Biology subjects

Monden, Y.

Publications and source records attributed to Monden, Y..

4 recordsLinked to original sources

bioRxiv2024

Polyphyletic domestication and inter-lineage hybridization magnified genetic diversity of cultivated melon, Cucumis melo L.

A total of 212 melon accessions with diverse geographical origins were classified into large and small seed-types by length of seed at the boundary of 9 mm, and into five populations based on polymorphisms in the nuclear genome. They were further divided into three maternal lineages, Ia, Ib, and Ic, by polymorphisms in the chloroplast genome. By combining these three classifications, the Europe/US subsp. melo and the East Asian subsp. agrestis were characterized as [large seed, Ib, PopA1 or A2] and [small seed, Ia, PopB1 or B2], respectively, indicating nearly perfect divergence in both nuclear and cytoplasm genomes. In contrast, in South and Southeast Asia, in addition to the Europe/US and East Asian types, recombinant types were also frequently found, indicating unclear genetic differentiation in South and Southeast Asia. Such an intermixed structure of genetic variation supported the Indian origin of Ia and Ib types of melon. Seed length was intermediate, between the large and small seed-types, and chloroplast type was a mixture of Ia and Ib in Momordica, suggesting its origin from the recombinant type. In Africa, three lineages of melon were distributed allopatrically and showed distinct divergence. Subsp. agrestis of the Ic type proved to be endemic to Africa, indicating its African origin.

evolutionary biology↗

bioRxiv2024

Genetic characterization of cucumber genetic resources in the NARO Genebank indicates their multiple dispersal trajectories to the East

The cucumber (Cucumis sativus) is an economically important vegetable crop cultivated and consumed worldwide. Despite its popularity, the manner in which cucumbers were dispersed from their origin in South Asia to the rest of the world, particularly to the east, remains a mystery due to the lack of written records. In this study, we performed genotyping-by-sequencing (GBS) on 723 worldwide cucumber accessions, mainly deposited in the Japanese National Agriculture and Food Research Organization (NARO) Genebank, to characterize their genetic diversity, relationships, and population structure. Analyses based on over 60,000 genome-wide single-nucleotide polymorphisms identified by GBS revealed clear genetic differentiation between Southeast and East Asian populations, suggesting that they reached their respective region independently, not progressively. A deeper investigation of the East Asian population identified two subpopulations with different fruit characteristics, supporting the traditional classification of East Asian cucumbers into two types thought to have been introduced by independent routes. Finally, we developed a core collection of 100 accessions representing at least 93.2% of the genetic diversity present in the entire collection. The genetic relationships and population structure, their associations with geographic distribution and phenotypic traits, and the core collection presented in this study are valuable resources for elucidating the dispersal history and promoting the efficient use and management of genetic resources for research and breeding in cucumber. Key messageGenotyping-by-sequencing of 723 worldwide cucumber genetic resources revealed that cucumbers were dispersed eastward via at least three distinct routes, one to Southeast Asia and two from different directions to East Asia.

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↗

bioRxiv2019

Genetic Mapping in Autohexaploid Sweet Potato with Low-coverage NGS-based Genotyping Data

Next-generation sequencing (NGS)-based genotyping methods can generate numerous genetic markers in a single experiment and have contributed to plant genetic mapping. However, the benefits of NGS-based methods are limited in autopolyploids as their genetic segregation mode is complex. Moreover, autopolyploids have large genomes and require abundant sequencing data to obtain sufficient genetic markers. There are several methods for genetic mapping in autopolyploids. These approaches may be impractical for plant genetic studies as they require large amounts of data and are not cost-effective. In the present study, we propose a simple strategy for genetic mapping of polyploids in a cost-effective manner. The allele dosage probabilities calculated from NGS read counts were used in association analyses to detect loci associated with specific phenotypes. This approach is superior to conventional methods of determining allele dosage, which usually result in the filtering of many genetic markers with low read depth. The validity of the strategy was demonstrated using real phenotype data from autohexaploid sweet potato populations to detect genetic loci for both qualitative and quantitative traits, the latter of which required the use of allele dosage probabilities for the detection of loci. We demonstrate that this proposed method is useful with reasonable NGS read counts.

genetics↗