Chrysanthemums are one of the most industrially important cut flowers worldwide. However, their segmental allopolyploidy and self-incompatibility have prevented the application of genetic analysis and modern breeding strategies. We thus developed a model strain, Gojo-0 (Chrysanthemum seticuspe), which is a diploid and self-compatible pure line. Here, we present the 3.05 Gb chromosome-level reference genome sequence, which covered 97% of the C. seticuspe genome. The genome contained more than 80% interspersed repeats, of which retrotransposons accounted for 72%. We identified recent segmental duplication and retrotransposon expansion in C. seticuspe, contributing to arelatively large genome size. Furthermore, we identified a retrotransposon family, SbdRT, which was enriched in gene-dense genome regions and had experienced a very recent transposition burst. We also demonstrated that the chromosome-level genome sequence facilitates positional cloning in C. seticuspe. The genome sequence obtained here can greatly contribute as a reference for chrysanthemum in front-line breeding including genome editing.

The recent whole-genome sequencing of soybean (Glycine max) revealed that soybean experienced whole-genome duplications 59 million and 13 million years ago, and it has an octoploid-like genome in spite of its diploid nature. We analyzed a natural green-cotyledon mutant line, Tenshin-daiseitou. The physiological analysis revealed that Tenshin-daiseitou shows a non-functional stay-green phenotype in senescent leaves, which is similar to that of the mutant of Mendel’s green-cotyledon gene I, the ortholog of SGR in pea. The identification of gene mutations and genetic segregation analysis suggested that defects in GmSGR1 and GmSGR2 were responsible for the green-cotyledon/stay-green phenotype of Tenshin-daiseitou, which was confirmed by RNA interference (RNAi) transgenic soybean experiments using GmSGR genes. The characterized green-cotyledon double mutant d1d2 was found to have the same mutations, suggesting that GmSGR1 and GmSGR2 are D1 and D2. Among the examined d1d2 strains, the d1d2 strain K144a showed a lower Chl a/b ratio in mature seeds than other strains but not in senescent leaves, suggesting a seed-specific genetic factor of the Chl composition in K144a. Analysis of the soybean genome sequence revealed four genomic regions with microsynteny to the Arabidopsis SGR1 region, which included the GmSGR1 and GmSGR2 regions. The other two regions contained GmSGR3a/GmSGR3b and GmSGR4, respectively, which might be pseudogenes or genes with a function that is unrelated to Chl degradation during seed maturation and leaf senescence. These GmSGR genes were thought to be produced by the two whole-genome duplications, and they provide a good example of such whole-genome duplication events in the evolution of the soybean genome.

This research was conducted to identify quantitative trait loci (QTL) associated with egg-related traits by constructing a genetic linkage map based on single nucleotide polymorphism (SNP) markers using restriction-site associated DNA sequencing (RAD-seq) in Japanese quail. A total of 138 F₂ females were produced by full-sib mating of F₁ birds derived from an intercross between a male of the large-sized strain with three females of the normal-sized strain. Eggs were investigated at two different stages: the beginning stage of egg-laying and at 12 weeks of age (second stage). Five eggs were analyzed for egg weight, lengths of the long and short axes, egg shell strength and weight, yolk weight and diameter, albumen weight, egg equator thickness, and yolk color (L*, a*, and b* values) at each stage. Moreover, the age at first egg, the cumulative number of eggs laid, and egg production rate were recorded. RAD-seq developed 118 SNP markers and mapped them to 13 linkage groups using the Map Manager QTX b20 software. Markers were spanned on 776.1 cM with an average spacing of 7.4 cM. Nine QTL were identified on chromosomes 2, 4, 6, 10, 12, and Z using the simple interval mapping method in the R/qtl package. The QTL detected affected 10 egg traits of egg weight, lengths of the long and short axes of egg, egg shell strength, yolk diameter and weight, albumen weight, and egg shell weight at the beginning stage, yellowness of the yolk color at the second stage, and age at first egg. This is the first report to perform a quail QTL analysis of egg-related traits using RAD-seq. These results highlight the effectiveness of RAD-seq associated with targeted QTL and the application of marker-assisted selection in the poultry industry, particularly in the Japanese quail.

In this study, we analyzed the complete sequence of the chloroplast genome of Chrysanthemum rupestre Matsum. et Koidz., 1910, a diploid disciform capitula species of Chrysanthemum endemic to Japan, formerly classified as Ajania rupestris (Matsum. & Koidz.) Muldashev, Bot. Zhurn. (Moscow & Leningrad), 1983. The chloroplast genome of C. rupestre has a typical conserved quadripartite structure of 151,061 bp in length, comprising a large single-copy region (82,846 bp), a small single-copy region (18,301 bp), and a pair of inverted repeat regions (each 24,957 bp). Phylogenetic analysis indicated that C. rupestre clustered with other Chrysanthemum species, including another former Ajania species, Chrysanthemum pacificum Nakai, 1928. However, Ajania variifolia (C.C.Chang) Tzvelev, 1961, which is a synonym of Phaeostigma variifolium (C.C.Chang) Muldashev, 1981, was placed outside the Chrysanthemum clade, thereby implying that the former genus Ajania includes heterogeneous species.