Genetic Diversity and Landscape Genomics of Carya dabieshanensis (M.C. Liu and Z.J. Li) in a Heterogenous Habitat

Genetic diversity defines the evolutionary potential of a species, yet mounting evidence suggests that epigenetic diversity could also contribute to adaptation. Elucidating the complex interplay between genetic and epigenetic variation in wild populations remains a challenge for evolutionary biologists, and the intriguing possibility that epigenetic diversity could compensate for the loss of genetic diversity is one aspect that remains basically unexplored in wild plants. This hypothesis is addressed in this paper by comparing the extent and patterns of genetic and epigenetic diversity of phylogenetically closely related but ecologically disparate species. Seven pairs of congeneric species from Cazorla mountains in south-eastern Spain were studied, each pair consisting of one endemic, restricted-range species associated to stressful environments, and one widespread species occupying more favourable habitats. The prediction was tested that endemic species should have lower genetic diversity due to population fragmentation, and higher epigenetic diversity induced by environmental stress, than their widespread congeners. Genetic (DNA sequence variants) and epigenetic (DNA cytosine methylation variants) diversities and their possible co-variation were assessed in three populations of each focal species using amplified fragment length polymorphism (AFLP) and methylation-sensitive AFLP (MSAP). All species and populations exhibited moderate to high levels of genetic polymorphism irrespective of their ecological characteristics. Epigenetic diversity was greater than genetic diversity in all cases. Only in endemic species were the two variables positively related, but the difference between epigenetic and genetic diversity was greater at populations with low genetic polymorphism. Results revealed that the relationship between genetic and epigenetic diversity can be more complex than envisaged by the simple hypothesis addressed in this study, and highlight the need of additional research on the actual role of epigenetic variation as a source of phenotypic diversity before a realistic understanding of the evolutionary relevance of epigenetic phenomena in plant adaptation can be achieved.

Invasive species are expected to undergo a reduction in genetic diversity due to founder effects, which should limit their ability to adapt to new habitats. Still, many invasive species achieve widespread distributions and dense populations. This paradox of invasions could potentially be overcome through multiple introductions or hybridization, both of which increase genetic diversity. We conducted a population genomics study of Japanese knotweed (Reynoutria japonica), which is a polyploid, clonally reproducing invasive species that has been notoriously successful worldwide despite supposedly low genetic diversity. We used genotyping by sequencing to collect 12,912 SNP markers from 88 samples collected at 38 locations across North America for the species complex. We used alignment-free k-mer hashing analysis in addition to traditional population genetic analyses to account for the challenges of genotyping polyploids. Genotypes conformed to three genetic clusters, likely representing Japanese knotweed, giant knotweed, and hybrid bohemian knotweed. We found that, contrary to previous findings, the Japanese knotweed cluster had substantial genetic diversity, though it had no apparent genetic structure across the landscape. In contrast, giant knotweed and hybrids showed distinct population groups. We did not find evidence of isolation by distance in the species complex, likely reflecting the stochastic introduction history of this species complex. The results indicate that clonal invasive species can show substantial genetic diversity and can be successful at colonizing a variety of habitats without showing evidence of local adaptation or genetic structure.

Genetic diversity is crucial for plants to respond to global climate change, and exploring relationships between genetic diversity and climatic factors may help predict how global climate change will shape the genetic diversity of plants in the future. So far, however, the extent and magnitude of the impact of climatic factors on the genetic diversity of plants has not been clarified. We collected data from 68 published papers on two widely used measures of genetic diversity of populations (average expected heterozygosity (He) and average observed heterozygosity (Ho)) and on localities of populations of 79 vascular plants, and extracted data on 19 climatic factors from WorldClim. We then explored the relationships between measures of genetic diversity and climatic factors using linear regressions. He of plant populations was significantly correlated with climatic factors in 58.7% (44) of the 75 species that used He as a measure of genetic diversity, and Ho was correlated with climatic factors in 65.1% (41) of the 63 species that used this genetic diversity measure. In general, Mean Temperature of Wettest Quarter, Precipitation Seasonality, Precipitation of Driest Quarter and Temperature Seasonality played a vital role in shaping He, and Ho was mostly correlated with Precipitation of Warmest Quarter, Mean Temperature of Wettest Quarter, Precipitation of Driest Quarter and Precipitation of Driest Month. Also, the proportion of the significant correlations between genetic diversity of populations and climatic factors was higher for woody than for herbaceous species, and different climatic factors played different roles in shaping genetic diversity of these two growth forms. Our results suggest that climate may play an important role in shaping genetic diversity of plant populations, that climatic change in the future may alter genetic diversity of plants, and that genetic diversity of different plant forms may respond to climatic change differently.

