Insertion of a transposon‐like sequence in the 5′‐flanking region of the YUCCA gene causes the stony hard phenotype

Abstract

Melting-flesh peaches produce large amounts of ethylene, resulting in rapid fruit softening at the late-ripening stage. In contrast, stony hard peaches do not soften and produce little ethylene. The indole-3-acetic acid (IAA) level in stony hard peaches is low at the late-ripening stage, resulting in low ethylene production and inhibition of fruit softening. To elucidate the mechanism of low IAA concentration in stony hard peaches, endogenous levels of IAA and IAA intermediates or metabolites were analysed by ultra-performance liquid chromatography-tandem mass spectrometry. Although the IAA level was low, the indole-3-pyruvic acid (IPyA) level was high in stony hard peaches at the ripening stage. These results indicate that YUCCA activity is reduced in ripening stony hard peaches. The expression of one of the YUCCA isogenes in peach, PpYUC11, was suppressed in ripening stony hard peaches. Furthermore, an insertion of a transposon-like sequence was found upstream of the PpYUC11 gene in the 5'-flanking region. Analyses of the segregation ratio of the stony hard phenotype and genotype in F1 progenies indicated that the transposon-inserted allele of PpYUC11, hd-t, correlated with the stony hard phenotype. On the basis of the above findings, we propose that the IPyA pathway (YUCCA pathway) is the main auxin biosynthetic pathway in ripening peaches of 'Akatsuki' and 'Manami' cultivars. Because IAA is not supplied from storage forms, IAAde novo synthesis via the IPyA pathway (YUCCA pathway) in mesocarp tissues is responsible for auxin generation to support fruit softening, and its disruption can lead to the stony hard phenotype.

Application of an antibody chip for screening differentially expressed proteins during peach ripening and identification of a metabolon in the SAM cycle to generate a peach ethylene biosynthesis model

“…As shown in Fig. 6a, b, the IAA concentration increased prior to a sharp increase in ethylene emission in CN13, while the silencing of YUC11 in CN16 turned off IAA production and ethylene generation, which was consistent with the experimental data 24,25 . IAA regulates ethylene production through the induction of Type-II ACS genes.…”

“…In addition to the metabolic reactions mentioned above, ACS1 expression is induced by IAA, which is catalyzed by YUCCA from the indole-3-pyruvic acid (IPyA) pathway; 24,25 the transcription of MetE has been reported to be linearly correlated with that of its substrate, Hcy 26 (Fig. 5).…”

Mikan Genome Database (MiGD): integrated database of genome annotation, genomic diversity, and CAPS marker information for mandarin molecular breeding

“…Recently, the molecular mechanism of various agronomically important traits in fruit trees is becoming apparent owing to the advances in deciphering the genome. Anthocyanin accumulation in blood orange (Butelli et al 2012), grape (Kobayashi et al 2004), and apple (Zhang et al 2019), columnar tree type in apple (Okada et al 2016), and non-melting flesh in stony hard peaches (Tatsuki et al 2018) is controlled by transcriptional regulation mediated by insertion or deletion of transposons. Therefore, the advancement of technologies in assembling hybrid genomes and long sequence reads is extremely important to assign transposons, retrotransposons, and repeat elements to accurate positions in the draft sequences.…”

Transposons played a major role in the diversification between the closely related almond (Prunus dulcis) and peach (P. persica) genomes: Results from the almond genome sequence

“…yellow fruit color (Falchi et al, 2013) hairy vs. glabrous fruit (Vendramin et al, 2014) and stonyhard vs. melting flesh texture (Tatsuki et al 2018) are caused by the action of transposon movement. MITE insertions have also been linked to crop traits, such as sex determination in melon (Martin et al 2009) or a drought tolerance phenotype in maize (Mao et al 2015).…”