Genotype-by-sequencing of global hyacinth bean (Lablab purpureus) collections provides genomic resources for crop conservation and improvement

Unravelling genetic divergence among tomato (Solanum lycopersicum L.) genotypes using simple sequence repeat marker profiling

Tomato (Solanum lycopersicum L.) is an economically important fruit vegetable crop valued for its nutritional benefits and income-generating potential. Its genetic improvement depends on the efficient use of diverse germplasm, yet molecular characterization of conserved genotypes remains limited, especially in developing regions. This study evaluated the population structure and genetic diversity among 43 tomato genotypes sourced from three distinct genetic resources in Taiwan, the United States of America, and Nigeria, using 12 polymorphic Simple Sequence Repeat markers out of 21 screened. A total of 39 alleles were detected, with an average of 3 alleles per locus, indicating substantial polymorphism. Major allele frequency ranged from 0.58 to 0.79, averaging 0.73, suggesting balanced allele distribution. The expected heterozygosity for the markers varied from 0.33 (SLM 6-12) to 0.40 (SLM 6-56). Gene diversity ranged from 0.33 to 0.59, indicating a moderately broad genetic base. The Polymorphic Information Content values, ranging from 0.28 to 0.53, demonstrated the markers' effectiveness in detecting polymorphisms and suitability for distinguishing the genotypes. Particularly, TP 122 and SLM 6-56 were identified as highly informative markers with PIC values above 0.40. Cluster analysis grouped the 43 genotypes into four main clusters. However, the groupings were independent of their geographic distribution. Likewise, the population structure (K = 4) supported the clustering result. Principal coordinate analysis revealed that the genotypes were distributed across the two axes with 86% of cumulative variation. The findings underscore a wide genetic base among the genotypes, offering valuable insights for planned hybridization schemes. The polymorphic markers used in this study may also be useful in variety identification and screening for distinctiveness in tomato breeding programmes.

Genetic characterization of a global collection of common buckwheat to harness genetic resources for agricultural diversity

Neglected and underutilized crops have great potential to diversify agroecosystems and human diets but require genetic improvement to make them economically viable alternatives to major crops. Common buckwheat ( Fagopyrum esculentum Moench) is valued for its excellent nutritional quality, its ecological importance and its benefits on crop rotation and soil health. However, low and highly variable yields, along with uneven seed ripening, have limited the crop’s usage in farming systems, highlighting the need for improved varieties. The availability of genetic resources and detailed genetic characterization are prerequisites for efficient breeding strategies. In this study, we elucidate the genetic diversity and phylogeography of a global germplasm collection comprising 170 common buckwheat accessions, including nine self-compatible accessions and eleven accessions with determinate growth habit. The collection was genetically characterized using double digest restriction-site associated DNA sequencing to generate accession-specific genome-wide allele frequency fingerprints (GWAFFs). Using accurate and repeatable GWAFFs based on 52,182 genome sites, an analysis of genetic admixture revealed seven subclusters within the collection. Our results show that common buckwheat accessions collected in specific regions of the world usually trace back to a single subcluster. Western Europe is an exception, as accessions from several different subcluster have been integrated into local cropping and food systems. These findings illustrate that most breeding programs for common buckwheat rely on only a fraction of the available genetic diversity. Therefore, the introduction of genetic material from different sources could increase the diversity of many local breeding programs. The precise genetic characterization of the collection with GWAFFs opens opportunities to apply modern breeding strategies such as genomics-assisted selection. True-to-type seed of 81 accessions of the collection were deposited in the Swiss National Gene Bank and are publicly available for cultivation and use in research and breeding.

