Search Results (42)

Germplasm resources embody the genetic diversity of plants and form the foundation for breeding and the ongoing improvement of elite cultivars. The establishment of germplasm banks, along with their systematic evaluation, constitutes a critical step toward the conservation, sustainable use, and innovative utilization of these resources. Liriodendron, a rare and endangered tree genus with species distributed in both East Asia and North America, holds considerable ecological, ornamental, and economic significance. However, a standardized evaluation system for Liriodendron germplasm remains unavailable. In this study, 297 Liriodendron germplasm accessions were comprehensively evaluated using 34 phenotypic traits and whole-genome resequencing data. Substantial variation was observed in most phenotypic traits, with significant correlations identified among several characteristics. Cluster analysis based on phenotypic data grouped the accessions into three distinct clusters, each exhibiting unique distribution patterns. This classification was further supported by principal component analysis (PCA), which effectively captured the underlying variation among accessions. These phenotypic groupings demonstrated high consistency with subsequent population structure analysis based on SNP markers (K = 3). Notably, several key traits exhibited significant divergence (p < 0.05) among distinct genetic clusters, thereby validating the coordinated association between phenotypic variation and molecular markers. Genetic diversity and population structure were assessed using 4204 high-quality single-nucleotide polymorphism (SNP) markers obtained through stringent filtering. The results indicated that the Liriodendron sino-americanum displayed the highest genetic diversity, with an expected heterozygosity (He) of 0.18 and a polymorphic information content (PIC) of 0.14. In addition, both hierarchical clustering and PCA revealed clear population differentiation among the accessions. Association analysis between three phenotypic traits (DBH, annual height increment, and branch number) and SNPs identified 25 highly significant SNP loci (p < 0.01). Of particular interest, the branch number-associated locus SNP_17_69375264 (p = 1.03 × 10⁻⁵) demonstrated the strongest association, highlighting distinct genetic regulation patterns among different growth traits. A minimal set of 13 core SNP markers was subsequently used to construct unique DNA fingerprints for all 297 accessions. In conclusion, this study systematically characterized phenotypic traits in Liriodendron, identified high-quality and core SNPs, and established correlations between key phenotypic and molecular markers. These achievements enabled differential analysis and genetic diversity assessment of Liriodendron germplasm, along with the construction of DNA fingerprint profiles. The results provide crucial theoretical basis and technical support for germplasm conservation, accurate identification, and utilization of Liriodendron resources, while offering significant practical value for variety selection, reproduction and commercial applications of this species. Full article

Eggplant (Solanum melongena) is a significant vegetable in the Solanaceae family. Significant progress has been made in genetic diversity analysis and fingerprinting construction for crops such as tomatoes and peppers within the same family, but research on eggplants in these aspects remains relatively limited. Current germplasm identification using fingerprinting primarily relies on traditional SSR markers, which suffer from limited polymorphism and labor-intensive workflows. This study aimed to identify high-quality single nucleotide polymorphisms (SNPs), develop reliable Kompetitive Allele-Specific PCR (KASP) markers for eggplant genotyping, and then conduct fingerprint construction and genetic diversity analysis. The ultimate goals were to achieve a precise identification of eggplant varieties and deeply explore the genetic background and evolutionary patterns of eggplant germplasm. In this study, 49 representative eggplant accessions were re-sequenced. After data quality control, sequence alignment, and multiple rounds of screening, 224 high-quality SNPs were identified. Based on these SNPs, 96 SNPs were selected to develop KASP markers. These markers can provide abundant genetic markers for eggplant genetic research, which are used to deeply explore the genetic background and conduct genetic diversity analysis. After multiple rounds of rigorous verification, 32 core candidate markers were finally screened out. The average polymorphic information content (PIC) and gene diversity (GD) values were 0.36 and 0.46, respectively. Phylogenetic tree, population structure, and principal component analyses divided the 280 eggplant accessions into eight distinct groups. Through the analysis of minimal core markers and core germplasm, 23 core SNP markers and a subset of 56 core germplasm accessions were identified, leading to the establishment of a comprehensive fingerprinting system for all 280 accessions. Our findings provide a foundational genetic resource for eggplant germplasm identification and offer significant support for future breeding efforts. Full article

