Genetic Differentiation Research Articles

Whole-Genome Resequencing Reveals Significant Genetic Differentiation Between Exserohilum turcicum Populations from Maize and Sorghum and Candidate Effector Genes Related to Host Specificity.

Exserohilum turcicum is a devastating fungal pathogen that infects both maize and sorghum, leading to severe leaf diseases of the two crops. According to host specificity, pathogenic isolates of E. turcicum are divided into two formae speciales, namely E. turcicum f. sp. zeae and E. turcicum f. sp. sorghi. To date, the molecular mechanism underlying the host specificity of E. turcicum is marginally known. In this study, the whole genomes of 60 E. turcicum isolates collected from both maize and sorghum were resequenced, which enabled identification of 233,022 single-nucleotide polymorphisms (SNPs) in total. Phylogenetic analysis indicated that all isolates are clustered into four genetic groups that have a close relationship with host source. This observation is validated by the result of principal component analysis. Analysis of population structure revealed that there is obvious genetic differentiation between two populations from maize and sorghum. Further analysis showed that 5,431 SNPs, including 612 nonsynonymous SNPs, are completely co-segregated with the host source. These nonsynonymous SNPs are located in 539 genes, among which 18 genes are predicted to encode secretory proteins, including six putative effector genes named SIX13-like, Ecp6, GH12, GH28-1, GH28-2, and CHP1. Sequence polymorphism analysis revealed various numbers of SNPs in the coding regions of these genes. These findings provide new insights into the molecular basis of host specificity in E. turcicum.

The conservation value of small population remnants: variability in inbreeding depression and heterosis of a perennial herb, the narrow-leaved purple coneflower (Echinacea angustifolia).

Anthropogenically fragmented populations may have reduced fitness due to loss of genetic diversity and inbreeding. The extent of such fitness losses due to fragmentation and potential gains from conservation actions are infrequently assessed together empirically. Controlled crosses within and among populations can identify whether populations are at risk of inbreeding depression and whether interpopulation crossing alleviates fitness loss. Because fitness depends on environment and life stage, studies quantifying cumulative fitness over a large portion of the lifecycle in conditions that mimic natural environments are most informative. To assess fitness consequences of habitat fragmentation, we leveraged controlled within-family, within-population, and between-population crosses to quantify inbreeding depression and heterosis in seven populations of Echinacea angustifolia within a 6400-hectare area. We then assessed cumulative offspring fitness after 14 years of growth in a natural experimental plot (N = 1136). Mean fitness of progeny from within-population crosses varied considerably, indicating genetic differentiation among source populations, even though these sites are all less than 9 km apart. The fitness consequences of within-family and between-population crosses varied in magnitude and direction. Only one of the seven populations showed inbreeding depression of high effect, while four populations showed substantial heterosis. Outbreeding depression was rare and slight. Our findings indicate that local crossings between isolated populations yield unpredictable fitness consequences ranging from slight decreases to substantial increases. Interestingly, inbreeding depression and heterosis did not relate closely to population size, suggesting that all fragmented populations could contribute to conservation goals as either pollen recipients or donors.

Genomics of historical museum collections clarifies species diversity in Cuban hutias (Capromys)

Abstract Specimen-based taxonomic research is essential for understanding diversity and setting management frameworks for threatened mammal faunas, and ancient DNA techniques are increasingly used to extract information from taxonomically relevant historical specimens. The largest survivors of the depleted Caribbean mammal fauna are hutias in the genus Capromys, which is usually interpreted as containing a single species, C. pilorides. Previous studies have demonstrated genetic differentiation of Capromys populations across Cuba, but infrageneric species diversity and nomenclature remain unclear. We conducted ancient DNA analysis of historical Capromys samples using cytochrome b and complete mitogenome data sets, and including the 19th-century holotypes of 2 species now considered synonyms, C. fournieri and C. geayi. Our analyses identify distinct western and central/eastern Capromys clades that diverged 1.75 Mya based upon mitogenome data. These clades are separated by the Havana–Matanzas Channel, which represented a barrier to dispersal throughout the Neogene–Quaternary. Divergence date comparisons with other hutia species provide support for interpreting divergence between Capromys populations as species-level differentiation. Although we were unable to yield amplifiable DNA from the C. fournieri holotype, our analyses confidently assign the C. geayi holotype to the western Capromys clade. We therefore recognize 2 extant Capromys species: C. geayi (western Cuba) and C. pilorides (central/eastern Cuba and Cayman Islands).