Genetic Diversity of the 4th-Cycle Breeding Population of Cunninghamia lanceolata (Lamb.) Hook. Using SSR Markers

: Cunninghamia lanceolata (Lamb.) Hook., a fast-growing timber species endemic to China, has been constrained in genetic improvement and marker-assisted breeding programs by the paucity of molecular-level genetic diversity information. In this study, 22 pairs of highly polymorphic SSR molecular markers were designed and developed based on transcriptome sequencing and public data, and subsequently employed for genetic diversity analysis of 258 germplasm accessions. These primers amplified 235 alleles across all accessions, averaging 10.682 alleles per marker. The mean observed heterozygosity (Ho) and expected heterozygosity (He) were 0.543 and 0.668, respectively, and the polymorphic information content (PIC) values ranged from 0.237 to 0.947, with a mean of 0.627, indicating substantial genetic diversity within the tested germplasm panel. Bayesian population structure analysis resolved the 258 accessions into 11 distinct genetic groups, with group 11 comprising 155 individuals and exhibiting the most complex provenance composition—a pattern independently corroborated by phylogenetic reconstruction and Principal Coordinate Analysis (PCoA). Among 11% of the genetic variation originated between populations and 89% from within populations. Pairwise estimates of Nei’s genetic distance and pairwise FST indicated frequent historical gene flow and close genetic relatedness among most groups. These findings provide a valuable empirical reference for germplasm evaluation and marker-assisted breeding in C. lanceolata .

Start Codon Targeted (SCoT) Markers Unraveled the Genetic Landscape and Population Structure of Dioscorea bulbifera L. Accessions from Kerala, India

Development of KASP molecular markers and construction of fingerprinting for cowpea (Vigna unguiculata (L.) Walp.) based on ddRAD-Seq

Cowpea (Vigna unguiculata (L.) Walp.) is a globally important legume crop. However, the scarcity of efficient molecular markers has hindered molecular breeding efforts and the protection of plant breeders’ rights. In this study, we employed double-digest restriction-site associated DNA sequencing (ddRAD-seq) to characterize the genetic diversity of 19 cowpea accessions. A total of 791,621 SNPs were identified, of which 13,469 high-quality SNPs were retained after filtering. Population structure and phylogenetic analyses revealed that these accessions clustered into three distinct groups. To facilitate cost-effective and rapid genotyping, we developed a panel of KASP (Kompetitive Allele-Specific PCR) markers. Through rigorous screening for polymorphism and stability, we identified six core KASP markers located in exonic regions. These six markers alone were sufficient to discriminate all 19 accessions. Based on these core markers, we constructed a unique DNA fingerprinting profile and assigned specific QR codes for each accession. This study demonstrates that selecting core KASP markers from ddRAD-seq data is a powerful strategy for germplasm identification. The developed fingerprinting system provides a robust, low-cost tool for seed purity testing, variety authentication, and marker-assisted selection in cowpea breeding programs.

Population structure and diversity of cowpea ( Vigna unguiculata [L.] Walp.): Genomic inference and preliminary distribution of breeding-relevant traits in a Niger-centred Sahelian diversity panel

The study of genetic diversity is essential for understanding population structure and optimizing breeding programs. To support cowpea breeding efforts, we conducted a diversity study on a panel of 185 accessions, including 125 newly collected accessions from Niger and additional accessions provided by research institutions in Nigeria, Burkina Faso, Senegal and Niger. This study aimed to analyse cowpea population structure and genomic diversity and to provide a preliminary assessment of phenotypic variation across genomic clusters. Genotyping-by-sequencing generated 20,918 single nucleotide polymorphisms (SNPs), which were used to assess population structure and genetic diversity. Population structure was inferred using a Bayesian approach (ADMIXTURE), and the resulting clustering pattern was corroborated by a multivariate method (DAPC). Seven genetic clusters were identified (A1–A7). Accessions from Niger were predominantly assigned to clusters A1, A2, A3 and A5; those from Senegal were mainly assigned to A4, whereas accessions from Nigeria were predominantly assigned to A7. Strong genetic differentiation was observed between accessions from Nigeria and those from Niger. The evaluation of phenological traits and yield components revealed marked differences among clusters. Most clusters showed low and multimodal grain and husk yield distributions, whereas cluster A5 consistently combined early maturity, high haulm yield and superior reproductive performance, highlighting its breeding potential. Overall, this study generated a large SNP marker dataset and provided integrated genomic and preliminary phenotypic information for a diverse cowpea germplasm panel. These resources will be useful for further studies of population genetics, breeding and association mapping in cowpea, an important legume crop for Sahelian countries.