Tilapia (Oreochromis spp.) is a globally important farmed fish. Analyses of genetic variation across different types of tilapia are essential for the development of superior breeding populations. We investigated the genetic structures of breeding populations of blue tilapia (Oreochromis aureus) (OA), Nile tilapia (Oreochromis niloticus) (ON), and red tilapia (Oreochromis spp.) (OS) by whole-genome resequencing. The results showed that the OS population had maintained high genetic diversity but significant genetic differentiation from the OA population. Principal component analysis, phylogenetic analysis, and genetic clustering analysis revealed a clear pattern of genetic differentiation among the three populations. The genetic structure of the ON population differed from that of the OA population but was similar to that of the OS population. Population kinship analysis revealed a close relationship between the ON and OS populations. Selective scanning analyses of three comparison groups (OA vs. ON, OA vs. OS, and ON vs. OS) revealed population-selected regions related to metabolism, endocrine, and immune systems, harboring key genes (qrsl1, pde4d, hras, ikbkb, prkag1, prkaa2, prkacb, irs2, and eif4e2). These key genes were related to growth, reproduction, and disease resistance, indicating that breeding programs have selected for these traits. Due to the lack of stable morphological characteristics of juvenile fish and the changes in external environmental conditions that lead to changes in individual morphological characteristics, SNP fingerprints were successfully constructed for the identification of the three populations based on the differences in SNPs. Based on the five core SNP markers, two combinations of SNP markers were developed to accurately identify the three populations of tilapia at the genomic level. These results provide new information about tilapia genetic resources and reference data for identification and breeding purposes. Full article

The analysis and identification of the genetic diversity of plant germplasm resources and varieties are crucial for plant breeding. DNA fingerprinting using genomic molecular markers is crucial for precisely identifying germplasm resources. In this study, the SLAF-seq was performed using 47 germplasm resources of the Wanzhou tea plant population and 5 common cultivated varieties from the Yunnan, Sichuan, and Fujian provinces. A total of 7,447,940 SNPs were identified from 1,641,569 SLAF tags with an averaged sequencing depth of 11.73 (Q30 94.93% and GC 41.37%), which were used to analyze the population composition and genetic diversity. Results showed a large degree of genetic diversity and genetic variation among the samples. The cluster analysis showed that the tea plant population was categorized into three groups, indicating that these germplasms could not be fully classified by their geographical origin, and the linkage disequilibrium analysis indicates that the population resources of the XJ production area are more modern in evolution. A total of 371 uniformly distributed SNP loci were selected and successfully employed to construct the first SNP fingerprint and quick response code (QR code) for tea resources in Wanzhou. These findings offer new insights for genotyping, classifying, and identifying germplasm and genetic resources in the breeding of the Wanzhou tea population. Full article

Auricularia heimuer is the second most widely cultivated edible fungus in China, with significant food and medicinal value, and is highly popular throughout Asia and globally. However, the differentiation of A. heimuer is simple, as its morphology is characterized by a small “black disc”, making it difficult to distinguish among germplasms with highly similar agronomic traits, thus posing challenges for germplasm identification. To address this issue, this study conducted whole-genome resequencing analysis on 150 A. heimuer germplasms. Through filtering 9,589,911 SNPs obtained from 280 G resequencing data, a total of 1,202,947 high-quality SNP sites were identified. Based on these high-quality SNPs, population structure analysis, principal component analysis (PCA), and phylogenetic tree analysis revealed that the 150 A. heimuer germplasms could be divided into five groups, with wild strains from the same geographical origin exhibiting significant geographical clustering patterns. This finding underscores the relationship between the genetic diversity of wild A. heimuer and its geographical distribution in China. A further selection of 71 SNP sites was made, and 61 KASP markers were successfully developed using kompetitive allele-specific PCR (KASP) technology, with 54 of them demonstrating good polymorphism. The average values for the polymorphism information content (PIC), minor allele frequency (MAF), gene diversity, and heterozygosity of these core KASP markers were 0.34, 0.35, 0.34, and 0.43, respectively. Based on the 54 core KASP markers, a DNA fingerprinting map of the 150 A. heimuer germplasms was constructed in this study. The findings provide important molecular marker resources and theoretical support for the identification of A. heimuer germplasm, molecular marker-assisted breeding, and the selection of superior varieties. Full article