Genetic diversity, population structure, and a genome-wide association study of sorghum lines assembled for breeding in Uganda.

Sorghum is an important source of food and feed worldwide. Developing sorghum core germplasm collections improves our understanding of the evolution and exploitation of genetic diversity in breeding programs. Despite its significance, the characterization of the genetic diversity of local germplasm pools and the identification of genomic loci underlying the variation of critical agronomic traits in sorghum remains limited in most African countries, including Uganda. In this study, we evaluated a collection of 543 sorghum accessions actively used in Ugandan breeding program across two cropping seasons at NaSARRI, Uganda, under natural field conditions. Phenotypic data analysis revealed significant (p<0.01) variation among accessions for days to 50% flowering, plant height, panicle exsertion, and grain yield, with broad-sense heritability (H²) estimates of 0.54, 0.9, 0.81, and 0.48, respectively, indicating a high genetic variability for these traits. We used a newly developed genomic resource of 7,156 single nucleotide polymorphism (SNP) markers to characterize the genetic diversity and population structure of this collection. On average, the SNP markers exhibited moderately high polymorphic information content (PIC = 0.3) and gene diversity (He = 0.3), while observed heterozygosity (Ho = 0.07) was low, typical for self-pollinating crops like sorghum. Admixture-based models, PCA, and cluster analysis all grouped the accessions into two subpopulations with relatively low genetic differentiation. Genome-wide association study (GWAS) identified candidate genes linked to key agronomic traits using a breeding diversity panel from Uganda. GWAS analysis using three different mixed models identified 12 genomic regions associated with days to flowering, plant height, panicle exsertion, grain yield, and glume coverage. Five core candidate genes were co-localized with these significant SNPs. The SNP markers and candidate genes discovered provide valuable insights into the genetic regulation of key agronomic traits and, upon validation, hold promise for genomics-driven breeding strategies in Uganda.

Small-scale geographic differences in multiple-driver environmental variability can modulate contrasting phenotypic plasticity despite high levels of gene flow

Climate change is altering not only the mean conditions of marine environments, but also their temporal variability and predictability. As these alterations are not uniform across seascapes, their biological effects are expected to accentuate intra-specific differences in the adaptive capacity (e.g., plasticity and evolutionary potential) of natural populations. To test this theoretical framework, we assessed the phenotypic and genetic profiles of mussel from three study sites across a multi-driver heterogeneous environmental mosaic in Chilean Patagonia. Our study reveals that temporal variability, predictability, and exposure to extreme events (low pH/low salinity), collectively, can modulate the plasticity and optimal conditions of mussels. Despite these phenotypic differences, we observed low genetic differentiation, likely resulting from significant gene flow induced by aquaculture, ultimately diminishing variation among individuals from different geographic areas. Our findings underscore how variability and predictability are essential factors shaping phenotypic diversity, even at small spatial scales. Balancing these factors could enhance species resilience and ecological success, crucial for biodiversity conservation amidst climate change.

Towards the understanding of genetic and morphological variations of a highly abundant seaweed-associated marine invertebrate

Unraveling the patterns of genetic structure and demographic history of marine species, as well as the factors that shape their genetic variations, is fundamental for informing conservation strategies for species and their environments. In this work, we investigate the current population structure and historical demographic patterns of the conspicuous seaweed-associated amphipod Hyale niger at a fine spatial scale in the subtropical SW Atlantic coast, in Brazil, by using both genome-wide and mitochondrial DNA markers. We also investigate how geographic distance, current oceanographic conditions, and variations in a key morphological trait contribute to the genetic variability of the amphipod. We observed an evident population genetic structure, even at a fine spatial scale, although genetic differentiation was lower than our expectations for a benthic direct brooder. Demographic history inferences were consistent across populations and showed two major demographic expansions on interglacial periods during the late Pleiostocene, before and after the last glacial maximum. We also demonstrated that isolation-by-environment (IBE) was the main driver of genetic differentiation, although we could not separate it from the effects of isolation-by-distance (IBD). Among environmental factors, nutrient concentrations in seawater were most relevant for explaining genetic structure. In addition, our data suggest that morphological variation in gnathopod 2 structure of males were not genetic-related and were probably plastic as a response to variations in macroalgae frond size. Our study reinforces the importance of using multiple molecular markers and analytical approaches to unveil patterns and processes generating genetic variation in natural populations.

