Determining Genetic Diversity and Population Structure of Common Bean (Phaseolus vulgaris L.) Landraces from Türkiye Using SSR Markers

SSR Genotyping and Marker-Trait Association with Yield Components in a Kazakh Germplasm Collection of Chickpea (Cicer arietinum L.)

Genetic diversity and marker-trait association with yield-related components were assessed in 39 chickpea accessions from a germplasm collection with either spring or autumn-sown seeds in South-Eastern Kazakhstan. Chickpea accessions originated from Azerbaijan, Germany, Kazakhstan, Moldova, Russia, Türkiye, Ukraine, Syria, and the International Center for Agricultural Research in the Dry Areas (ICARDA). Eleven SSR markers were used for molecular genotyping. Yield and yield components were evaluated in nine traits in experiments with spring and autumn seed sowing. The number of alleles of polymorphic markers varied from 2 to 11. The greatest polymorphism was found in the studied chickpea genotypes using SSR marker TA22 (11 alleles), while NCPGR6 and NCPGR12 markers were monomorphic. In the studied chickpea accessions, unique alleles of the SSR loci TA14, TA46, TA76s, and TA142 were found that were not previously described by other authors. An analysis of correlation relationships between yield-related traits in chickpea revealed the dependence of yield on plant height, branching, and the setting of a large number of beans. These traits showed maximal values in experiments with chickpea plants from autumn seed sowing. An analysis of the relationship between the SSR markers applied and morphological yield-related traits revealed several informative markers associated with important traits, such as plant height, height to first pod, number of branches, number of productive nodes, number of pods per plant, hundred seed weight, seed weight per plant, and seed yield.

Chromosome-scale genomes of five Hongmu species in Leguminosae

The Legume family (Leguminosae or Fabaceae), is one of the largest and economically important flowering plants. Heartwood, the core of a tree trunk or branch, is a valuable and renewable resource employed for centuries in constructing sturdy and sustainable structures. Hongmu refers to a category of precious timber trees in China, encompassing 29 woody species, primarily from the legume genus. Due to the lack of genome data, detailed studies on their economic and ecological importance are limited. Therefore, this study generates chromosome-scale assemblies of five Hongmu species in Leguminosae: Pterocarpus santalinus, Pterocarpus macrocarpus, Dalbergia cochinchinensis, Dalbergia cultrata, and Senna siamea, using a combination of short-reads, long-read nanopore, and Hi-C data. We obtained 623.86 Mb, 634.58 Mb, 700.60 Mb, 645.98 Mb, and 437.29 Mb of pseudochromosome level assemblies with the scaffold N50 lengths of 63.1 Mb, 63.7 Mb, 70.4 Mb, 61.1 Mb and 32.2 Mb for P. santalinus, P. macrocarpus, D. cochinchinensis, D. cultrata and S. siamea, respectively. These genome data will serve as a valuable resource for studying crucial traits, like wood quality, disease resistance, and environmental adaptation in Hongmu.

Genetic Diversity and Relationship of Shanlan Upland Rice Were Revealed Based on 214 Upland Rice SSR Markers

Shanlan upland rice (Oryza sativa L.) is a unique upland rice variety cultivated by the Li nationality for a long time, which has good drought resistance and high utilization value in drought resistance breeding. To explore the origin of Shanlan upland rice and its genetic relationship with upland rice from other geographical sources, 214 upland rice cultivars from Southeast Asia and five provinces (regions) in southern China were used to study genetic diversity by using SSR markers. Twelve SSR primers were screened and 164 alleles (Na) were detected, with the minimum number of alleles being 8 and the maximum number of alleles being 23, with an average of 13.667. The analysis of genetic diversity and analysis of molecular variance (AMOVA) showed that the differences among the materials mainly came from the individuals of upland rice. The results of gene flow and genetic differentiation revealed the relationship between the upland rice populations, and Hainan Shanlan upland rice presumably originated from upland rice in Guangdong province, and some of them were genetically differentiated from Hunan upland rice. It can be indirectly proved that the Li nationality in Hainan is a descendant of the ancient Baiyue ethnic group, which provides circumstantial evidence for the migration history of the Li nationality in Hainan, and also provides basic data for the advanced protection of Shanlan upland rice, and the innovative utilization of germplasm resources.

