Search Results (62)

Rice (Oryza sativa) provides a major food resource worldwide, playing an important role in the global economy. Leptocorisa acuta (Hemiptera: Alydidae), commonly known as the rice seed bug, is a major pest of paddy crops in many rice-growing regions and it is considered a potential invasive pest in the United States. Here, we investigated the genetic structure and demographic history of 18 populations sampled from China and southeast Asia using double-digest restriction site-associated DNA sequencing (ddRAD-seq). Then, we performed niche modeling based on occurrence records under current and future climate scenarios. Our analyses suggested that the lack of genetic structure among populations of L. acuta is related to recent diversification, strong flight, and dispersal capability, leading to a high level of gene flow. The demographic history was not strongly affected by the last glacial maximum. Ecological niche modeling predicts that future suitable areas will expand in Asia and America, relative to the current conditions. The ecological niche results demonstrated that L. acuta is a potentially invasive pest to the United States (mainly Florida and nearby areas) under current and future scenarios. Moreover, the moderately and highly suitable areas will increase in America (primarily located in North America, namely Florida and nearby areas, and Mexico), Central American and Caribbean countries, and some regions of South America. Some South American countries have extensive rice crops and broadly suitable habitats that may indicate a higher invasion risk. Through population genetics, our study supports the strong dispersal capacity of this insect pest and calls for vigilance against its invasion in some countries in the Americas. Full article

The Atlas cedar Cedrus atlantica is a relict and endemic conifer from Morocco and Algeria, although plantations may be found in several locations aside from its natural range. Recurrent droughts have been widely related to Atlas cedar dieback, growth decline, and mortality, but the genetic basis of potential adaptive capacity is unknown. We used the double digest restriction-site associated DNA sequencing technique (ddRAD-seq) to describe the genetic structure and variability of Atlas cedar along an aridity gradient in Morocco. Furthermore, we investigated the potential genetic origin of three Spanish plantations, also along an aridity gradient. The obtained single nucleotide polymorphisms (SNPs) were used to perform genotype–environment associations (GEAs) to define SNPs related to bioclimatic variables of temperature and precipitation. The vulnerability of this species to environmental variations was also estimated by its risk of non-adaptedness (RONA). Population structure showed a divergence between the Moroccan natural stands and some of the Spanish plantations, with each Moroccan nucleus being genetically distinct. The genetic variability was significantly lower in plantations than in natural populations. The drier Spanish plantations (easternmost) were genetically very similar to the driest Moroccan population (southernmost), suggesting that as its origin. A total of 41 loci under selection were obtained with the Moroccan dataset. In relation to temperature and precipitation variables, isothermality showed the highest number of associated loci (10) in GEA studies, and genotype–phenotype associations (GPAs) showed one locus associated with the Specific Leaf Area. RONA value was higher in the southernmost High Atlas population, where rising temperature was the main driver of expected genetic offset by allele frequency changes under the worst emissions scenario. In contrast, Spanish plantations would need smaller genetic changes to cope with the expected climate change. Likely gene flow from southern to northern areas suggests a latitudinal heading, where Spanish plantations might operate as an assisted migration. Moreover, one locus showed a northern/southern pattern in saplings but not in adults, suggesting a potential latitudinal pattern of selection. Our results are discussed on the basis of their management and conservation. Full article

The present research investigates the fine-scale spatial genetic structure (SGS) and gene flow dynamics in the endangered relict tree Tetracentron sinense, a keystone species in China’s montane ecosystems facing severe habitat fragmentation and genetic erosion. Utilizing genome-wide SNPs from 378 individuals across four natural populations (BMXS, MGFD, GLGS, SXFP), derived from ddRAD-seq, we quantified genetic diversity, SGS (Sp statistic), and dispersal patterns through spatial autocorrelation, parentage analysis, and age-class stratification. Results indicated critically low heterozygosity (observed heterozygosity, H_O = 0.019–0.022) and high inbreeding coefficient (Fis = 0.147–0.304), with moderate SGS (Sp = 0.0076–0.021) suggesting restricted gene flow (effective dispersal radius: 11–32 m). Seed-mediated dispersal was predominant, but topography and rainfall constrained dispersal (<5% beyond 50 m). Saplings exhibited stronger SGS, and the SXFP population experienced 100% sapling mortality due to inbreeding depression. Conservation efforts should prioritize assisted gene flow, habitat restoration, and ex situ sampling at distances greater than 115 m to preserve genetic diversity and adaptive potential. This study highlights the urgent need for genomics-informed conservation strategies in fragmented montane ecosystems. Full article