Analysis of genetic diversity and genetic structure of indigenous chicken populations in Guizhou province based on genome-wide single nucleotide polymorphism markers

Guizhou province in China is rich in indigenous chicken breeds, playing an essential role in the genetic improvement of modern chickens. Genetic diversity has decreased in recent decades due to accelerated breeding processes and changing conservation priorities. To determine the genetic diversity and population structure of Guizhou indigenous chicken breeds, we used 55K genotyping arrays to conduct population genetic analysis on 233 individuals from 8 Guizhou indigenous breeds and 263 individuals from 9 Guizhou indigenous chicken populations. We evaluated the genetic diversity parameter (heterozygosity, proportion of polymorphic markers, and nucleotide diversity), linkage disequilibrium (LD), population structure, and genetic differentiation (FST and genetics distance). Genetic diversity results indicated that the genetic diversity of chicken breeds in Guizhou province is relatively affluent. Among Guizhou breeds, Baiyi black-bone and Guizhou yellow chicken displayed the lowest genetic diversity, as the 2 breeds exhibit lower PN and heterozygosity, the extent of linkage disequilibrium is higher. According to the LD pattern, Guizhou indigenous breeds can be divided into 3 categories. Population structure analysis showed a certain degree of genetic differentiation among local chickens in Guizhou. We argue that Chishui black-bone and Puan black-bone chickens are 2 different geographical regional groups of the same breed. In principal component analysis, individuals from the 2 groups clustered together, and the phylogenetic tree results showed that the 2 groups clustered together to form a branch independent of other breeds, and they displayed an identical pattern of ancestral lineage composition. The research results will provide a reference for protecting local chicken genetic resources in Guizhou Province and promote the protection and utilization of genetic resources.

Landscape Heterogeneity Drives Genetic Diversity in the Highly Dispersive Moss Funaria hygrometrica Hedw.

Funaria hygrometrica, a cosmopolitan moss species known for its remarkable dispersal capacity, was selected as the focal organism to investigate the relationship between landscape features and genetic diversity. Our study encompassed samples collected from two distinct regions: the Spanish Sierra Nevada Mountains (SN), characterized by a diverse landscape with an altitudinal difference of nearly 3500 m within a short distance, and the Murcia Region (MU) in Southeast Spain, characterized by a uniform landscape akin to the lowlands of Sierra Nevada. Genotyping analysis targeted three genetic regions: the nuclear ribosomal internal transcribed spacer (nrITS), the chloroplast rps3-rpl16 region, and the mitochondrial rpl5-rpl16 spacer. Through this analysis, we aimed to assess genetic variability and population structure across these environmentally contrasting regions. The Sierra Nevada populations exhibited significantly higher haplotype diversity (Hd = 0.78 in the highlands and 0.67 overall) and nucleotide diversity (π% = 0.51 for ITS1) compared to the Murcia populations (Hd = 0.35, π% = 0.14). Further investigation unveiled that samples from the lowlands of Sierra Nevada showed a closer genetic affinity to Murcia than to the highlands of Sierra Nevada. Furthermore, the genetic differentiation between highland and lowland populations was significant (ΦST = 0.55), with partial Mantel tests and ResistanceGA analysis revealing a strong correlation between ITS1-based genetic diversity and landscape features, including altitude and bioclimatic variables. Our study elucidated potential explanations for the observed genetic structuring within F. hygrometrica samples' populations. These included factors such as a high selfing rate within restricted habitats, a limited average dispersal distance of spores, hybrid depression affecting partially incompatible genetic lineages, and recent migration facilitated via human activities into formerly unoccupied areas of the dry zones of Southeast Spain.

