Flower color is one of the key trait that determines the marketability of chrysanthemums. However, genetic research on chrysanthemum remains limited because of numerous environmental factors and the complexity of the chrysanthemum genome. To gain a deeper understanding of the genetic mechanisms underlying flower color in chrysanthemum, this study conducted genotyping analysis on 94 F₁ progenies derived from a cross between two wild chrysanthemum parents, ‘CWT2’ and ‘CWT8,’ which exhibit distinct flower colors. Genotyping-by-sequencing (GBS) was used for SNP identification, resulting in 79,002 single nucleotide polymorphisms (SNPs). After stringent filtering, 2,548 SNP markers were selected to construct a GBS-SNP linkage map, which was subsequently used to detect quantitative trait loci (QTLs) associated with flower color. Four QTL were identified, encompassing genes involved in carotenoid biosynthesis, carotenoid degradation, and the methylerythritol phosphate pathway. Among the 16 candidate genes analyzed for their potential role in flower color determination, three genes (VDE, CYP707A4, and CYP707A2) were ultimately selected for molecular marker development. The findings of this study provide a valuable foundation for understanding the genetic basis of carotenoid degradation in chrysanthemums. Future in-depth research is expected to facilitate the development of new chrysanthemum varieties for breeding programs through marker-assisted selection in breeding programs.

Brassica juncea, a member of the Brassicaceae family commonly referred to as mustard, is an allotetraploid (AABB, 2n=36) resulting from interspecific hybridization between Brassica rapa (AA, 2n=20) and Brassica nigra (BB, 2n=16). In this study, microspores were cultured using F₁ hybrids between two selected B. juncea double haploid (DH) lines with high anthocyanin and glucosinolate contents in the maternal versus leafy paternity. The results of the microspore culture showed that the total number of cultured buds, obtained embryos, and embryos per bud were 2,010, 15,526, and 7.62, respectively. Colchicine was used to induce the amphidiploids (AABB). We found that 149 of the 218 regenerated plants (68.3%) were amphidoploid. Among them, 117 individuals underwent ripening and seed harvesting and were used for subsequent phenotype analysis. Leaf color, length, and other agricultural traits exhibited various patterns owing to the recombination of the parental allele. The glucosinolate (GSL) content ranged from a maximum of 29.27 μmol/g dry weight to a minimum of 6.39 μmol/g dry weight, exceeding the range of parental value. The composition of GSL was mainly aliphatic, with sinigrin accounting for approximately 89% of the total aliphatic GSL content. These DH lines and their respective unique phenotypic traits are crucial for crop breeding and are valuable resources for advancing functional genomics and developing molecular markers in B. juncea.

Pear (Pyrus spp.) is an economically important fruit tree that grows extensively worldwide. To facilitate the identification of agronomically important traits and provide new information for genetic and genomic research concerning this fruit tree, a high-density genetic linkage map of pear was constructed using 178 F₁ populations derived from a cross between ‘Manpungbae’ and ‘Oharabeni’. Single nucleotide polymorphisms (SNPs) detected by genotyping-by-sequencing (GBS) and simple sequence repeats (SSRs) developed from pears were analyzed to construct a genetic linkage map. SSR markers were used to locate the corresponding chromosome number for each linkage group (LG). A total of 1,807 GBS-SNPs and 41 SSRs were anchored to the integrated genetic linkage map. Seventeen LGs were identified, covering a genetic distance of 1,519.4 cM with an average marker density of 0.87 cM. The lengths of the LGs ranged from 70.9 cM (LG 14) to 160.4 cM (LG 15). Each LG had SSR markers from 1 to 5, except for LGs 7, 8, and 9. Our integrated genetic map of pear could be used as a basic frame map for comparative analysis of genomic structure between different pear research groups.

Fruit development period (FDP), defined as the time between full bloom and maturity, varies greatly in peaches (Prunus persica L. Batsch). It is necessary to develop molecular markers associated with maturity date to extend the harvest season in new peach cultivars. We designed the 260 SSR primer set covering the entire genome of approximately 300 kb to 1 Mb based on P. persica cultivar ‘Mihong’ genome sequence. The SSR markers were used to survey the relationship between the parentages ‘Yumeyong’ and ‘Chiyomaru’ and their offspring cultivars ‘Mihong’, ‘Yumi’, ‘Misshong’ and ‘Soomee’. Male cultivar ‘Chiyomaru and its offspring cultivars ‘Mihong’, Yumi’, and ‘Misshong’ are early and middle maturity cultivars with FDP of 77, 76, 82, and 108 days, respectively, whereas female cultivar ‘Yumyeong’ and its offspring cultivar ‘Soomee’ are late maturity cultivars with FDP of 128 days. Three regions of SSR markers could distinguish between early, middle, and late maturity cultivars. In the early stages of breeding, these markers will be used for marker-assisted selection (MAS) in the parentages ‘Yumyeong’ and ‘Chiyomaru’ and their offspring cultivars.