The closely related Naupactini species Naupactus leucoloma, Naupactus peregrinus, and Naupactus minor—collectively known as “white-fringed weevils”—form a monophyletic group within the N. leucoloma species group. Mostly parthenogenetic, a few sexually reproducing populations of both N. leucoloma and N. peregrinus occur in their native ranges (Argentinian Mesopotamian region), where they overlap. In 2013, after several decades during which only females had been recorded, a few males potentially belonging to these species were discovered. To clarify their taxonomic identity and understand the group’s evolutionary dynamics, we analyzed their mitochondrial and nuclear genetic markers to assess their genetic variation distribution and infer their phylogenetic relationships. Molecular phylogenetic analyses revealed that these males constitute an independently evolving lineage, whereas morphological comparisons produced inconclusive results. Statistical tests confirmed introgression between these unidentified males and N. leucoloma. These findings uncover unexpected levels of genetic divergence within this group of Neotropical weevils. 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

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

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

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

The radiation of cichlid species in the East African Great Lakes is remarkable and rapid. The population genetics of two deep-water Cyphotilapia species along the east coast of Lake Tanganyika from Burundi to southern Tanzania was determined using ddRAD-seq. A combination of ADMIXTURE, PCA, genome polarization, and 2D site frequency spectrum analyses confirmed the presence of two species, C. frontosa in the north and C. gibberosa in the south, as documented in other studies. We also found evidence of a potential hybrid zone connecting the two species at a sharp genetic cline centered in the middle of the lake and apparent introgression in both directions, but predominantly from ‘gibberosa’ into ‘frontosa’. The highest proportion of introgressed ‘gibberosa’ ancestry was present in the southernmost populations of C. frontosa collected near Karilani Island and Cape Kabogo. At the intra-specific level, there was support for between 1 and 3 populations of C. frontosa, whereas the results indicated only a single homogeneous population of C. gibberosa. The presence of different morphs in the lake despite the low levels of heterozygosity suggests that a small number of loci may be involved in the morphological variation and/or that there is a more complex interplay between genetics and the environment in different locations. Full article

In the framework of a Collaboration Agreement between CREA and ARSIAL, a morpho-phenological, chemical, and genetic characterization of maize populations native to the Lazio region was carried out. During 2022 and 2023, a set of 50 accessions, belonging both to ARSIAL and CREA maize collections, were multiplied in Bergamo. Morpho-phenological descriptors were recorded in the field: plant height, ear height, and male and female flowering time. The grain chemical composition in terms of protein, lipid, starch, ash and fiber was evaluated by near-infrared spectroscopy (NIRS). A double-digest restriction-site-associated DNA sequencing (ddRADseq) strategy was used to genotype the landraces. The two collections were not significantly different in terms of grain chemical composition. On the other hand, the ARSIAL and CREA germplasm showed a different distribution in the three cluster-based population structure obtained by ddRADseq, which largely corresponded to the distribution map of their collection sites. The materials from the Lazio region maintained by ARSIAL and CREA were revealed to be different. The comparison between the two groups of landraces showed the importance of characterizing germplasm collections to promote the recovery and valorization of local biodiversity. Full article

A joint analysis of dendrochronological and genomic data was performed to identify genetic mechanisms of adaptation and assess the adaptive genetic potential of Siberian stone pine (Pinus sibirica Du Tour) populations. The data obtained are necessary for predicting the effect of climate change and mitigating its negative consequences. Presented are the results of an association analysis of the variation of 84,853 genetic markers (single nucleotide polymorphisms—SNPs) obtained by double digest restriction-site associated DNA sequencing (ddRADseq) and 110 individual phenotypic traits, including dendrophenotypes based on the dynamics of tree-ring widths (TRWs) of 234 individual trees in six natural populations of Siberian stone pine, which have a history of extreme climatic stresses (e.g., droughts) and outbreaks of defoliators (e.g., pine sawfly [Neodiprion sertifer Geoff.]). The genetic structure of studied populations was relatively weak; samples are poorly differentiated and belong to genetically similar populations. Genotype–dendrophenotype associations were analyzed using three different approaches and corresponding models: General Linear Model (GLM), Bayesian Sparse Linear Mixed Model (BSLMM), and Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK), respectively. Thirty SNPs were detected by at least two different approaches, and two SNPs by all three. In addition, three SNPs associated with mean values of recovery dendrophenotype (Rc) averaged across multiple years of climatic stresses were also found by all three methods. The sequences containing these SNPs were annotated using genome annotation of a very closely related species, whitebark pine (P. albicaulis Engelm.). We found that most of the SNPs with supposedly adaptive variation were located in intergenic regions. Three dendrophenotype-associated SNPs were located within the 10 Kbp regions and one in the intron of the genes encoding proteins that play a crucial role in ensuring the integrity of the plant’s genetic information, particularly under environmental stress conditions that can induce DNA damage. In addition, we found a correlation of individual heterozygosity with some dendrophenotypes. Heterosis was observed in most of these statistically significant cases; signs of homeostasis were also detected. Although most of the identified SNPs were not assigned to a particular gene, their high polymorphism and association with adaptive traits likely indicate high adaptive potential that can facilitate adaptation of Siberian stone pine populations to the climatic stresses and climate change. Full article