Analysis of genetic diversity and environmental associations of wild citron (Citrus medica L.) in northeast India

Citron (Citrus medica L.) is a major citrus fruit crop known for its medicinal, nutritional, and aromatic uses. Native to northeast India, Myanmar, and south China, citron is cultivated mostly in the Mediterranean and South Asian countries. The truly wild populations of citron are found in the hills and valleys of northeast India. The extent of genetic diversity in wild citron in relation to environmental variables has not been documented. In the present study, we analyzed genetic diversity and environmental association of wild populations of C. medica in northeast India using 15 polymorphic nuclear SSR (simple sequence repeat) markers and 21 environmental variables. SSR profiling revealed a moderate genetic diversity (Ho = 0.40; He = 0.41; I = 0.70). Neighbor-joining (NJ) and principal coordinate analysis (PCoA) grouped 16 natural populations into two genetic clusters. Bayesian structure results showed two genetic populations with a high admixture of individuals. Analysis of molecular variance (AMOVA) revealed low genetic differentiation (Fst = 0.14; P < 0.001), indicative of high gene flow (Nm = 1.53) in citron. The isolation by distance (IBD) analysis showed a weak correlation, indicating that geographic distance was not a determining factor for genetic distance in C. medica populations. The higher metrics of outcrossing rate (tm > 0.9) revealed outbreeding nature of the species. The genetic diversity of citron showed a positive correlation with precipitation of driest month and precipitation of coldest quarter, but negative with mean diurnal range and isothermality. Overall, the results of the present study could benefit the conservation and management of citron resources and their natural habitat in northeast India. Genetically highly diverse populations identified in the present study can be used for conservation and utilization of citron genetic resources.

Whole-genome resequencing reveals genetic diversity and selection signatures in five populations of Mandarin Fish (Siniperca chuatsi)

Mandarin fish is an important freshwater economic fish in China, and the genome of mandarin fish population may have specific selection signatures after long-term selection, and studying these selection signatures is one of the important strategies for screening functional genes. In this study, the whole genome was resequenced from five mandarin fish populations (HLJ, HN, AH, FJ, and BJ), and a total of high-quality SNPs with 1659,318 single nucleotide polymorphisms were obtained, and the genetic differentiation index and nucleotide polymorphism ratio between populations were used to detect the selected genomic regions. The results showed that all individuals were divided into two branches, with the HLJ population forming an independent cluster, and the HN, AH, FJ, and BJ populations clustering together. Selection signal analysis on the HLJ mandarin fish population and other mandarin fish populations using the FST and π HLJ/other methods. Finally, we identified 26 important candidate genes based on the enrichment pathways related to fat traits such as Glycerolipid metabolism, acyl-CoA oxidase activity, Wnt signaling pathway, and Notch signaling pathway, including notch3, pla2g12a and acox1. This study explores the genetic diversity and genetic structure of mandarin fish from a whole-genome perspective, identifies candidate genes related to fat traits, and provides references for the protection and utilization of mandarin fish genetic resources.

Population genetic structure of Montipora digitata coral-algal symbiosis in the South China Sea

Species genetic diversity can reflect their adaptability to environmental changes. Coral reefs worldwide are in rapid decline due to climate change and human activities, highlighting the need for conservation intervention. The South China Sea (SCS) is an important biodiversity hotspot, particularly in the Xisha Islands (XS) that contain the majority of coral species in the SCS. However, few studies exist on coral genetic diversity in the SCS. Montipora digitata is the dominant reef-building coral species in the XS. In this study, two mitochondrial DNA fragments and 11 microsatellite markers were employed to investigate the genetic diversity of coral host of M. digitata, and ITS amplicon sequencing was employed to investigate the Symbiodiniaceae community structure. We sampled five wild populations of M. digitata in Hainan Island and the Xisha Islands. Montipora digitata showed low genetic diversity across populations in the SCS. We found significant genetic differentiation between the Sanya (SY) and XS populations but no significant genetic differentiation within XS populations. We identified four Symbiodiniaceae genera, with Cladocopium and Durusdinium being the most common, as well as Gerakladium and Fugacium. The Symbiodiniaceae types of SY and XS are significantly different, C15 is abundant in all populations, while D1a is also abundant in SY. We analyzed the correlation between 16 environmental factors and the genetic diversity of symbionts, genetic diversity of coral host and Symbiodiniaceae community was significantly correlated with sea surface temperature (SST) and other environmental factors. Our study provided a detailed paradigm from the perspective of genetic diversity of how a dominant coral species can be indicative of poor environmental adaptation potential.