Prunus persica “Mihong” cultivar is a domesticated white peach that was generated from the crossing between “Yumyeong” and “Chiyomaru” cultivars in the Republic of Korea in 1995. We launched “Mihong” genome sequencing in 2018 and “Mihong” reached to 200 scaffold and 241 Mb sequences using long-read sequencing and Hi-C technology. F₁ populations of ”Kawanakajima Hakuto,” “Mihong,” “Changhowon Hwangdo,” and “Yumi” were developed in NIHHS. These four cultivars were sequenced and assembled using the SOAPdenovo version 2.04. First, we surveyed the SSRs in “Mihong” assembly sequences and extracted the ±300 bp flanking sequences containing SSRs. Second, the assembly sequences of three cultivars were aligned and mapped against “Mihong” ±300 bp flanking sequences using BLASTn (version 2.2.29+). We anticipated the differential length in SSRs among the four cultivars. We sorted the primers with a standard deviation over 4.5 (STEV > 4.5) among the four cultivars. In addition, we surveyed the primers having difference in over 10 bp with “Kawanakajima Hakuto” and “Mihong” for polymorphic markers in the mapping population. All primer pairs were designed to generate amplicons of 150-200 bp in coating SSR regions using primer3 (version 3-2.2.3). We selected 260 SSR markers with a physical distance of average per 1 Mb. These SSR markers accounted for 74% polymorphism in the four genotypes. Finally, a F₁ population of “Kawanakajima Hakuto” and “Mihong” covered 884.5 cM with 465 SNPs and 86 SSRs and this genetic map matched correctly to the HI-C pseudomolecule of P. persica.

Three Brassica species, namely, Brassica rapa, B. nigra, and B. oleracea are considered economically important as they are grown for human consumption and biogas production. Like other crops facing agricultural constraints, selective crossing or hybridization in cruciferous vegetables has helped farmers to improve them. This study conducted a comparative evaluation across and within the species through cytogenetic analysis to provide fresh insights into their chromosome structures and evolutionary relationships. A new karyomorphological parameter confirmed symmetric karyotypes in all the accessions, thereby allowing for the depiction of the ancestral chromosome karyotype. Several lines of B. rapa, B. nigra, and B. oleracea were subjected to physical mapping using a fluorescence in situ hybridization technique to elucidate the chromosomal distribution of the two types of rDNAs. The signal number and distribution of 18S rDNA across the metaphase chromosomes of B. rapa accessions did not vary as compared to 5S rDNA, which was also observed in several lines of B. nigra. In contrast, the number and distribution of 5S rDNA loci across the chromosomes in several lines of B. oleracea were found to be more conserved than those corresponding to the 18S rDNA. Overall, this study revealed the evolutionary dynamics of rDNA, which may play an important role in shaping the chromosome karyotypes of Brassica species.

Amphidiploid Brassica juncea (AABB, 2n=36) contains the synthesized genome of the diploid ancestors of Brassica rapa (AA, 2n=20) and Brassica nigra (BB, 2n=16), proven the ‘triangle of U’ model. Varieties of the B. juncea include vegetables, oilseed crops, and medicinal plants in South Asia, China, and other regions. ‘Dolsangat’, one of the cultivars of B. juncea is widely used as the main ingredient for ‘KatKimchi’, a kind of Korean traditional food Kimchi. To develop an efficient polyploidization protocol of B. juncea, we used twenty accessions. Among them, we could induce the amphidiploid plants with 0.23% in natural. A successful of polyploidization, it is essential of chromosome doubling regent treatment of B. juncea. At first, we tried to colchicine treatment in the embryo stage and it was very harmful to the embryo and could get few plants. The second, we made the regeneration plants from embryo to rooting phase and shocked them in 0.34% colchicine contained distilled water. We could induce amphidiploid plants with a success rate of 63.4%. Also, we surveyed glucosinolate content and JB1, Alsami, and JD6 showed high total contents. These plants will use for genetic materials for breeding, genetic and molecular studies.

High-density genetic linkage mapping is critical for undertaking marker-assisted selection and confirming quantitative trait loci, as well as helping to build pseudomolecules of genomes. We constructed a genetic map using 94 F₁ populations generated from the interspecific cross between Korean cultivar “Wonwhang” (Pyrus pyrifolia, NCBI BioSample SAMN05196235) and European cultivar “Bartlett” (Pyrus communis). We designed a total of 24,267 SSR markers based on the genome sequences of “Wonwhang” for this. To select the markers that are linked to the traits important in pear breeding programs, SSR-containing genomic sequences were subjected to nucleotide sequence homology searches, which resulted in 510 SSR markers with high similarity to genes encoding proteins with putative functions such as transcription factors, resistance proteins, flowering time, and regulatory genes. Of these, 70 markers showed polymorphisms in parents and segregating populations and were used to construct a genetic linkage map, together with the unpublished 579 SNPs obtained from genotyping by sequencing analysis. The genetic linkage map covered 3,784.2 cM and the average distance between adjacent markers was 5.8 cM. Seventy SSR markers were distributed across 17 chromosomes with more than one locus.