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In peach, the flat phenotype is caused by a partially dominant allele in heterozygosis ( Ss ), fruits from homozygous trees ( SS ) abort a few weeks after fruit setting. Previous research has identified a SSR marker (UDP98–412) highly associated with the trait, found suitable for marker assisted selection (MAS). Here we report a ∼10 Kb deletion affecting the gene  PRUPE.6G281100 , 400 Kb upstream of UDP98-412, co-segregating with the trait. This gene is a leucine-rich repeat receptor-like kinase (LRR-RLK) orthologous to the  Brassinosteroid insensitive 1-associated receptor kinase 1  ( BAK1 ) group. PCR markers suitable for MAS confirmed its strong association with the trait in a collection of 246 cultivars. They were used to evaluate the DNA from a round fruit derived from a somatic mutation of the flat variety ‘UFO-4’, revealing that the mutation affected the flat associated allele ( S ). Protein BLAST alignment identified significant hits with genes involved in different biological processes. Best protein hit occurred with  AtRLP12 , which may functionally complement  CLAVATA2 , a key regulator that controls the stem cell population size. RT-PCR analysis revealed the absence of transcription of the partially deleted allele. The data support  PRUPE.6G281100  as a candidate gene for flat shape in peach.

A deletion affecting an LRR-RLK gene co-segregates with the fruit flat shape trait in peach