Phylogeographic history of the Japanese alpine butterfly Erebia niphonica (Lepidoptera, Nymphalidae): fragmentation and secondary contactThe authors chose Erebia niphonica that is one of alpine butterflies, and studied about the distribution change of alpine organisms in the Japanese islands during Quaternary.For molecular information, we studied the haplotypes of base sequences of 942 bp in total using ND5 gene (432 bp) and CO 1 gene (510 bp) of mitochondrial DNA.Samples are 425 individuals collected in various parts of Hokkaido and Honshu in the Japanese islands.We also checked 2 individuals each from Khangai Mountains in Mongolia and Amur region in Russia for reference.We inferred past historical events by analyzing the haplotypes by Nested Clade Phylogeographical Analysis (NCPA).As a result it has been suggested that Erebia niphonica group went through reproductive isolation in more than one refugia in Hokkaido and more than one in Honshu during warm interglacials, and they fragmented into different lineages within the Japanese islands.Also we specified the secondary contact points which support the NCPA analysis which inferred that range fragmentation and dispersal were repeated.
Hybrid sterility is a reproductive barrier that prevents gene flow between species. In Oryza species, some hybrid sterility loci, which are classified as gamete eliminators, cause pollen and seed sterility and sex-independent transmission ratio distortion (siTRD) in hybrids. However, the molecular basis of siTRD has not been fully characterized because of lacking information on causative genes. Here, we analyze one of the hybrid sterility loci, S2, which was reported more than forty years ago but has not been located on rice chromosomes. Hybrids between African rice (Oryza glaberrima) and a near-isogenic line that possesses introgressed chromosomal segments from Asian rice (Oryza sativa) showed sterility and siTRD, which confirms the presence of the S2 locus. Genome-wide SNP marker survey revealed that the near-isogenic line has an introgression on chromosome 4. Further substitution mapping located the S2 locus between 22.60 Mb and 23.54 Mb on this chromosome. Significant TRD in this chromosomal region was also observed in a calli population derived from cultured anther in hybrids of another cross combination of African and Asian rice species. This indicates that the pollen abortion caused by the S2 locus occurs before callus induction in anther culture. It also suggests the wide existence of the S2-mediated siTRD in this interspecific cross combination. Chromosomal location of the S2 locus will be valuable for identifying causative genes and for understanding of the molecular basis of siTRD.
In F1 hybrids of Oryza sativa (Asian rice) and O. glaberrima (African rice), heterozygosity leads to a complete gamete abortion because of allelic conflict at each of the 13 hybrid sterility (HS) loci. We systematically produced 19 plants from the F1 hybrids of both the rice species by the anther culture (AC) method. Five of the 19 interspecific hybrid plants were fertile and able to produce seeds. Unlike ordinal doubled haploid plants resulting from AC, these regenerated plants showed various ploidy levels (diploid to pentaploid) and different zygosities (completely homozygous, completely heterozygous, and a combination). These properties were attributable to meiotic anomalies in the interspecific hybrid F1 plants. Examination of the genetic structures of the regenerated plants suggested meiotic non-reduction took place in the interspecific hybrid F1 plants. The centromeric regions in the regenerated plants revealed that the abnormal first and/or second divisions of meiosis, namely the first division restitution (FDR) and/or second division restitution (SDR), had occurred in the interspecific hybrid. Immunohistochemical observations also verified these phenomena. FDR and SDR occurrences at meiosis might strongly lead to the formation of diploid microspores. The results demonstrated that meiotic anomalies functioned as a reproductive barrier occurred before the HS genes acted in gamete of the interspecific hybrid. Although such meiotic anomalies are detrimental to pollen development, the early rescue of microspores carrying the diploid gamete resulted in the fertile regenerated plants. The five fertile plants carrying tetraploid genomes with heterozygous alleles of the HS loci produced fertile diploid pollens, implying that the diploid gametes circumvented the allelic conflicts at the HS loci. We also proposed how diploid male gametes avoid HS with the killer-protector model.
In this study, a lightweight phenotyping system that combined the advantages of both deep learning-based panicle detection and the photogrammetry based on light consumer-level UAVs was proposed. A two-year experiment was conducted to perform data collection and accuracy validation. A deep learning model, named Mask Region-based Convolutional Neural Network (Mask R-CNN), was trained to detect panicles in complex scenes of paddy fields. A total of 13 857 images were fed into Mask R-CNN, with 80% used for training and 20% used for validation. Scores, precision, recall, Average Precision (AP), and F1-score of the Mask R-CNN, were 82.46%, 80.60%, 79.46%, and 79.66%, respectively. A complete workflow was proposed to preprocess flight trajectories and remove repeated detection and noises. Eventually, the evident changed in rice growth during the heading stage was visualized with geographic distributions, and the total number of panicles was predicted before harvest. The average error of the predicted amounts of panicles was 33.98%. Experimental results showed the feasibility of using the developed system as the high-throughput phenotyping approach. Keywords: panicle detection, vision-based phenotyping, deep learning, unmanned aerial vehicle (UAV) DOI: 10.25165/j.ijabe.20211401.6025 Citation: Lyu S X, Noguchi N, Ospina R, Kishima Y. Development of phenotyping system using low altitude UAV imagery and deep learning. Int J Agric & Biol Eng, 2021; 14(1): 207–215.
Additional file 2: Table S1. List of Mekong Delta rice accessions examined in this study. Table S2. Phenotypic features for the standard evaluation system (SES) scores. Table S3. Preliminary test for salinity-tolerant/sensitive groups with 50 and 100 mM NaCl. Table S4. SES scores and phenotypic values in the 97 MDI accessions and their rankings. Table S5. Concentrations (mg/gDW) for mineral ions (Na+, K+, Ca2+, and Mg2+) and Na2+/K+ ratio in roots, stems, and leaves of 20 accessions exposed to 100 mM NaCl for 20 days (20 DUT) and control samples. Table S6A. SNPs above the threshold of p-value at 1.00E–04 in a Manhattan plot for SES score at 20 DUT (Fig. 5A). Table S6B. SNPs above the threshold of p-value at 1.00E–04 in a Manhattan plot for shoot dry weight ratio (Fig. 5B).
'%3e%3ccircle r='9'/%3e%3cg id='d'%3e%3cg id='c'%3e%3cg id='b'%3e%3cpath d='m-19 0 1.169 1.169L0 0l-17.831-1.169z'/%3e%3cpath id='a' d='m-.884.116.05.05L0 0z' transform='scale(19.2381)'/%3e%3cuse xlink:href='%23a' transform='scale(1 -1)'/%3e%3c/g%3e%3cuse xlink:href='%23b' transform='rotate(45)'/%3e%3c/g%3e%3cuse xlink:href='%23c' transform='rotate(90)'/%3e%3c/g%3e%3cuse xlink:href='%23d' transform='rotate(180)'/%3e%3cg transform='translate(-2.02)'%3e%3cg id='f' transform='translate(37.962)'%3e%3cpath id='e' d='M5 0 1.618 1.176l-.073 3.58-2.163-2.854-3.427 1.037L-2 0z'/%3e%3cuse xlink:href='%23e' transform='scale(1 -1)'/%3e%3c/g%3e%3cuse xlink:href='%23f' transform='rotate(120)'/%3e%3cuse xlink:href='%23f' transform='rotate(-120)'/%3e%3c/g%3e%3c/g%3e%3c/svg%3e)