This study aims to characterize Iraqi pigeon breeds’ population structure and genetic diversity using Microsatellite (SSR) markers to obtain detailed insights into their genetic variation, differentiation, and evolutionary dynamics. This study represents the first comprehensive analysis of Iraqi pigeon breeds’ population structure and genetic diversity. The genetic diversity analysis revealed moderate to high allelic diversity, with the number of alleles (Na) ranging from 16 to 25 and the number of effective alleles (Ne) from 11.95 to 20.56. Observed heterozygosity (Ho) ranged from 0.27 to 0.53, while expected heterozygosity (He) was consistently high (0.92 to 0.95). FST values indicated significant genetic differentiation among pigeon breeds, ranging from 0.40 to 0.54, and gene flow (Nm) values suggested limited migration between subpopulations. The Principal Component Analysis (PCA) identified five distinct clusters, explaining 76.02% of the total variance, which reflects pronounced genetic boundaries and distinct genetic identities among the breeds. Genetic structure analysis using admixture with K=3 clusters highlighted distinct ancestral contributions. The genetic distance analysis revealed close genetic relationships among populations like Kirkuk, Baghdad, and Mosul White, with lower genetic distances (0.06 to 0.08). In contrast, Fadadi, Zangi, and Yellow breeds exhibited higher genetic differentiation (distances up to 0.15). The Analysis of Molecular Variance (AMOVA) indicated significant genetic variation among populations, with a variance component of 10.92 and a Phi-statistic of 0.58, demonstrating moderate to high genetic differentiation and substantial genetic diversity within populations. This comprehensive analysis underscores significant genetic variation and distinct population structures among Iraqi pigeons, with clear differentiation and diverse genetic contributions across breeds. The findings highlight the effectiveness of SSR markers in capturing the genetic landscape, providing essential insights for the conservation and management of genetic diversity within these pigeon populations. This study contributes valuable information for understanding Iraqi pigeon breeds’ genetic dynamics and evolutionary relationships, supporting future genetic and conservation efforts.

Higher genetic diversity and gene flow in wild populations of Miscanthus sinensis in southwest China

Genetic diversity and structure within and between wild and cultivated Saccharina japonica (Laminariales, Phaeophyta) revealed by SSR markers

Understanding landscape processes driving patterns of population genetic differentiation and diversity has been a long-standing focus of ecology and evolutionary biology. Gene flow may be reduced by historical, ecological or geographic factors, resulting in patterns of isolation by distance (IBD) or isolation by environment (IBE). Although IBE has been found in many natural systems, most studies investigating patterns of IBD and IBE in nature have used anonymous neutral genetic markers, precluding inference of selection mechanisms or identification of genes potentially under selection. Using landscape genomics, the simultaneous study of genomic and ecological landscapes, we investigated the processes driving population genetic patterns of White-breasted Nuthatches (Sitta carolinensis) in sky islands (montane forest habitat islands) of the Madrean Archipelago. Using more than 4000 single nucleotide polymorphisms and multiple tests to investigate the relationship between genetic differentiation and geographic or ecological distance, we identified IBE, and a lack of IBD, among sky island populations of S.carolinensis. Using three tests to identify selection, we found 79 loci putatively under selection; of these, seven matched CDS regions in the Zebra Finch. The loci under selection were highly associated with climate extremes (maximum temperature of warmest month and minimum precipitation of driest month). These results provide evidence for IBE - disentangled from IBD - in sky island vertebrates and identify potential adaptive genetic variation.

