In contrast with wild species, cultivated crop genomes consist of reshuffled recombination blocks, which occurred by crossing and selection processes. Accordingly, recombination block-based genomics analysis can be an effective approach for the screening of target loci for agricultural traits. We propose the variation block method, which is a three-step process for recombination block detection and comparison. The first step is to detect variations by comparing the short-read DNA sequences of the cultivar to the reference genome of the target crop. Next, sequence blocks with variation patterns are examined and defined. The boundaries between the variation-containing sequence blocks are regarded as recombination sites. All the assumed recombination sites in the cultivar set are used to split the genomes, and the resulting sequence regions are termed variation blocks. Finally, the genomes are compared using the variation blocks. The variation block method identified recurring recombination blocks accurately and successfully represented block-level diversities in the publicly available genomes of 31 soybean and 23 rice accessions. The practicality of this approach was demonstrated by the identification of a putative locus determining soybean hilum color. We suggest that the variation block method is an efficient genomics method for the recombination block-level comparison of crop genomes. We expect that this method will facilitate the development of crop genomics by bringing genomics technologies to the field of crop breeding.

The soybean development goal in Korea has changed over time, but the pattern of genetic diversity in modern varieties has not yet been well characterized. In this study, 20 simple sequence repeat (SSR) markers are shown to generate a total of 344 alleles, where the number of alleles ranges from 7 to 29, with an average of 17.2 per locus, and the polymorphism informative content (PIC) values range from 0.6799 to 0.9318, with an average of 0.8675. Five different clusters are classified using the unweighted pair group mean arithmetic (UPGMA) method. The genetic distance between clusters I and V (0.3382) is the farthest, and that between clusters III and IV (0.0819) is the closest. The genetic distance between all pairings of groups, according to the time period of their release, is lowest (0.1909) between varieties developed in the 1990s and those from 2000 onward, and highest (0.5731) between varieties developed in the 1980s and those from 2000 onward. Model-based structure analysis revealed the presence of three sub-populations and 17 admixtures in the Korean soybean varieties. All 172 Korean soybean varieties were tested for discrimination using six SSR markers. The numbers of varieties that were clustered in each step are as follows: 7 (4.1%) in step 1 (Sat_076), 73 (42.4%) in step 2 (Sat_417), 69 (40.1%) in step 3 (Sat_043), 13 (7.6%) in step 4 (Satt197), 8 (4.6%) in step 5 (Satt434), and 2 (1.2%) in step 6 (Satt179). These results, based on the analysis of genetic resources, can contribute to the creation of a core collection for soybean conservation and breeding, as well as to the development of future varieties with useful traits.

This study was carried out to investigate the variations in protein and isoflavone contents of 300 soybean germplasms introduced from domestic and foreign countries and to compare their contents in terms of size, colour and country of origin. The protein content ranged from 28.7 g 100 g⁻¹ to 44.5 g 100 g⁻¹, with an average of 39.0 g 100 g⁻¹. In a comparison of protein according to country of origin, the highest content was seen in soybeans from Korea (39.7 g 100 g⁻¹), followed by North Korea (39.2 g 100 g⁻¹), China (39.0 g 100 g⁻¹), Japan (38.8 g 100 g⁻¹), the USA (38.0 g 100 g⁻¹) and Russia (37.2 g 100 g⁻¹). The total isoflavone content ranged from 207.0 µg g⁻¹ to 3561.8 µg g⁻¹, with an average of 888.8 µg g⁻¹. In the comparison of isoflavone content according to country, the highest average content was shown in soybeans from Japan (951.3 µg g⁻¹), followed by the USA (918.7 µg g⁻¹), Korea (902.2 µg g⁻¹), North Korea (870.0 µg g⁻¹) and Russia (710.6 µg g⁻¹). Daidzein, glycitein and genistein isoflavone contents were positively correlated, while total isoflavone and protein showed a low negative correlation.

Italian ryegrass (Lolium multiflorum, IRG) and perennial ryegrass (Lolium perenne L., PRG) are widely cultivated as forage grasses in Korea using heterogeneous and polycross techniques, which promote genetic diversity within varieties. However, their genetic diversity patterns in Korea remain underexplored. This study evaluated the genetic diversity of IRG (eight varieties, including one exotic) and PRG (two exotic varieties) using 66 simple sequence repeat (SSR) markers. Across 87 samples (nine IRG and two PRG varieties), 655 alleles were identified, averaging 9.9 per locus. Key genetic parameters included heterozygosity (0.399), observed heterozygosity (0.675), fixation index (0.4344), and polymorphic informative content (0.6428). The lowest within-variety genetic distance was observed in ‘Hwasan 104ho’ (0.469), while ‘IR901’ had the highest (0.571). Between varieties, the closest genetic distance was between ‘Greencall’ and ‘Greencall 2ho’ (0.542), and the furthest was between ‘Kowinmaster’ and ‘Aspire’ (0.692). Molecular variance analysis showed 90% variation within varieties and 10% among varieties. Five clusters (I–V) were identified, with cluster I primarily including diploid IRG varieties and the tetraploid ‘Hwasan 104ho.’ Structural analysis differentiated diploid from tetraploid varieties (K = 2) and further separated tetraploid IRG and PRG (K = 3). Principal component analysis confirmed these groupings, with ‘Greencall’ and ‘Greencall 2ho’ exhibiting the closest genetic distance (0.227) and ‘Greencall’ and ‘Aspire’ the furthest (0.384). These findings provide a foundational resource for marker-assisted breeding to improve agronomic traits and enhance the efficiency of ryegrass breeding programs.