The critically endangered Vietnamese Pond Turtle (Mauremys annamensis), an endemic species occurring in a small lowland area in central Vietnam, has been virtually extirpated from its natural range. As a result, reintroduction of held individuals worldwide, especially from Europe, the United States, and Vietnam, will play a vital role in species recovery programs. Nevertheless, the discordance between different molecular markers in inferring the placements of two closely related species, M. annamensis and M. mutica, and the existence of two distinct mitochondrial lineages within M. annamensis, have hindered conservation strategies to properly maintain the genetic integrity of held populations to release individuals back to their natural habitat in the future. In this study, we sequenced 732 bps of a mitochondrial gene (ND4) and 1038 bps of an intron fragment of the RNA fingerprint protein 35 (R35) gene for 18 samples collected from the local trade in five provinces in Vietnam and 20 samples from founders in the Turtle Conservation Centre, Cuc Phuong National Park, Vietnam. DNA sequences analyzed by Bayesian Inference, Maximum Likelihood, and NeighborNet methods show that the Vietnamese Pond Turtle is a well-defined species and that the population of M. mutica from Hainan Island likely evolved through introgression between a lineage distantly related to true M. mutica and M. annamensis and a lineage closely related to the two mitochondrial haplotypes of M. annamensis. Interestingly, our analyses of samples collected from the local trade and those with known localities reveal that the two extant mitochondrial lineages within M. annamensis are geographically isolated and evolutionarily significant. Based upon the new findings, we recommend genetic screening for all held populations in Vietnam and elsewhere and that animals with different genetic histories be managed separately. In addition, it is important to use other molecular markers, such as microsatellites and single nucleotide polymorphisms (SNPs), to determine potential hybrids between the two mitochondrial haplotypes and remove them from conservation breeding programs before releasing the turtles back to their natural habitat. Full article

Pleurotus pulmonarius is prized by consumers for its distinct flavor, strong aroma, and dense, crispy texture. Although China has extensive germplasm resources for P. pulmonarius, only a limited number of cultivars are commercially available. A comprehensive evaluation and detailed analysis of P. pulmonarius germplasm, alongside the exploration of superior germplasm resources, are essential for developing new varieties. In this study, we resequenced the genomes of 47 P. pulmonarius strains collected nationwide, identifying a total of 4,430,948 single nucleotide polymorphism (SNP) loci. After filtering based on minor allele frequency and data integrity, 181,731 high-quality SNP markers were retained. Phylogenetic analysis grouped the strains into six clusters, with strains from similar geographical regions clustering together. Most CBS strains formed a single cluster; cultivated varieties exhibited higher genetic similarity, whereas wild strains displayed greater diversity. Principal component analysis (PCA) and population structure analyses, using the same SNP markers, corroborated the phylogenetic findings. DNA fingerprinting, derived from 369 core SNPs, further underscored the genetic diversity among strains. Significant morphological variation was observed, with strains in groups ZP, CBS, and WHLJ exhibiting notably higher yields and cap widths compared to other groups. Correlation analysis revealed associations among various phenotypes, while genome-wide association study (GWAS) identified multiple SNP markers within candidate genes linked to agronomic traits, most of which were controlled by multiple genes. This research offers a molecular-level characterization and evaluation of P. pulmonarius germplasm resources, providing a scientific basis for enriching available germplasm and advancing breeding materials. Full article

Cacao (Theobroma cacao L.) is a tropical tree species belonging to the Malvaceae, which originated in the lowland rainforests of the Amazon. It is a major agricultural commodity, which contributes towards the Gross Domestic Product of West African countries, where it accounts for about 70% of the world’s production. Understanding the genetic diversity of genetic resources in a country, especially for an introduced crop such as cacao, is crucial to their management and effective utilization. However, very little is known about the genetic structure of the cacao germplasm from Sierra Leone and Togo based on molecular information. We assembled cacao germplasm accessions (235 from Sierra Leone and 141 from Togo) from different seed gardens and farmers’ fields across the cacao-producing states/regions of these countries for genetic diversity and population structure studies based on single nucleotide polymorphism (SNP) markers using 20 highly informative and reproducible KASP–SNPs markers. Genetic diversity among these accessions was assessed with three complementary clustering methods, including model-based population structure, discriminant analysis of principal components (DAPC), and phylogenetic trees. STRUCTURE and DAPC exhibited some consistency in the allocation of accessions into subpopulations or groups, although some discrepancies in their groupings were noted. Hierarchical clustering analysis grouped all the individuals into two major groups, as well as several sub-clusters. We also conducted a network analysis to elucidate genetic relationships among cacao accessions from Sierra Leone and Togo. Analysis of molecular variance (AMOVA) revealed high genetic diversity (86%) within accessions. A high rate of mislabeling/duplicate genotype names was revealed in both countries, which may be attributed to errors from the sources of introduction, labeling errors, and lost labels. This preliminary study demonstrates the use of KASP–SNPs for fingerprinting that can help identify duplicate/mislabeled accessions and provide strong evidence for improving accuracy and efficiency in cacao germplasm management as well as the distribution of correct materials to farmers. Full article

