Biology subjects

Onoue, N.

Publications and source records attributed to Onoue, N..

4 recordsLinked to original sources

bioRxiv2026

Accumulation of two distinct alleles causes astringency loss in cultivated polyploid persimmon

Persimmon fruit accumulates high levels of proanthocyanidins (PAs), causing extreme astringency. In pollination-constant and non-astringent (PCNA) cultivars, PA accumulation ceases early in fruit development. Although the PCNA trait is recessively controlled by the ASTRINGENCY (AST) locus, its causal gene has remained unknown. Using haplotype-resolved forward genetics in a hexaploid genetic background, we identified the previously uncharacterized TANNIN (TAN) as the causal gene. Long-read sequencing revealed that PCNA originated through the accumulation of independently derived ast alleles that cause transcriptional deficiency of TAN. These findings resolve the complex genetic basis of natural astringency loss in persimmon and provide a framework for molecular breeding. Further investigation of TAN function would uncover mechanisms underlying massive accumulation of PAs in persimmon fruit and insight into specialized metabolite sequestration.

plant biology↗

bioRxiv2025

Physiological characterization in a somaclonal mutant for fruit shape derived from persimmon 'Hiratanenashi'

Fruit shape is an essential agronomic trait that contributes to the commercial value of fruit crops; however, the physiological mechanisms determining fruit shape have been studied only in a few model crops. Persimmon (Diospyros kaki Thunb.), a major fruit crop in East Asia, shows diversity in fruit shape among cultivars. The underlying molecular mechanisms that determine fruit shape remain unclear. A comparative physiological analysis was conducted to investigate the differences between a major Japanese cultivar, Hiratanenashi with a "flat" fruit shape, and its somaclonal mutant cultivar, Koushimaru with a "round" fruit shape. Through principal component analysis (PCA) with the elliptic Fourier descriptor, the fruit shape transitions in these two cultivars were measured over the fruit differentiation period (40-53 days after anthesis). Histological observation of the mesocarp cells in the fruit shape differentiation stage indicated that not only cell proliferation patterns but also multiple vectors involving cell shapes or sizes are possible determinants of differences in fruit shape. Transcriptome analysis at the fruit shape differentiation stage detected differentially expressed genes between the two cultivars. The hierarchical clustering with expression patterns throughout the fruit development/maturation stages defined four main clusters, including candidate genes determining fruit shapes. We focused on one of these genes, DKAch04a32073.t1, annotated as WUSCHEL related homeobox 13 (WOX13), which has been reported to be a key factor in callus formation (or stem cell proliferation) and the reconnection of organs in Arabidopsis thaliana. Future functional analyses of the candidate genes would provide a better understanding of the mechanisms underlying persimmon fruit shape.

plant biology↗

bioRxiv2023

Genetic basis of lineage-specific evolution of fruit traits in hexaploid persimmon

Frequent polyploidization events in plants have led to the establishment of many lineage-specific traits representing each species. Little is known about the genetic bases for these specific traits in polyploids, presumably due to plant genomic complexity and their difficulties of applying genetic approaches. Hexaploid Oriental persimmon (Diospyros kaki) has evolved specific fruit characters, including wide variations in fruit shapes and astringency. In this study, using whole-genome diploidized/quantitative genotypes from ddRAD-Seq data of 173 persimmon cultivars, we examined their population structures and potential correlations between their structural transitions and variations in nine fruit traits. The population structures of persimmon cultivars were highly randomized and not substantially correlated with the representative fruit traits focused on in this study, except for fruit astringency. With genome-wide association analytic tools considering polyploid alleles, we identified the loci associated with the nine fruit traits; we mainly focused on fruit-shape variations, which have been numerically characterized by principal component analysis of elliptic Fourier descriptors. The genomic regions that putatively underwent selective sweep exhibited no overlap with the loci associated with these persimmon-specific fruit traits. These insights will contribute to understanding of the genetic mechanisms by which fruit traits are independently established, possibly due to polyploidization events.

plant biology↗

bioRxiv2022

Ongoing rapid evolution of a post-Y region revealed by chromosome-scale genome assembly of a hexaploid monoecious persimmon (Diospyros kaki)

Sex chromosomes have evolved independently in many plant lineages. They have often undergone rapid structural degeneration and extension of non-recombining regions, which is conventionally considered to be strongly associated with the expression of sexually dimorphic traits. In this study, we assembled a monoecious hexaploid persimmon (Diospyros kaki) in which the Y chromosome had lost its function in male determination. Comparative genomic analysis among D. kaki and its dioecious relatives revealed that the non-functional Y chromosome (Ym) via silencing of the sex-determining gene, OGI, arose approximately two million years ago. Comparative analyses of the whole X and Ym chromosomes suggested that the non-functional male-specific region of the Y-chromosome (MSY), or post-MSY, retained certain conserved characteristics of the original functional MSY. Specifically, comparison of the functional MSY in D. lotus and the non-functional post-MSY in D. kaki indicated that the post-MSY had been rapidly rearranged mainly via ongoing transposable element bursts, as well as in the functional MSY. These results suggest a novel interpretation that the rapid evolution of the post-MSY (and possibly also MSYs in dioecious Diospyros species) might reflect the ancestral genomic properties of these regions, rather than the evolution of male-determining functions and/or sexually dimorphic traits.

plant biology↗