Population structure analysis of Phlebotomus papatasi populations using transcriptome microsatellites: possible implications for leishmaniasis control and vaccine development

BackgroundPhlebotomus papatasi is considered the primary vector of Leishmania major parasites that cause zoonotic cutaneous leishmaniasis (ZCL) in the Middle East and North Africa. Phlebotomus papatasi populations have been studied extensively, revealing the existence of different genetic populations and subpopulations over its large distribution range. Genetic diversity and population structure analysis using transcriptome microsatellite markers is important to uncover the vector distribution dynamics, essential for controlling ZCL in endemic areas.MethodsIn this study, we investigated the level of genetic variation using expressed sequence tag-derived simple sequence repeats (EST-SSRs) among field and colony P. papatasi samples collected from 25 different locations in 11 countries. A total of 302 P. papatasi sand fly individuals were analyzed, including at least 10 flies from each region.ResultsThe analysis revealed a high-level population structure expressed by five distinct populations A through E, with moderate genetic differentiation among all populations. These genetic differences in expressed genes may enable P. papatasi to adapt to different environmental conditions along its distribution range and likely affect dispersal.ConclusionsElucidating the population structuring of P. papatasi is essential to L. major containment efforts in endemic countries. Moreover, the level of genetic variation among these populations may improve our understanding of Leishmania–sand fly interactions and contribute to the efforts of vaccine development based on P. papatasi salivary proteins.Graphical

The genetic consequences of historic climate change on the contemporary population structure of a widespread temperate North American songbird

Studies of widely distributed species can inform our understanding of how past demographic events tied to historic glaciation and ongoing population genetic processes interact to shape contemporaneous patterns of biodiversity at a continental scale. In this study, we used whole-genome resequencing to investigate the current population structure and genetic signatures of past demographic events in the widespread migratory American goldfinch (Spinus tristis). Phylogenetic relationships inferred from whole mitochondrial genomes were poorly resolved. In contrast, a genome-wide panel of > 4.5 million single nucleotide polymorphisms (SNPs) strongly supported the existence of eastern and western populations separated by western mountain ranges and additional population structuring within the western clade. Demographic modeling estimated that the eastern and western populations diverged approximately one million years ago, and both populations experienced subsequent population bottlenecks during the last glacial period. Species distribution models showed a severe contraction of suitable habitat for the American goldfinch during this period, with predicted discontinuities that are consistent with multiple, isolated glacial refugia that coincide with present-day population structure. Low overall genetic differentiation between the eastern and western populations (FST ∼ 0.01) suggests ongoing gene flow accompanied divergence, and individuals with admixed genomic signatures were sampled along a potential contact zone. Nevertheless, outlier SNPs were identified near genes associated with feather color, song, and migratory behavior and provide strong candidates for further study of the mechanisms underlying reproductive isolation and speciation in birds.

Relationship Between Genetic and Phenotypic Variations in Natural Populations of Perennial and Biennial Sagebrush.

Plant responses to environmental heterogeneity depend on life-history traits, which could relate to phenotypical and genetic characteristics. To elucidate this relationship, we examined the variation in population genetics and functional traits of short- and long-lived Artemisia species that are co-occurring in the steppes of Mongolia. Mongolian steppes represent stressful and water-limited habitats, demanding phenotypic modifications in the short term and/or genetic adaptation in the long term. However, detailed knowledge is missing about both plant phenotypic and genetic differentiation, and their interrelationships in temperate grasslands. Here, we investigated 21 populations of the widely distributed subshrub Artemisia frigida and the herbaceous biennial Artemisia scoparia. Genetic variation was assessed with newly developed simple sequence repeats (SSRs) markers. Functional trait data were collected from each individual, and data on environmental variables was collected for each population. We detected significantly higher genetic diversity in the biennial species (H E = 0.86) compared with the perennial (H E = 0.79). For both species, the largest share of genetic variation was partitioned within populations (96%). Population genetic structure in the biennial A. scoparia was weak, while the perennial A. frigida showed some spatial genetic structure, which was impacted by geographical factors, soil nutrients, and precipitation amount. Morphology-related functional traits (i.e., plant height) were predominantly associated with environmental variables rather than with genetic variation, whereas physiology-related trait (i.e., specific leaf area [SLA]) was partly genetically determined.

Molecular Identification and Genetic Diversity Analysis of Papaya Leaf Curl China Virus Infecting Ageratum conyzoides.