Capsicum frutescens (C. frutescens) has rich germplasm resources, but there have been no reports on its genetic diversity analysis alone using simplified genome sequencing technology (GBS). To provide a basis for the breeding of new pepper varieties and the later development of C. frutescens SNP molecular markers, this study used GBS technology to sequence 65 collected pepper germplasm resources. A total of 1,399,391 SNP sites were obtained by GBS simplified genome sequencing, and there were 1,465,897 SNP variant sites. Through population genetic structure analysis, the population structure and phylogenetic tree of 65 C. frutescens germplasms were constructed. The GBS method is also suitable for the genetic relationship analysis of C. frutescens, and it also shows that there is an obvious separation of materials from different origins, and there is also a certain degree of genetic exchange. Most of C. frutescens varieties from Fujian Province and its surrounding areas are clustered together; C. frutescens varieties from western China are also clustered together. We selected T62 and T60 with a genetic distance of 0.2796 and a spiciness level of nine as the female and male parent combinations, respectively, and bred a new high-yield C. frutescens combination, ‘Mingjiao 308’. C. frutescens varieties from the same geographical origin are usually clustered together. These germplasms may contain the ancestry of multiple varieties. This result can also provide basic data for the later construction of an SNP fingerprint database. Full article

The plant species Cedrela odorata has been largely exploited in the timber industry due to the high demand for its wood. Therefore, C. odorata has been considered a vulnerable species since 1994, under the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). C. odorata is a key timber species included in the management and conservation plans for the Amazon and Central American rainforests. These plans include the development of genetic and genomic resources to study local populations of the species in Colombia. In this study, two novel chloroplast (cp) genomes were assembled and annotated using the MinION long-read sequencing technology. The new cp genomes were screened for sequence variants (SVs), and a total of 16 SNPs were identified, presumably unique to populations from the Amazon region in Colombia. Comparative genomics with other reported cp genomes from different populations of C. odorata support the hypothesis of intraspecific diversity associated with their place of origin. These cp genome sequences of C. odorata from Colombian individuals represent valuable genomic resources for the species, suitable for identifying novel DNA fingerprinting and barcoding applications. Full article

High-throughput genomic technologies are enabling the identification of thousands or even millions of single-nucleotide polymorphisms (SNPs). SNP markers are frequently used to analyze crop varieties, with the marker data summarized in a common VCF file. At present, it is difficult to identify the minimal SNP set, the smallest sets that can distinguish between all crop varieties listed in a VCF file, due to the absence of available ready-to-use tools capable of such characterization. Here, we describe the development of the ready-to-use open-source tool MDSearch (Minimal Discriminatory SNP Set Search) based on the identification of the MDS (minimal discriminatory set) of SNPs using random walking staring from the maximal discriminatory set. MDSearch can be used for disploid as well as poliploid species and both phased and unphased VCF files. MDSearch has been validated using a publicly available dataset of barley SNPs obtained by genotyping-by-sequencing. As a result, we have successfully identified a discriminating set of 19 SNP markers capable of distinguishing all 254 barley varieties included in our study. We expect that this program will prove useful to genomics researchers to support a variety of certifications. Full article

Leucaena is a versatile legume shrub/tree used as tropical livestock forage and in timber industries, but it is considered a high environmental weed risk due to its prolific seed production and broad environmental adaptation. Interspecific crossings between Leucaena species have been used to create non-flowering or sterile triploids that can display reduced weediness and other desirable traits for broad use in forest and agricultural settings. However, assessing the success of the hybridisation process before evaluating the sterility of putative hybrids in the target environment is advisable. Here, RNA sequencing was used to develop breeding markers for hybrid parental identification in Leucaena. RNA-seq was carried out on 20 diploid and one tetraploid Leucaena taxa, and transcriptome-wide unique genetic variants were identified relative to a L. trichandra draft genome. Over 16 million single-nucleotide polymorphisms (SNPs) and 0.8 million insertions and deletions (indels) were mapped. These sequence variations can differentiate all species of Leucaena from one another, and a core set of about 75,000 variants can be genetically mapped and transformed into genotyping arrays/chips for the conduction of population genetics, diversity assessment, and genome-wide association studies in Leucaena. For genetic fingerprinting, more than 1500 variants with even allele frequencies (0.4–0.6) among all species were filtered out for marker development and testing in planta. Notably, SNPs were preferable for future testing as they were more accurate and displayed higher transferability within the genus than indels. Hybridity testing of ca. 3300 putative progenies using SNP markers was also more reliable and highly consistent with the field observations. The developed markers pave the way for rapid, accurate, and cost-effective diversity assessments, variety identification and breeding selection in Leucaena. Full article