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

Dali tea (Camellia taliensis), serving as a primitive wild species within the section Thea, represents a crucial genetic source for the domestication of Pu-erh tea (C. sinensis var. assamica) due to its strong stress tolerance and unique biochemical composition. It is of key value for the conservation of tea genetic resources and breeding innovation. Utilizing the SLAF-seq (Specific-Locus Amplified Fragment Sequencing) technique, this study systematically analyzed the genetic diversity and evolutionary relationships among five geographic populations (16 C. taliensis and 4 C. sinensis var. assamica accessions) within the Lancang River basin. Results revealed significant genetic differentiation among the C. taliensis populations. Pronounced genetic isolation was observed between the Lincang Daxueshan and Dali Nanjian populations. Localized gene introgression occurred between wild C. taliensis (Nanjian population) and C. sinensis var. assamica.The wild Lincang Daxueshan population formed a monophyletic clade at the base of the phylogenetic tree, exhibiting strong genetic isolation and high differentiation levels (Fst = 0.364) but low genetic diversity. In contrast, the cultivated population (Banna Germplasm Repository) displayed a mixed genetic background, with wild genetic components constituting only 50%-60%. The Lincang Daxueshan wild population showed a low minor allele frequency (MAF = 0.204) and a mild inbreeding coefficient (Fis = 0.09), indicating a potential risk of genetic erosion. Conversely, the Banna Germplasm Repository population exhibited the highest genetic diversity (Shannon Index = 0.318), highlighting the effectiveness of ex situ conservation and its potential as a vital gene donor for tea breeding. This study underscores the unique status of the upper Lancang River basin in Yunnan as a core conservation area for C. taliensis genetic diversity. We propose strategies of "delineating priority zones for in situ conservation" and "facilitating inter-population germplasm exchange," providing a molecular basis for conserving wild tea resources and breeding for stress resistance. Employing high-density SNP markers, we obtained 5,182,931 loci with an average sequencing depth of 19.30x. This enabled quantification of gene flow between wild and cultivated populations (Nm = 0.18) and clarified the contribution of introgressive domestication to the genetic makeup of cultivated tea. These findings provide a theoretical foundation for understanding interspecific interaction mechanisms in tea plant evolution and hold significant implications for promoting regional ecological conservation and biodiversity maintenance.

Glycyrrhiza uralensis is an endangered and national-protected medicinal plant species distributed in semi-arid and arid areas of North China. This study addresses the genetic diversity and relationship between populations in different habitats by amplified fragment length polymorphism (AFLP). The plant materials consisted of 50 individuals from 5 different populating areas of Chifeng (Inner Mongolia), Hengjinqi (Inner Mongolia), Minqin (Ganshu), Aletai (Xinjiang) and Kashi (Xinjiang). Eight AFLP primer combinations generated a total of 1025 bands with 52.7% polymorphism. Unweighted pair group method based on arithmetic average (UPGMA) analysis was performed on Jaccard’s similarity coefficient matrix. According to results, the genetic resources and diversity in wild populations of G. uralensis were rich (polymorphism = 54.3%, He = 0.1932). The polymorphism among populations was Chifeng > Hangjinqi > Minqin > Aletai > Kashi and the genetic diversity varied from 0.1794 - 0.2061 and was in the order of Minqin > Chifeng > Hangjinqi > Aletai > Kashi. Genetic diversity was significantly correlated with annual mean precipitation and soil pH. Aletai and Kashi populations had close genetic relationship, and so Minqin and Chifeng populations. Conservational efforts have to be strengthened for all populations of the plant species in different habitats. Key words: Genetic characteristic, plant population, liquorice, semi-arid and arid area, biodiversity conservation.