Papaya leaf curl China virus (PaLCuCNV) is a damaging plant pathogen causing substantial losses to crop. The complete genomes of three PaLCuCNV isolates from Ageratum conyzoides were obtained and combined with the 68 reference isolates in GenBank for comprehensive genetic diversity analyses using specialized computational tools. Sequence alignment revealed nucleotide sequence similarity ranging from 85.3% to 99.9% among 71 PaLCuCNV isolates. Employing phylogenetic analysis, 71 PaLCuCNV sequences were clustered into five groups, with no significant correlation observed between genetic differentiation and either host species or geographical origin. Additionally, 13 recombination events across all PaLCuCNV isolates were identified. Genetic diversity analysis indicated the ongoing expansion and evolution of PaLCuCNV populations, supported by a neutral model. Moreover, significant genetic differentiation was observed among distinct viral populations, primarily attributed to genetic drift. Overall, our findings provide valuable insights into the detection, genetic variation, and evolutionary dynamics of PaLCuCNV.

Limited Migration From Physiological Refugia Constrains the Rescue of Native Gastropods Facing an Invasive Predator.

Biological invasions have caused the loss of freshwater biodiversity worldwide. The interplay between adaptive responses and demographic characteristics of populations impacted by invasions is expected to be important for their resilience, but the interaction between these factors is poorly understood. The freshwater gastropod Amnicola limosus is native to the Upper St. Lawrence River and distributed along a water calcium concentration gradient within which high-calcium habitats are impacted by an invasive predator fish (Neogobius melanostomus, round goby), whereas low-calcium habitats provide refuges for the gastropods from the invasive predator. Our objectives were to (1) test for adaptation of A. limosus to the invasive predator and the low-calcium habitats, and (2) investigate if migrant gastropods could move from refuge populations to declining invaded populations (i.e., demographic rescue), which could also help maintain genetic diversity through gene flow (i.e., genetic rescue). We conducted a laboratory reciprocal transplant of wild F0 A. limosus sourced from the two habitat types (high calcium/invaded and low calcium/refuge) to measure adult survival and fecundity in home and transplant treatments of water calcium concentration (low/high) and round goby cue (present/absent). We then applied pooled whole-genome sequencing of 12 gastropod populations from across the calcium/invasion gradient. We identified patterns of life-history traits and genetic differentiation across the habitats that are consistent with local adaptation to low-calcium concentrations in refuge populations and to round goby predation in invaded populations. We also detected restricted gene flow from the low-calcium refugia towards high-calcium invaded populations, implying that the potential for demographic and genetic rescue is limited by natural dispersal. Our study highlights the importance of considering the potentially conflicting effects of local adaptation and gene flow for the resilience of populations coping with invasive predators.

Characterising the Genomic Landscape of Differentiation Between Annual and Perennial Rye.

Annuality and perenniality represent two different life-history strategies in plants, and an analysis of genomic differentiation between closely related species of different life histories bears the potential to identify the underlying targets of selection. Additionally, understanding the interactions between patterns of recombination and signatures of natural selection is a central aim in evolutionary biology, because patterns of recombination shape the evolution of genomes by affecting the efficacy of selection. Here, our aim was to characterise the landscape of genomic differentiation between weedy annual rye (Secale cereale L.) and wild perennial rye (Secale strictum C. Presl), and explore the extent to which signatures of selection are influenced by recombination rate variation. We used population-level sequence data of annual and perennial rye to analyse population structure and their demographic history. Based on our analyses, annual and perennial rye diverged approximately 26,500 years ago (ya) from an ancestral population size of ~85,000 individuals. We analysed patterns of genetic diversity and genetic differentiation, and found highly differentiated regions located in low-recombination regions, indicative of linked selection. Although all highly differentiated regions, as revealed by F ST-outlier scans, were located in low-recombining regions, not all chromosomes showed this tendency. We therefore performed a gene ontology enrichment analysis, which showed that highly differentiated regions comprise genes involved in photosynthesis. This enrichment was confirmed when F ST outlier scans were performed separately in low- and intermediate-recombining regions, but not in high-recombining regions, suggesting that local recombination rate variation in rye affects outlier scans. Cultivated rye is an annual crop, but the introduction of perenniality may be advantageous in regions with poor soil quality or under low-input farming. Although the resolution of our analysis is limited to a broad-scale, knowledge about the evolutionary divergence between annual and perennial rye might support breeding efforts towards perennial rye cultivation.

