Combination of genetic analysis and ancient literature survey reveals the divergence of traditional Brassica rapa varieties from Kyoto, Japan

京の伝統野菜ミブナの育種の歴史を解明. 京都大学プレスリリース. 2021-06-02.Since ancient times, humans have bred several plants that we rely on today. However, little is known about the divergence of most of these plants. In the present study, we investigated the divergence of Mibuna (Brassica rapa L. subsp. nipposinica L. H. Bailey), a traditional leafy vegetable in Kyoto (Japan), by combining genetic analysis and a survey of ancient literature. Mibuna is considered to have been bred 200 years ago from Mizuna, another traditional leafy vegetable in Kyoto. Mibuna has simple spatulate leaves, whereas Mizuna has characteristic serrated leaves. The quantitative trait loci (QTL) and gene expression analyses suggested that the downregulation of BrTCP15 expression contributed to the change in the leaf shape from serrated to simple spatulate. Interestingly, the SNP analysis indicated that the genomic region containing the BrTCP15 locus was transferred to Mibuna by introgression. Furthermore, we conducted a survey of ancient literature to reveal the divergence of Mibuna and found that hybridization between Mizuna and a simple-leaved turnip might have occurred in the past. Indeed, the genomic analysis of multiple turnip cultivars showed that one of the cultivars, Murasakihime, has almost the same sequence in the BrTCP15 region as Mibuna. These results suggest that the hybridization between Mizuna and turnip has resulted in the establishment of Mibuna

Genet assignment and population structure analysis in a clonal forest-floor herb, Cardamine leucantha, using RAD-seq

To study the genetic structure of clonal plant populations, genotyping and genet detection using genetic markers are necessary to assign ramets to corresponding genets. Assignment is difficult as it involves setting a robust threshold of genetic distance for genet distinction as neighbouring genets in a plant population are often genetically related. Here, we used restriction site-associated DNA sequencing (RAD-seq) for a rhizomatous clonal herb, Cardamine leucantha [Brassicaceae] to accurately determine genet structure in a natural population. We determined a draft genome sequence of this species for the first time, which resulted in 66,617 scaffolds with N50 = 6,086 bp and an estimated genome size of approximately 253 Mbp. Using genetic distances based on the RAD-seq analysis, we successfully distinguished ramets that belonged to distinct genets even from a half-sib family. We applied these methods to 372 samples of C. leucantha collected at 1-m interval grids within a 20 × 20 m plot in a natural population in Hokkaido, Japan. From these samples, we identified 61 genets with high inequality in terms of genet size and patchy distribution. Spatial autocorrelation analyses indicated significant aggregation within 7 and 4 m at ramet and genet levels, respectively. An analysis of parallel DNA microsatellite loci (simple sequence repeats, SSR) suggested that RAD-seq can provide data that allows robust genet assignment. It remains unclear whether the large genets identified here became dominant stochastically or deterministically. Precise identification of genets will assist further study and characterization of dominant genets

Jaw Laterality and Related Handedness in the Hunting Behavior of a Scale-Eating Characin, Exodon paradoxus

BACKGROUND: Asymmetry in animal bodies and behavior has evolved several times, but our knowledge of their linkage is limited. Tanganyikan scale-eating cichlids have well-known antisymmetry in their bodies and behavior; individuals open their mouths leftward (righty) or rightward (lefty), and righties always attack the right flank of the prey, whereas lefties attack the left. This study analyzed the morphological asymmetry in a scale-eating characiform, Exodon paradoxus, and its behavioral handedness. METHODOLOGY/PRINCIPAL FINDINGS: Each eight E. paradoxus was observed for 1-h with a prey goldfish in an aquarium to detect the behavioral handedness. Following the experiment, the lateral differences in the mandibles and head-inclination of these eight and ten additional specimens were analyzed. Both measurements on the morphology showed a bimodal distribution, and the laterality identified by these two methods was always consistent within a given individual, indicating that the characin has morphological antisymmetry. Furthermore, this laterality significantly corresponded to behavioral handedness; that is, lefties more often rasped scales from the right flank of the prey and vice versa. However, the correlation between laterality and handedness is the opposite of that in the cichlids. This is due to differences in the feeding apparatus and technique. The characin has cuspids pointing forward on the external side of the premaxilla, and it thrusts its dominant body side outward from its body axis on the flank of the prey to tear off scales. By contrast, the cichlids draw their dominant body side inward toward the axis or rotate it to scrape or wrench off scales with the teeth lined in the opened mouth. CONCLUSIONS/SIGNIFICANCE: This study demonstrated that the antisymmetry in external morphology and the corresponding behavioral handedness have evolved in two lineages of scale-eating fishes independently, and these fishes adopt different utilization of their body asymmetry to tear off scales

Predominance of cross-predation between lateral morphs in a largemouth bass and a freshwater goby.

The predator-prey relationship between largemouth bass, Micropterus salmoides, and freshwater goby, Rhinogobius spp., in Lake Biwa, Japan, was examined with respect to their morphological antisymmetry (laterality). Largemouth bass and Rhinogobius gobies exhibited lateral dimorphism in the height of the mandible and the length of the dentary, respectively. Populations of both species were composed of both left-developed and right-developed individuals. Each predation event was categorized as either cross-predation (a predator caught prey of the opposite morph) or parallel-predation (a predator caught prey of the same morph). Stomach contents analysis revealed that cross-predation events predominated over parallel-predation. Annual sampling for eight years demonstrated that in both largemouth bass and Rhinogobius gobies, the ratio of right-developed individuals in the population fluctuated temporally around 0.5. As the predominance of cross-predation was found in the relationship between the exotic largemouth bass and an endemic goby, the predominance may be caused by a kinematical interplay at each predation event

捕食-被食相互作用における魚類の左右性 : 行動学的視点からの解明

京都大学0048新制・課程博士博士(理学)甲第16673号理博第3785号新制||理||1547(附属図書館)29348京都大学大学院理学研究科生物科学専攻(主査)教授 堀 道雄, 准教授 渡辺 勝敏, 教授 沼田 英治学位規則第4条第1項該当Doctor of ScienceKyoto UniversityDA

Electronic Supplementary Materials Online Resource 3, R script to save motion file

BVHconvert.R is R script to convert the 3D coordinates of fish motion saved in CSV format into BVH format.<div>motion1_fortest.csv is a data to test this script. By using this script, motion1_fortest.csv is converted into motion1_fortest.bvh.<br></div

3DCG Medaka Fish Creation Manual (in Japanese)

Manual for making fish polygons and associating the motion file with the polygon model, and creating an animation of the model swimming

3DCG Medaka Fish Creation Manual (in English)

Manual for making fish polygons and associating the motion file with the polygon model, and creating an animation of the model swimming