Efficiency of RAPD and SCoT Markers in the Genetic Diversity Assessment of the Common Bean

Knowledge about the genetic diversity of the available common bean germplasm can help breeders properly direct the choice of genetic material in the breeding process. The aim of the present work was to estimate the usefulness of 10 RAPD and 10 SCoT markers in genetic diversity detection among 33 common bean genotypes. Both molecular marker systems were able to generate high levels of polymorphism in the genetic material, which was supported by the relatively high polymorphic information content (PIC) values observed for the used markers. The Diversity Detection Index (DDI) and Marker Index (MI) were used to compare the effectiveness of RAPD and SCoT markers. For both techniques, high values of MI and DDI were calculated, representing their effectivity. The SCoT markers showed higher values of the parameters used (MI = 7.474, DI = 2.265) than the RAPD markers (MI = 5.323, DDI = 1.612), indicating their higher efficiency in the detection of molecular variability. Three constructed dendrograms and PCoA plots were created using RAPD and SCoT, and both methods combined confirmed sufficient separation of the bean genotypes from each other. At the same time, a higher efficiency of SCoT markers compared to RAPD markers in the detection of the genetic diversity of beans was also proven. The results may be of future interest in the choice of genetically distant material for breeding purposes.

Genetic Diversity and Population Structure in Türkiye Bread Wheat Genotypes Revealed by Simple Sequence Repeats (SSR) Markers

Wheat genotypes should be improved through available germplasm genetic diversity to ensure food security. This study investigated the molecular diversity and population structure of a set of Türkiye bread wheat genotypes using 120 microsatellite markers. Based on the results, 651 polymorphic alleles were evaluated to determine genetic diversity and population structure. The number of alleles ranged from 2 to 19, with an average of 5.44 alleles per locus. Polymorphic information content (PIC) ranged from 0.031 to 0.915 with a mean of 0.43. In addition, the gene diversity index ranged from 0.03 to 0.92 with an average of 0.46. The expected heterozygosity ranged from 0.00 to 0.359 with a mean of 0.124. The unbiased expected heterozygosity ranged from 0.00 to 0.319 with an average of 0.112. The mean values of the number of effective alleles (Ne), genetic diversity of Nei (H) and Shannon's information index (I) were estimated at 1.190, 1.049 and 0.168, respectively. The highest genetic diversity (GD) was estimated between genotypes G1 and G27. In the UPGMA dendrogram, the 63 genotypes were grouped into three clusters. The three main coordinates were able to explain 12.64, 6.38 and 4.90% of genetic diversity, respectively. AMOVA revealed diversity within populations at 78% and between populations at 22%. The current populations were found to be highly structured. Model-based cluster analyses classified the 63 genotypes studied into three subpopulations. The values of F-statistic (Fst) for the identified subpopulations were 0.253, 0.330 and 0.244, respectively. In addition, the expected values of heterozygosity (He) for these sub-populations were recorded as 0.45, 0.46 and 0.44, respectively. Therefore, SSR markers can be useful not only in genetic diversity and association analysis of wheat but also in its germplasm for various agronomic traits or mechanisms of tolerance to environmental stresses.

Identification of Novel QTLs Associated with Frost Tolerance in Winter Wheat (Triticum aestivum L.)

Low temperature (cold) and freezing stress is a major problem during winter wheat growth. Low temperature tolerance (LT) is an important agronomic trait in winter wheat and determines the plants' ability to cope with below-freezing temperatures; thus, the development of cold-tolerant cultivars has become a major goal of breeding in various regions of the world. In this study, we sought to identify quantitative trait loci (QTL) using molecular markers related to freezing tolerance in winter. Thirty-four polymorphic markers among 425 SSR markers were obtained for the population, including 180 inbred lines of F₁₂ generation wheat, derived from crosses (Norstar × Zagros) after testing with parents. LT₅₀ is used as an effective selection criterion for identifying frost-tolerance genotypes. The progeny of individual F₁₂ plants were used to evaluate LT50. Several QTLs related to wheat yield, including heading time period, 1000-seed weight, and number of surviving plants after overwintering, were identified. Single-marker analysis illustrated that four SSR markers with a total of 25% phenotypic variance determination were linked to LT50. Related QTLs were located on chromosomes 4A, 2B, and 3B. Common QTLs identified in two cropping seasons based on agronomical traits were two QTLs for heading time period, one QTL for 1000-seed weight, and six QTLs for number of surviving plants after overwintering. The four markers identified linked to LT₅₀ significantly affected both LT₅₀ and yield-related traits simultaneously. This is the first report to identify a major-effect QTL related to frost tolerance on chromosome 4A by the marker XGWM160. It is possible that some QTLs are closely related to pleiotropic effects that control two or more traits simultaneously, and this feature can be used as a factor to select frost-resistant lines in plant breeding programs.