Leishmania infantum is the primary cause of visceral and cutaneous leishmaniasis in the European Mediterranean region. Subspecies-level characterization of L. infantum aids epidemiological studies by offering insights into the evolution and geographical distribution of the parasite and reservoir identity. In this study, conducted in north-east Spain, 26 DNA samples of L. infantum were analyzed, comprising 21 from 10 humans and 5 from 5 dogs. Minicircle kinetoplast DNA (kDNA) polymerase chain reaction assays using primers MC1 and MC2, followed by sequencing, were employed to assess intraspecific genetic variability. Single-nucleotide polymorphism (SNP) analysis detected seven genotypes (G1, G2, G12*–G15*, and G17*), with five being reported for the first time (*). The most prevalent was the newly described G13 (54%), while the other currently identified genotypes were predominantly found in single samples. The in silico restriction fragment length polymorphism (RFLP) method revealed five genotypes (B, F, N, P, and W), one of them previously unreported (W). Genotype B was the most prevalent (85%), comprising three SNP genotypes (G1, G2, and G13), whereas the other RFLP genotypes were associated with single SNP genotypes. These kDNA genotyping methods revealed significant intraspecific genetic diversity in L. infantum, demonstrating their suitability for fingerprinting and strain monitoring. Full article

China possesses abundant wild germplasm resources and a wide range of cultivated strains of Stropharia rugosoannulata. However, issues such as genetic diversity and unclear genetic relationships have had an impact on the classification and preservation of germplasm resources, the breeding of new varieties, and the promotion of superior strains. There is an urgent need for genetic diversity analysis and assessment of germplasm resources. In this study, we conducted whole-genome resequencing of 50 cultivated and wild strains collected from various regions across the country. After applying a series of filtering parameters, we obtained 888,536 high-quality Single Nucleotide Polymorphism (SNP) markers. Using these SNP markers, we performed principal component analysis, population structure analysis, and phylogenetic clusters analysis on the 50 strains. Most cultivated strains exhibited high genetic similarity, while significant genetic diversity was observed among wild strains. Based on factors such as marker distribution throughout the entire genome and marker quality, we selected 358 core SNP markers to construct SNP fingerprints. Two-dimensional barcodes were generated for each strain to enable specific identification. Additionally, the mycelial growth rate of strains was evaluated on Potato Dextrose Agar (PDA) and substrate culture media. We also assessed their lignin degradation capability using guaiacol agar plates assay. It was observed that the mycelial growth rate on PDA and substrate culture medium exhibited a significant correlation with the diameter of the mycelial colony on guaiacol agar medium. Additionally, the correlation between the mycelial growth rate on the substrate medium and that on the guaiacol agar plate was stronger than that on PDA medium. This study provided molecular-level identification and assessment of germplasm resources. It clarified the genetic relationships among strains and the characteristics of mycelium growth-related agronomic traits of each strain. This research contributed to the enrichment and development of utilizable germplasm resources and breeding materials for S. rugosoannulata, offering a scientific basis for further research. Full article

Germplasm identification is essential for plant breeding and conservation. In this study, we developed a new method, DT-PICS, for efficient and cost-effective SNP selection in germplasm identification. The method, based on the decision tree concept, could efficiently select the most informative SNPs for germplasm identification by recursively partitioning the dataset based on their overall high PIC values, instead of considering individual SNP features. This method reduces redundancy in SNP selection and enhances the efficiency and automation of the selection process. DT-PICS demonstrated significant advantages in both the training and testing datasets and exhibited good performance on independent prediction, which validates its effectiveness. Thirteen simplified SNP sets were extracted from 749,636 SNPs in 1135 Arabidopsis varieties resequencing datasets, including a total of 769 DT-PICS SNPs, with an average of 59 SNPs per set. Each simplified SNP set could distinguish between the 1135 Arabidopsis varieties. Simulations demonstrated that using a combination of two simplified SNP sets for identification can effectively increase the fault tolerance in independent validation. In the testing dataset, two potentially mislabeled varieties (ICE169 and Star-8) were identified. For 68 same-named varieties, the identification process achieved 94.97% accuracy and only 30 shared markers on average; for 12 different-named varieties, the germplasm to be tested could be effectively distinguished from 1,134 other varieties while grouping extremely similar varieties (Col-0) together, reflecting their actual genetic relatedness. The results suggest that the DT-PICS provides an efficient and accurate approach to SNP selection in germplasm identification and management, offering strong support for future plant breeding and conservation efforts. Full article