Drivers of phenotypic variation and plasticity to drought in populations of a Mediterranean shrub along an environmental gradient

Assessing the factors driving intraspecific phenotypic variation is crucial to understand the evolutionary trajectories of plant populations and predict their vulnerability to climate change. Environmental gradients often lead to phenotypic divergence in functional traits and their plasticity across populations. We studied the entire environmental range of the Mediterranean gypsum endemic shrub Helianthemum squamatum to evaluate the factors underlying quantitative population differentiation and phenotypic plasticity to drought, using a common garden with 16 populations that covered the main geographic and the entire climatic range of the species. Sampling followed a hierarchical approach to assess trait genetic variation within and among four distinct geographical regions. We found high but similar plastic responses across populations, which were consistent with adaptive plasticity to drought, including advanced phenology, more sclerophyllous leaves, higher water use efficiency and larger seeds in dry conditions. Despite these generally similar plastic responses, we found significant population differentiation in quantitative traits, part of which was structured at the regional scale. Such differentiation was not associated with environmental variation, including differences in climate and soil conditions. This suggests that non-adaptive processes might have had a role on genetic differentiation in H. squamatum, likely due to the island-like configuration of gypsum habitats and the lack of effective seed dispersal of the study species. Our results emphasize the role of phenotypic plasticity in adaptive drought response and the importance of considering both adaptive and non-adaptive processes shaping intraspecific phenotypic variation, which is crucial for predicting plant population vulnerability to climate change.

Assessment of Genetic Parameters and Diversity Organization of Ginger Accessions Cultivated in Burkina Faso as Revealed by Microsatellite Markers

Rhizomes of Ginger (Zingiber officinale Rosc.) are widely used as a spice across the world. It has originated from South-east Asia and introduced to many parts of the world, and has been cultivated as a spice and for medicinal purpose. Ginger is a high value crop in Burkina Faso. The genetic diversity organization in ginger species is not well-known in Burkina Faso. Genetic resources are imperative for varietal selection. The importance of genetic resources depends on the levels of their diversity. The present investigation aims to assess the diversity of ginger accessions collected from Burkina Faso. Forty-seven ginger accessions collected from three provinces, Comoé (03), Léraba (14), Kénédougou (30), located in the southwestern zone of Burkina Faso were genotyped for their molecular traits using microsatellite markers. A total of 24 alleles were revealed by electrophoresis. All the simple-sequence repeats (SSR) set primers used revealed high polymorphic rate (100%) with the expected heterozygosity (0.499), showing their ability in assessment of the diversity levels and genetic organization of ginger accessions due to their codominance. The dendrogram obtained by the Neighbor-Joining method revealed three main genetic groups. The genetic differentiation index value (0.313) showed that the accessions of the three provinces were different, with an interesting diversity observed from kénédougou ginger accessions. Information from this study could be used in the development of effective management strategies for the conservation and effective use of the genetic resources within ginger accessions grown in Burkina Faso.

Seascape Genetics and Distinct Intraspecific Diversification of the Decapod Nephrops norvegicus in the Adriatic Sea.

Norway lobster Nephrops norvegicus, a prized decapod crustacean species, is found at different depths across the East Atlantic Ocean and Mediterranean Sea. Despite management efforts, the stocks are globally characterised as overexploited. In the present study, the impact of biogeographical boundaries on the phylogeographical and demographic population status was investigated within the Adriatic Sea, addressing important genetic indices for decapod functional conservation management. Central Mediterranean, Adriatic Sea A total of 482 individuals of Nephrops divided into the 12 samples were collected across biogeographical range of the Adriatic Sea. Using the mtDNA D-loop and microsatellite markers, methods of phylogeography and seascape genetics were applied to infer offshore versus coastal population divergence, demography and structure. Significant findings include genetic differentiation between offshore and coastal samples, with higher diversity indices in open waters. The limited gene flow observed between these two areas emphasises the self-sustained nature of coastal populations. Recent demographic changes in coastal populations reflect geographical constraints, fishing pressures and fluctuations in self-recruitment success. Additionally, the study reveals historical biogeographic events shaping the Adriatic populations, with evidence suggesting lineage divergence during the upper Pleistocene and postglacial recolonisation from southern Adriatic refugia. The role of biogeographical conditions in shaping genetic structure and limited gene flow between inshore and offshore areas underscore the need for improved management strategies, emphasising the importance of marine protected areas in conserving coastal populations and maintaining overall genetic diversity of the Norway lobster in the Adriatic Sea. Genomic monitoring within current management practices is recommended.