Abstract
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.
Highlights
Fruits are the edible part of many cultivated species and their study is one of the major topics in plant research
The SNPs closest to UDP98-412 annotated in the peach genome database occur 363.5 kb upstream of this marker, with 20 SNPs in a 26.5 kb region (Pp06: 26,254,140.26,254,809)
Considering the high level of variability observed genome-wide between round and flat peaches[22] the large extension of LD in peach[23, 24] and the codominant mode of action of the flat and round alleles, which must be in heterozygosis in flat varieties, we expected to find a substantial level of heterozygosis in the region flanking the SSR marker associated with the trait (UDP98-412)
Summary
Fruits are the edible part of many cultivated species and their study is one of the major topics in plant research. While little is known about the genetic mechanisms regulating fruit morphogenesis in fruit trees, many genetic studies have aimed to unravel such process in the model species Arabidopsis. In this species leucine-rich receptor like kinases like ERECTA and CLAVATA-1, show functional implications in the maintenance, size and shape meristem[2, 3]. Fruit shape has been most studied in tomato. The flat shape of the peach fruit is determined in the early stages of flower development by a single gene S/s (for saucer-shaped) mapped in the distal part of chromosome 615. The SSR UDP98-412 has been reported to be tightly linked to the S locus and works efficiently in marker assisted selection (MAS)[18]
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