Biology subjects

Itai, A.

Publications and source records attributed to Itai, A..

7 recordsLinked to original sources

bioRxiv2026

A coordinated regeneration-selection strategy enables genetic transformation and rapid flowering in apple x pear intergeneric hybrids

Wide hybridization between related species and genera provides valuable opportunities for broadening genetic diversity and introducing desirable traits. In the tribe Maleae (Rosaceae), Malus (apple) and Pyrus (pear) are phylogenetically closely related, and apple x pear hybrids represent promising materials such as for disease-resistance breeding. However, the effective utilization of such hybrids in breeding programs is constrained by long juvenile period. In this study, we established a tissue culture-based regeneration and genetic transformation platform for apple x pear hybrids. Key stages affecting adventitious shoot regeneration were optimized, and appropriate ranges of antibiotic selection pressure and bacterial elimination conditions were systematically evaluated. Regeneration capacity was predominantly genotype-dependent and became further restricted under Agrobacterium infection, necessitating precise balancing between regeneration competence and selection pressure. Using the highly competence line and the established transformation system, MdFT1 gene was successfully introduced and over-expressed in intergeneric hybrids, resulting in transgenic plants exhibiting floral bud initiation approximately six months after infection under in vitro conditions. This study provides a practical and efficient regeneration-transformation framework for apple x pear hybrids and demonstrates its applicability for FT-mediated early flowering. The established system offers technical support for accelerated breeding strategies and facilitates the utilization of novel resources in genetic improvement of pome fruit.

plant biology↗

bioRxiv2025

Spatially resolved analysis of growth dynamics in pome and drupe fruits of Rosaceae using 3D Gaussian Splatting

Fruit growth has long been described using single- or double-sigmoid curves; however, these temporal models cannot fully capture the spatial heterogeneity that ultimately shapes a fruit. Here, we present a three-dimensional analysis pipeline that non-destructively tracks spatial fruit growth dynamics from field-collected imaginary. Surface landmarks were drawn, and video recordings were taken throughout development for three pome fruits, apple (Malus x domestica), Japanese pear (Pyrus pyrifolia) and European pear (Pyrus communis), and two drupe fruits, peach (Prunus persica) and Japanese apricot (Prunus mume), to track their motion. Using 3D Gaussian Splatting, we successfully reconstructed 3D models of the fruits, and the landmark displacement could be measured with high accuracy, with R2 [≥] 0.98 when compared to manual recordings. We found a common spatial growth gradient in the longitudinal growth shared in the pomes and drupes of the Rosaceae; proximal (stem-end) regions exhibited more pronounced growth than the distal (stylar) end. An exception was found in European pear Bartlett, which showed relatively vigorous growth in the distal region, explaining its distinct shape with expanded distal end. Transverse expansion varied far less than longitudinal expansion, with a possible association with initial fruit morphology. Inter-fruit growth variability peaked in the fastest-growing regions, particularly in the distal area of the European pear, highlighting the link between growth vigor and phenotypic variance. These results provide foundational insights into the developmental dynamics of both pome and drupe fruits of the Rosaceae family, contributing to the optimization of fruit size, shape, and uniformity.

plant biology↗

bioRxiv2023

Propagation path of a flowering cherry (Cerasus x yedoensis) cultivar 'Somei-Yoshino' traced by somatic mutations

Flowering cherry cultivar Somei-Yoshino (Cerasus x yedoensis) has been clonally propagated and spread all around the world including Japan. Somei-Yoshino is thought to be an interspecific hybrid derived from C. spachiana and C. speciosa; however, its origin is unclear. Since somatic mutations are randomly induced in genomes and stably transmitted through generations, we aimed to identify somatic mutations in the genome of Somei-Yoshino to trace its propagation path. A total of 46 Somei-Yoshino clones were collected from all over Japan and subjected to whole-genome sequencing. The results revealed 684 single nucleotide variants, of which 71 were found in more than two clones. Clustering analysis of the 46 clones using these 71 variants revealed six groups, four of which contained 40 of the 46 clones. In addition, because each of the four clones closely planted in Ueno Park, Tokyo, Japan, clustered into the four different groups, we considered that these four clones could be the ancestors of the Somei-Yoshino clones found in Japan. Furthermore, based on the comparison of mutant alleles with the genomes of Cerasus species, one of the four trees was concluded as the closest to the origin. Here, we propose that the origin of Somei-Yoshino is a chimera derived from at least four somatic mutants.

plant biology↗

bioRxiv2021

Transcriptome Dynamics of Floral Organs Approaching Blooming in the Flowering Cherry (Cerasus x yedoensis) Cultivar 'Somei-Yoshino'