Genetic Relationships of 118 Castanea Specific Germplasms and Construction of Their Molecular ID Based on Morphological Characteristics and SSR Markers

To understand the genetic relationships of Castanea species, 16 phenotypic traits were measured, simple sequence repeat (SSR) markers were analyzed, and molecular identity cards (IDs) were constructed for 118 Castanea materials using fluorescent capillary electrophoresis. The coefficient of variation values of the 16 morphological traits of the test materials ranged from 11.11% to 60.38%. A total of 58 alleles were detected using six pairs of SSR core primers, with an average number of 9.7 alleles per locus. The average number of valid alleles per locus was 3.9419 and the proportion of valid alleles was 40.78%. A total of 105 genotypes were detected, and the number of genotypic species that could be amplified per primer pair ranged from 8 to 26. The mean value of the observed heterozygosity was 0.4986. The variation in the He, H, and PIC values was similar; the size of I value was approximately 2.21 times larger, and its mean number of variations was 0.7390, 0.7359, 0.6985, and 1.6015, respectively. The classification of 118 Castanea species was performed using three analytical methods: structure analysis, neighbor-joining (NJ) cluster analysis, and principal coordinate analysis (PCoA), and the results of the three methods were in high agreement. Six pairs of SSR core primers with high polymorphism and strong discriminatory properties were used to identify 118 Castanea plants, and a unique molecular ID card was constructed for each material. These results provide insight into the genetic diversity and population structure of Castanea plants and a theoretical basis for improving the phenomenon of mixed varieties and substandard plants in the Castanea plant market.

Assessment of the Genetic Diversity and Population Structure of the Peruvian Andean Legume, Tarwi (Lupinus mutabilis), with High Quality SNPs

Lupinus mutabilis Sweet (Fabaceae), “tarwi” or “chocho”, is an important grain legume in the Andean region. In Peru, studies on tarwi have mainly focused on morphological features; however, they have not been molecularly characterized. Currently, it is possible to explore the genetic parameters of plants with reliable and modern methods such as genotyping by sequencing (GBS). Here, for the first time, we used single nucleotide polymorphism (SNP) markers to infer the genetic diversity and population structure of 89 accessions of tarwi from nine Andean regions of Peru. A total of 5922 SNPs distributed along all chromosomes of tarwi were identified. STRUCTURE analysis revealed that this crop is grouped into two clusters. A dendrogram was generated using the UPGMA clustering algorithm and, like the principal coordinate analysis (PCoA), it showed two groups that correspond to the geographic origin of the tarwi samples. AMOVA showed a reduced variation between clusters (7.59%) and indicated that variability within populations is 92.41%. Population divergence (Fst) between clusters 1 and 2 revealed low genetic difference (0.019). We also detected a negative Fis for both populations, demonstrating that, like other Lupinus species, tarwi also depends on cross-pollination. SNP markers were powerful and effective for the genotyping process in this germplasm. We hope that this information is the beginning of the path towards a modern genetic improvement and conservation strategies of this important Andean legume.

Genetic Diversity, Conservation, and Utilization of Plant Genetic Resources

Plant genetic resources (PGRs) are the total hereditary material, which includes all the alleles of various genes, present in a crop species and its wild relatives. They are a major resource that humans depend on to increase farming resilience and profit. Hence, the demand for genetic resources will increase as the world population increases. There is a need to conserve and maintain the genetic diversity of these valuable resources for sustainable food security. Due to environmental changes and genetic erosion, some valuable genetic resources have already become extinct. The landraces, wild relatives, wild species, genetic stock, advanced breeding material, and modern varieties are some of the important plant genetic resources. These diverse resources have contributed to maintaining sustainable biodiversity. New crop varieties with desirable traits have been developed using these resources. Novel genes/alleles linked to the trait of interest are transferred into the commercially cultivated varieties using biotechnological tools. Diversity should be maintained as a genetic resource for the sustainable development of new crop varieties. Additionally, advances in biotechnological tools, such as next-generation sequencing, molecular markers, in vitro culture technology, cryopreservation, and gene banks, help in the precise characterization and conservation of rare and endangered species. Genomic tools help in the identification of quantitative trait loci (QTLs) and novel genes in plants that can be transferred through marker-assisted selection and marker-assisted backcrossing breeding approaches. This article focuses on the recent development in maintaining the diversity of genetic resources, their conservation, and their sustainable utilization to secure global food security.