits.