Search Results (160)

Guadua angustifolia, a native bamboo species of ecological and economic importance, has been widely studied in Colombia. This study focused on evaluating the genetic diversity and population structure of G. angustifolia from six natural populations in the Department of Nariño, Colombia, using restriction site-associated DNA sequencing (RADseq). A total of 224,996 high-quality SNPs were identified across 48 individuals. Observed heterozygosity (Ho) ranged from 0.398 in Consacá to 0.78 in Tumaco, while expected heterozygosity (He) was lower in all cases, ranging from 0.291 to 0.597. All populations exhibited negative inbreeding coefficients (FIS), from −0.316 to −0.763, indicating an excess of heterozygotes and suggesting predominantly outcrossing reproduction. Analysis of molecular variance (AMOVA) revealed that most genetic variation resides within individuals (92.54%), with low differentiation among populations (7.46%). Population structure and phylogenetic analyses identified two main genetic clusters, likely reflecting the origin of the planting material. Our results revealed that chromosomes CM070500.1, CM070502.1, CM070503.1, CM070504.1, CM070508.1, and CM070510.1 exhibited the highest SNP density, suggesting the presence of genomic regions with elevated variability. In contrast, chromosomes with lower SNP density suggested conservated genes related to Flavone Synthase II. This study is the first to evaluate genetic materials from the Department of Nariño. These findings highlight the significant genetic diversity in G. angustifolia and the density of SNPs, and provide suggestions for conservation planning and the development of targeted breeding programs for this non-model tropical species. Full article

Chinese Cymbidium are prized for their ornamental beauty, ecological significance, and economic value. However, genomic resources crucial for breeding studies within this genus remain scarce, which has hindered the identification of key genes controlling economically important traits and posed challenges for conservation efforts. We performed a comprehensive identification of whole-genome simple sequence repeats (SSRs) and single-nucleotide polymorphism (SNP) markers using the restriction-site associated DNA sequencing (RADseq) on C. goeringii and C. faberi. A total of 49,640 SSR loci were identified across both species, with an average density of 12.7 SSRs/Mb. Among these, 17,637 SSRs were common to both C. goeringii and C. faber, while 17,676 and 14,329 SSRs were uniquely identified in C. goeringii and C. faberi, respectively. Additionally, we identified 405,416 SNPs and 26,870 InDels, with average densities of 105.2/Mb and 6.5/Mb. Furthermore, we validated two SSRs (located at Chr01:78857480-78860461 and Chr01:93382182-93384869) and developed an efficient method for identifying hybrids among the progeny resulting from crosses between C. goeringii and C. faberi. We also validated two SNP markers that showed a close association with the petal and lip length using Sanger sequencing. Our findings revealed that the Chr01_99657375 SNP achieved 73% predictive accuracy for identifying long-petal/lip phenotypes. The results are expected to greatly benefit marker-assisted breeding efforts in Cymbidium orchids and lay a solid foundation for the molecular breeding process of improving flower shape traits in orchid plants. Full article

The genus Rhododendron presents significant challenges for systematic classification due to extensive hybridization and adaptive radiation. Here, we employed double-digest restriction site-associated DNA sequencing (ddRAD-seq) to resolve phylogenetic relationships among nine ecologically significant Rhododendron species (34 accessions) endemic to Zhejiang Province, China, a biodiversity hotspot for this genus. Using R. simsii as the reference genome, we generated 39.40 Gb of high-quality sequencing data with a Q30 score of 96.65% and a GC content of 39.63%, achieving an average alignment rate of 92.79%. Through stringent filtering (QD ≥ 2, MQ ≥ 40), we identified 14,048,702 genome-wide single nucleotide polymorphism (SNP), predominantly characterized by the mutation types T:A>C:G and C:G>T:A. The widespread R. simsii and R. simsii var. putuoense exhibited significant genetic diversity, whereas the low-altitude widespread R. molle and the endemic R. simiarum exhibited lower genetic diversity. Moderate genetic differentiation (F_st = 0.097) was observed between R. simsii and R. simsii var. putuoense, while substantial genetic differentiation was detected among the other Rhododendron species. Principal component analysis (PCA), combined with phylogenomic reconstruction, demonstrated that the Rhododendron genus can be stratified into six well-supported genetic clades. Furthermore, this study provides the first genomic validation of the sibling relationship between R. simsii and its variety, R. simsii var. putuoense, and clarifies the systematic position of R. huadingense, suggesting that it should be classified as a new subgenus. This study establishes ddRAD-seq as a cost-effective tool, providing both a theoretical framework for SNP-based phylogenetics and critical insights for conserving China’s azalea biodiversity. Full article

Lantana camara L. is sold worldwide for ornamental purposes, although it is also characterized by high invasiveness potential. Genetic and molecular data available for L. camara are still poor, and breeding is performed through conventional methods. This study focused on a molecular genotyping analysis through the ddRADseq method on an experimental collection of lantana clonal lines to evaluate the potential of molecular techniques in performing marker-assisted breeding, in favour of variety registration and in guaranteeing plant variety protection for the species. Although high genetic uniformity was observed in the population, a unique molecular profile was assigned to every line, indicating the effectiveness of the approach used. Interestingly, low degrees of heterozygosity were observed. In addition, the possibility of inferring ploidy levels through SNP profiles was assessed since it would avoid the necessity of previous biological knowledge and the use of fresh materials. Ploidy analysis is of high interest for lantana breeding to obtain less invasive triploids. Flow cytometry and chromosome counting were used for inference assessment. An nQuack framework provided correct results for the majority of the clonal lines, confirming its effectiveness. These findings encourage the adoption of molecular systems to help breed minor species such as L. camara. Full article

Silverside fishes in Chile, abundant in marine and freshwater habitats, are classified in two genera: Odontesthes and Basilichthys. Both genera have widespread distributions across southern South America, with marine origins. Despite extensive information on Chilean freshwater silversides and their overlapping distributions along a latitudinal gradient, their taxonomy and diversification remain contentious. This study examines the diversity of Chilean silversides using RADseq genomic data from 78 Odontesthes and 60 Basilichthys individuals, covering most of their range. The phylogenetic and structural analyses of approximately 20,000 SNPs reveal some geographic variation but indicate no differentiation between Odontesthes mauleanum and O. brevianalis. The genus Basilichthys, in contrast, presents a disjunct distribution, with populations in coastal rivers of Peru (B. semotilus) that are separated from Chilean populations by the Atacama Desert. Chilean Basilichthys, traditionally classified as B. microlepidotus and B. australis until 2012, also show no genetic differentiation consistent with species boundaries but exhibit latitudinal differences consistent with isolation by distance. The contrasting patterns of genetic differentiation exhibited by species of these genera may be explained by the more frequent exchange with marine species for Odontesthes that do not occur in Basilichthys, in addition to the recent geological history of glaciations affecting the southern range of their distribution. Full article

Wheat (Triticum aestivum) is one of the most important cereal crops globally, with significant economic value. The Arabidopsis Tóxicos en Levadura (ATL) gene family, which comprises members of ubiquitin ligase enzymes (E3s), functions in substrate protein tagging during ubiquitin-mediated protein modification. Recent studies have demonstrated its involvement in stress responses. However, the ATL gene family in wheat remains poorly characterized. This study aimed to identify the members of the ATL gene family in wheat and investigate their roles under salt stress. We identified 334 TaATL genes in the wheat genome, all of which contain either RING-H2, RING U-box, or RAD18 superfamily domains, exhibiting a remarkably low proportion of intron-containing genes. The Ka/Ks (non-synonymous to synonymous substitution rate) analysis and cis-acting element analysis of the TaATL gene family indicate that its sequences are highly conserved and functionally constrained, suggesting that it may participate in abiotic stress responses through the ABA, MeJA, and MYB signaling pathways. Both RNA-seq analysis and RT-qPCR data demonstrated that the expression levels of the TaATL gene family were significantly upregulated under stress conditions, indicating their crucial roles in stress responses. This study demonstrates that the targeted regulation of stress-responsive signaling pathways mediated by superior TaATL gene family members can effectively enhance wheat salt tolerance, thereby providing a viable strategy for the development of high-yielding cultivars adapted to saline agricultural ecosystems. Full article

Sunflower Verticillium Wilt and Leaf Mottle (SVW), caused by Verticillium dahliae Kleb., is a globally prevalent disease affecting sunflower production. In this study, we identified a major quantitative trait locus (QTL) on chromosome 10 and other genomic regions associated with SVW resistance by integrating biparental and association mapping in sunflower populations from the National Institute of Agricultural Technology. Nine replicated field trials were conducted in highly infested V. dahliae reservoirs to assess disease incidence and severity. Both mapping populations were genotyped using double-digest restriction-site-associated DNA sequencing (ddRADseq). Association mapping with 18,161 SNPs and biparental QTL mapping with 1769 SNPs identified a major QTL on chromosome 10 explaining up to 30% of phenotypic variation for disease incidence at flowering and for the area under the disease progress curve for disease incidence, and which contributes to a lesser extent to disease severity reduction. Additional QTLs on chromosomes 17, 8, 9, 14, 13, and 11 were associated with reduced disease incidence, severity, or both. Candidate genes were identified within these associated regions, 39 of which are in the major QTL on Chromosome 10. These findings demonstrate the value of integrating complementary QTL mapping strategies for validating resistance loci and advancing sunflower breeding for SVW resistance. Full article

Long-term clonality has profound consequences for genetic structure despite offering an alternative means of reproductive assurance under unfavorable conditions for sexual reproduction. Vanilla shenzhenica Z. J. Liu & S. C. Chen (Orchidaceae), the only endangered Vanilla species in China, exhibits a clear tendency towards asexual propagation, as evidenced by its small, fragmented wild populations. To develop effective conservation strategies for this species, it is essential to assess the extent of clonality and evaluate genetic diversity both within and among populations. In this study, we sampled 43 individuals from cultivated and wild populations of V. shenzhenica and analyzed their phylogenetic relationships, genetic structure, and diversity based on single-nucleotide polymorphisms (SNPs). Our results indicate that all the studied wild populations are predominantly sustained by vegetative growth, each forming a monoclonal patch with a single genotype. The overall genetic diversity within V. shenzhenica is low likely due to a combination of factors, including clonality, reduced effective population size, and environmental disturbances. These findings underscore the urgent need for the conservation management of this species. Conservation plans should prioritize ex situ conservation efforts, focusing on promoting assisted sexual reproduction to produce viable seeds and offspring that combine diverse genotypes from different populations. This study provides valuable insights in relation to effective conservation planning for endangered clonal species. Full article

The evolutionary history of the Caribbean candelabrum octocorals from the genus Eunicea (Plexauridae: Octocorallia) remains unknown despite their high diversity and abundance in reef environments. Understanding the evolutionary relationships between and within the Eunicea species is critical to accurately measuring the group diversity. Furthermore, this group has a high potential for cryptic diversity and new species, particularly given the rich morphological variability. Conventional molecular markers, however, have not provided a precise positioning for the species inside the genus. Here, we provide the first phylogenomic reconstruction of these candelabrum octocorals employing NextRAD, a reduced-representation sequencing technique, to generate thousands of SNPs. We include 15 morphospecies sampled between valid and new species throughout the Caribbean. At large, the phylogeny is well supported and resolved. In total, 13 species-level clades are discernible, including two lineages with demonstrated genetic and morphological variation that are considered and described as two new species, Eunicea criptica sp. nov. and E. colombiensis sp. nov., both previously assigned as E. clavigera and the second as the “thick morphotype”, thereby increasing the diversity of the group. Understanding the magnitude of species diversity within Eunicea is essential for directing conservation initiatives and clarifying the biological processes in reef ecosystems. Full article

Voles and lemmings (subfamily Arvicolinae) remain some of the most difficult groups for disentangling phylogenetic relations owing to recent and very fast explosive radiation. The rapid radiation events are challenging for phylogenetic analysis and produce bushes of various shapes that are impossible to resolve with a straightforward approach using individual loci. Here using the quaddRAD-seq technique and transcriptomes, we tested whether data from the nuclear genome are consistent with trees inferred earlier from individual loci and from mitogenomes in topology and divergence dating. Both the transcriptome and quaddRAD-seq data convincingly place Arvicola as the earliest derivative within Arvicolini. This result is in agreement with the fossil record and conventional taxonomy. For the first time, whole-genome sequencing data resolved relations within the third radiation wave of the subfamily’s taxa, namely the tribes Arvicolini, Lagurini, and Ellobiusini, which have formed polytomy in mitochondrial trees in earlier articles. This study indicates that divergence dating is highly dependent on the number and position of calibration points in a tree and on taxa sampling. In terms of phylogenetic inference, the position of nodes with insufficient taxa representation is the most susceptible to errors. Full article

Cotyledon color is one of the important indices for identifying faba bean variety purity and measuring processing quality. Therefore, an in-depth study of the genetic mechanism of cotyledon color is vital for promoting faba bean industry development. We used the yellow cotyledon variety Qingcan 16 and the green cotyledon variety Qingcan 17 as parent plants to construct hybrid combinations. F₁-, F₂-, BC₁F₁-, and BC₂F₁-generation single-plant cotyledon colors were counted to clarify cotyledon color inheritance. F₂-generation individuals were genotyped using ddRAD-Seq to construct a genetic linkage map and identify QTLs for cotyledon color. Green cotyledons were controlled by one pair of recessive nuclear genes. Using the screened 1991 SNP markers, a high-density linkage map was constructed, with a coverage length of 1476.95 cM and an average map distance of 0.96 cM. The green cotyledon trait was located using WinQTL Cart, and a vfGC candidate interval explaining 34.30 to 49.40% of the phenotypic variation was identified at LG02 (101.952 cM to 115.493 cM) and at LOD = 16.0, corresponding to chr1L 1,077,051,302 bp to 1,636,400,339 bp (559.35 Mb). The above interval contained 2021 genes, 20 of which were involved in photosynthesis, but no SGR or genes with similar functions were identified. However, the published faba bean vfSGR was located within the vfGC candidate interval, confirming that our localization interval was reliable. The above findings provided further clues for the fine localization of genes regulating green cotyledons and the development of molecular linked markers in faba bean. Full article

A comprehensive study of the genetic characteristics of endangered species is a prerequisite for their effective conservation and management. Rhododendron farinosum is an endangered ornamental species with extremely small populations located in northeastern Yunnan Province. To unravel the reasons behind the endangerment of this species and provide guidance for the rational conservation of this species, this study obtained a large number of SNP loci by using double-digest restriction-site-associated DNA sequencing (ddRAD-seq) to evaluate the genetic diversity and genetic structure of R. farinosum, as well as to infer the population history of this species. Our findings reveal that, at the population level, R. farinosum exhibited a high genetic diversity (π = 0.1948 ± 0.0020, H_E = 0.1880 ± 0.0020). The F_ST values (0.1383–0.2231) indicated high genetic differentiation among the three populations. The AMOVA revealed that 62.83% of the genetic variation originated within populations and 37.17% between populations. The PCA, Structure, and UPGMA consistently depicted that the three populations of R. farinosum are clearly distinguished into three clusters. Furthermore, the effective population size of R. farinosum was inferred to date back to 95,000 years ago using the stairway plot, with a continuous decline from 3292 years. Based on these findings, we propose conservation strategies and management measures for R. farinosum. Full article

Glyptostrobus pensilis is an endangered tree species, and detecting its genetic diversity can reveal the mechanisms of endangerment, providing references for the conservation of genetic resources. Samples of 137 trees across seven populations within Fujian Province were collected and sequenced using double-digest restriction site-associated DNA (ddRAD-seq). A total of 3,687,189 single-nucleotide polymorphisms (SNPs) were identified, and 15,158 high-quality SNPs were obtained after filtering. The genetic diversity in the populations was found to be low (H_o = 0.08630, H_e = 0.03475, π = 0.07239), with a high genetic differentiation coefficient (F_st). When K = 4, the coefficient of variation (CV) error value was minimized, suggesting that the 137 individuals could be divided into four groups, with frequent gene flow between them. Principal component analysis (PCA) divided the seven populations into two major categories based on their north–south geographic location. The clustering was consistent with those obtained from the PCA. The main reasons for the endangerment of G. pensilis are likely to be poor natural regeneration, human disturbances, and climatic factors. It is recommended that methods such as in situ conservation, ex situ conservation, and the establishment of germplasm banks be implemented to maintain the genetic diversity of G. pensilis populations. Full article

A comprehensive understanding of the pattern of genetic variation among populations and adaptations to environmental heterogeneity is very important for conservation and genetic improvement. Forest tree species are ideal resources for understanding population genetic differentiation and detecting signatures of selection due to their adaptations to heterogeneous landscapes. Ulmus lamellosa is a tree species that is endemic to northern China. In this study, using restriction-site-associated DNA sequencing (RAD-seq) data, 12,179 single-nucleotide polymorphisms were identified across 51 individuals from seven populations. There was a high level of genetic diversity and population differentiation in U. lamellosa. Population genetic structure analyses revealed a significant genetic structure related to the configuration of the mountains. Additionally, we found that the isolation-by-distance pattern explained the genetic differentiation best, and environmental heterogeneity also played a role in shaping the landscape genetics of this species inhabiting mountain ecosystems. The F_ST-based outlier and genotype–environment association approaches were used to explore the genomic signatures of selection and local adaptation and detected 317 candidate outlier loci. Precipitation seasonality (coefficient of variation), precipitation in the driest month, and enhanced vegetation index were important determinants of adaptive genetic variation. This study provides abundant genetic resources for U. lamellosa and insights into the genetic variation patterns among populations. Full article

Variety characterization is crucial in the seed trade, particularly for protecting variety rights. However, the identification of roselle (Hibiscus sabdariffa L.) varieties, known for their beneficial effects on human health and high processing potential, has traditionally relied on morphological traits due to limited genetic information. To investigate genetic polymorphisms of roselle germplasms and to develop breeder-accessible genotyping tools, this study first phenotyped a roselle collection from diverse geographical origins for the selection of core varieties, and then utilized double-digest restriction-associated DNA sequencing (ddRAD-seq) to identify 53,746 single nucleotide polymorphisms (SNPs) across 17 core varieties. Cluster analysis of the SNP data effectively grouped varieties with similar genetic backgrounds. From this genetic information, we selected nine SNPs as a toolkit to simplify core variety discrimination. These SNPs were then converted into breeder-friendly kompetitive allele-specific PCR (KASP) markers, facilitating the classification of an additional 54 roselle accessions. In conclusion, this research contributes novel insights into the genetic relationships among roselle varieties, and establishes a robust framework utilizing ddRAD-seq and KASP markers for improved genetic resource identification and application in breeding programs. Full article