In China, PBR (Plant Breeder’s Right) applications of chrysanthemum rank first among all of the applications of ornamental crops in China due to the plant’s significant ornamental, edible, and medicinal values. However, issues of variety infringement and disputes have become increasingly prominent, and traditional molecular markers are difficult to use due to the high heterozygosity and complex ploidy of chrysanthemum. Our study explored the availability of MNP (Multiple Nucleotide Polymorphism) markers in this regard. In total, 30 representative varieties of five types were selected for the screening of MNPs, and another 136 varieties were selected for validation of the screened MNPs. Based on ddRAD-seq (Double Digest Restriction site-associated DNA sequencing) of the 30 varieties, 26,147 SNPs were screened for genetic analysis，and 487 MNPs were screened with a length from 139 to 274 bp, an average of 6.6 SNPs individually, and a repeatability rate of 99.73%. Among the 487 MNPs, 473 MNP markers were found to cover all 27 chromosomes of chrysanthemum. Performance of our MNPs in the 136 varieties was similar to those in the 30 varieties, where the average Ho (observed heterozygosity) was 71.48%, and the average DP (discriminative power) was 82.77%, preliminarily indicating the stability of the 487 MNPs. On the other hand, clustering results based on the 487 MNPs were also generally consistent with those based on the 26,147 SNPs, as well as those based on phenotypic traits, and initial grouping, likewise, further indicating the robust capability of our MNPs in variety discrimination, which is similar to their correspondence with numerous SNPs. Therefore, our MNP markers have great potential in the accurate and rapid identification of chrysanthemum varieties, and, accordingly, in fostering breeding innovation and promoting chrysanthemum marketing.

Seed vigour is a key trait determining field seedling establishment and storage longevity in rice. In this study, we aimed to systematically evaluate the vigour variation patterns of rice germplasm from different sub-populations and geographic origins under artificial ageing and explore the feasibility of multi-spectral imaging for non-destructive vigour assessment. Specifically, we selected 244 rice accessions covering seven sub-populations and originating from six continents. After 0, 10 and 15 days of accelerated ageing, standard germination tests combined with multi-spectral image analysis were conducted to determine the germination rate, germination potential and vigour index. The results showed that accelerated ageing significantly inhibited the germination ability of all seeds, and this effect exhibited significant sub-population specificity. Among the sub-populations, aus and Asian-origin accessions displayed the strongest ageing tolerance, while the temperate japonica sub-population and European-origin accessions were highly sensitive, with vigour almost completely lost after 10 days of ageing. Multi-spectral data analysis revealed that reflectance in the 780–970 nm wavelength band was highly significantly correlated with the vigour index. In conclusion, the genetic background and geographical ecotype may be key determinants of seed storability in rice; the aus sub-population and Asian-origin accessions appear to be promising sources of ageing tolerance; and multi-spectral imaging can serve as an effective high-throughput, non-destructive tool for seed vigour evaluation. It should be noted that, given the limited sample size in this study and the fact that geographic origin and sub-population composition may not be independent in the evaluated germplasm panel, the conclusions are only representative of this particular set of accessions. The generalisability of the results therefore requires further validation with additional and more balanced samples.

Carnation is one of the most popular ornamental flowers worldwide. Due to its high ornamental and economic value, breeding techniques have advanced rapidly, leading to the continuous emergence of new varieties. However, this has also resulted in issues such as synonymy and homonymy. Therefore, utilizing DNA fingerprinting for rapid and accurate variety identification can play a crucial role in germplasm identification and the resolution of intellectual property disputes. In this study, we performed reduced-representation genome sequencing on 50 carnation accessions to develop single nucleotide polymorphism (SNP) markers. After filtering, 82,584 high-quality SNPs were obtained. These SNPs were used to conduct principal component analysis, population structure analysis, and cluster analysis on the 50 carnation accessions. From these high-quality SNPs, 130 SNP loci were further selected and converted into Kompetitive Allele-Specific PCR (KASP) markers. Preliminary screening using 92 carnation accessions yielded 53 KASP markers, and a subsequent screening with 217 carnation accessions identified 45 core KASP markers. Using these core markers, a fingerprint database was successfully constructed for 309 carnation accessions, achieving a distinguishing power of 99.987%. This study employed SNP fingerprinting and genetic analysis for the screening and identification of carnations, broadening the genetic basis at the molecular level and supporting subsequent variety protection efforts, thereby providing a scientific basis for carnation selection and identification.

Pepper breeding in China faces challenges including narrow genetic backgrounds, variety homogenization, and authenticity issues in the seed market. The original SSR-based variety identification system (NY/T 2475-2013) has limitations such as low polymorphism and uneven marker distribution, failing to meet current efficiency requirements. In this study, 240 pepper varieties were used. Fluorescent capillary electrophoresis was employed to analyze issues in the original system. A total of 150 SSR primer pairs was screened using eight phenotypically distinct varieties, followed by rescreening with 96 varieties from different origins. After marker optimization, a new identification system was established, validated using 144 varieties, and a DNA fingerprint database was constructed. Phenotypic experiments were conducted to evaluate applicability. The new system comprises 26 core primer pairs: 12 newly selected and 14 retained from the original standard. These primers are evenly distributed across chromosomes, with annealing temperatures optimized to 57 °C and grouped into seven multiplex panels. Across 240 pepper varieties, the 26 primer pairs detected 153 allelic variants and 293 genotypes. Average polymorphism information content (PIC) increased from 0.43 to 0.49 compared to the original system, and the discrimination efficiency reached 99.975% among 28,680 pairwise variety combinations. Phylogenetic and population structure analyses divided the 240 pepper varieties into six groups. Varieties with molecular genetic distance approaching zero showed high phenotypic similarity. The newly developed SSR-based system demonstrated excellent performance and strong applicability. It can be used for authenticity and purity identification, parentage testing, and auxiliary selection in DUS testing, supporting new variety rights protection and providing technical support for standardized management of the pepper seed industry.