To gain insights into the genetic mechanisms underlying blooming and petal movement in flowering cherry (Cerasus x yedoensis), we performed time-course RNA-seq analysis of the floral buds and open-flowers of the most popular flowering cherry cultivar, Somei-Yoshino. Independent biological duplicate samples of floral buds and open-flowers were collected from Somei-Yoshino trees grown at three different locations in Japan. RNA-seq reads obtained from floral bud and open-flower samples collected in the current study (in 2019) and in a previous study (in 2017) were aligned against the genome sequence of Somei-Yoshino to quantify gene transcript levels. Clustering analysis of RNA-seq reads revealed dynamic changes in the transcriptome, with genes in seven modules predominantly expressed at specific time points, ranging from 5 weeks before flowering to 2 weeks after flowering. Based on the identified gene modules and Gene Ontology (GO) terms enriched at different floral stages, we speculate that the genetic mechanisms underlying petal movement and flower opening in cherry involve the processes of development, cell wall organization, reproduction, and metabolism, which are executed by genes encoding transcription factors, phytohormones, transporters, and polysaccharide metabolic enzymes. Furthermore, we propose a method for cherry bloom forecasting, based on gene expression levels at different time points before flowering as RNA markers.

plant biology↗

bioRxiv2021

Genome sequencing and analysis of two early-flowering cherry (Cerasus x kanzakura) varieties, 'Kawazu-zakura' and 'Atami-zakura'

To gain genetic insights into the early-flowering phenotype of ornamental cherry, also known as sakura, we determined the genome sequences of two early-flowering cherry (Cerasus x kanzakura) varieties, Kawazu-zakura and Atami-zakura. Since the two varieties are interspecific hybrids, likely derived from crosses between Cerasus campanulata (early-flowering species) and Cerasus speciosa, we employed the haplotype-resolved sequence assembly strategy. Genome sequence reads obtained from each variety by single molecule real-time sequencing (SMRT) were split into two subsets, based on the genome sequence information of the two probable ancestors, and assembled to obtain haplotype-phased genome sequences. The resultant genome assembly of Kawazu-zakura spanned 519.8 Mb with 1,544 contigs and an N50 value of 1,220.5 kb, while that of Atami-zakura totaled 509.6 Mb with 2,180 contigs and an N50 value of 709.1 kb. A total of 72,702 and 72,528 potential protein-coding genes were predicted in the genome assemblies of Kawazu-zakura and Atami-zakura, respectively. Gene clustering analysis identified 2,634 clusters uniquely presented in the C. campanulata haplotype sequences, which might contribute to its early-flowering phenotype. Genome sequences determined in this study provide fundamental information for elucidating the molecular and genetic mechanisms underlying the early-flowering phenotype of ornamental cherry tree varieties and their relatives.

genomics↗

bioRxiv2020

Chromosome-scale genome assembly of Japanese pear (Pyrus pyrifolia) variety 'Nijisseiki

AimThe Japanese pear (P. pyrifolia) variety Nijisseiki is valued for its superior flesh texture, which has led to its use as a breeding parent for most Japanese pear cultivars. However, in the absence of genomic resources for Japanese pear, the parents of the Nijisseiki cultivar remain unknown, as does the genetic basis of its favorable texture. The genomes of pear and related species are complex due to ancestral whole genome duplication and high heterozygosity, and long-sequencing technology was used to address this. Methods and ResultsDe novo assembly of long sequence reads covered 136x of the Japanese pear genome and generated 503.9 Mb contigs consisting of 114 sequences with an N50 value of 7.6{square}Mb. Contigs were assigned to Japanese pear genetic maps to establish 17 chromosome-scale sequences. In total, 44,876 protein-encoding genes were predicted, 84.3% of which were supported by predicted genes and transcriptome data from Japanese pear relatives. As expected, evidence of whole genome duplication was observed, consistent with related species. Conclusion and PerspectiveThis is the first genome sequence analysis reported for Japanese pear, and this resource will support breeding programs and provide new insights into the physiology and evolutionary history of Japanese pear.

genomics↗

bioRxiv2019

Phased genome sequence of an interspecific hybrid flowering cherry, Somei-Yoshino (Cerasus x yedoensis)

We report the phased genome sequence of an interspecific hybrid, the flowering cherry Somei-Yoshino (Cerasus x yedoensis). The sequence was determined by single-molecule real-time sequencing technology and assembled using a trio-binning strategy in which allelic variation was resolved to obtain phased sequences. The resultant assembly consisting of two haplotype genomes spanned 690.1 Mb with 4,552 contigs and an N50 length of 1.0 Mb. We predicted 95,076 high-confidence genes, including 94.9% of the core eukaryotic genes. Based on a high-density genetic map, we established a pair of eight pseudomolecule sequences, with highly conserved structures between two genome sequences with 2.4 million sequence variants. A whole genome resequencing analysis of flowering cherry varieties suggested that Somei-Yoshino is derived from a cross between C. spachiana and either C. speciose or its derivative. Transcriptome data for flowering date revealed comprehensive changes in gene expression in floral bud development toward flowering. These genome and transcriptome data are expected to provide insights into the evolution and cultivation of flowering cherry and the molecular mechanism underlying flowering.

genomics↗