Common wild rice (Oryza rufipogon Griff.) is a valuable germplasm resource for rice genetic improvement. However, it is endangered due to habitat loss. Assessment of its genetic diversity is essential for germplasm characterization, utilization, and conservation. In the present study, we developed a 79,422-single-nucleotide polymorphism genome-wide array by specific-locus amplified fragment sequencing (SLAF-seq) and used it to genotype 110 common wild rice accessions from different agroclimatic zones in Guangdong Province, China. The number of SNPs on each chromosome was consistent with the physical length of the chromosome, and the average marker density was approximately 4.83 kb/SNP. The genome-wide linkage disequilibrium decayed to its half maximum within 0.52 kb for O. rufipogon. The common wild rice accessions were clustered into four subgroups, with some overlap in principal component analysis and a neighbor-joining tree that was also confirmed by model-based admixture. Analysis of molecular variance revealed significant genetic differentiation among individuals, accounting for 90.64% of the total molecular variance; however, the differences between the subgroups (Enping, Lufeng, Suixi and Fogang) were not significant. The significant genetic variations in resources collected in different years were observed in Enping and Suixi subgroups, but there was no significant genetic variation in Fogang subgroup. The pairwise fixation index (FST) suggested that the populations from Enping and Lufeng were most differentiated while those from Enping and Fogang were least differentiated. Our results illustrated clear genetic relationships among 110 common wild rice accessions, showing a potential molecular marker-based strategy for preserving the genetic diversity and accelerating the systematic utilization of these important wild rice resources.

Conservation of genetic diversity in livestock breeds is important since it is, both within and between breeds, under threat. The availability of large numbers of SNP markers has resulted in new opportunities to estimate genetic diversity in more detail, and to improve prioritization of animals for conservation of genetic diversity. The aim of this thesis was to further explore the potential of SNP markers for estimation and conservation of genetic diversity within livestock breeds. This was evaluated analyzing Holstein cattle populations, genotyped with a commonly used 50k SNP chip. Genetic diversity was estimated with SNP markers and compared to genetic diversity estimated with pedigree information. Both methods could detect differences in overall genetic diversity, even between two closely related populations. With SNP markers, differences in genetic diversity at the chromosomal level could be identified as well. Subsequently, SNP markers and pedigree information were used to prioritize animals for conservation in a gene bank using optimal contributions. SNP based prioritization was slightly more effective than pedigree based information, both over the whole genome and at specific regions of the genome. We extended the optimal contribution method to simultaneously conserve a single allele at a specific frequency and maximize the overall genetic diversity conserved in a gene bank. The loss of overall genetic diversity was larger when the target frequency for animals conserved in the gene bank differed more from the original frequency in the population. It can be concluded that dense SNP data form a powerful tool for estimation and conservation of genetic diversity in livestock breeds. Although pedigree information gives a good representation of the overall genetic diversity, SNP markers can provide more detailed information about the genetic diversity over the genome. Especially for small populations, SNP markers can play an important role in conservation of unique alleles, while simultaneously minimizing the loss of genetic diversity at the rest of the genome.

Context Genetic diversity between parental lines is closely linked to the extent of heterosis in crops such as rice (Oryza sativa L.). Diversifying indica lines through incorporation of tropical japonica genome has been shown to enhance heterosis in rice. Nevertheless, it is crucial to assess newly developed lines from inter-subspecific crosses for agronomic and quality traits for exploitation. Aims Assessing the genetic diversity of inter-subspecific rice derivatives and identifying superior lines with desirable agronomic/quality traits using a multi-trait index. Methods Diversity of 88 breeding lines was estimated using the unweighted pair group method with arithmetic mean (UPGMA) clustering method for eight agronomic and three quality traits. Multi-trait genotype ideotype selection indices and yield*trait biplot analysis were used to select superior lines. Key results The traits total number of spikelets per panicle, gelatinisation temperature, and apparent amylose content exhibited high genetic variation and heritability, while single plant yield expressed moderate heritability. The lines were grouped into eight distinct clusters, thus harbouring substantial genetic diversity. Significant selection gains for yield and other traits, such as number of spikelets per panicle, productive tillers, and apparent amylose content were noticed. Four lines, CB ITJ 123, CB ITJ 42, CB ITJ 35, and CB ITJ 66, emerged as superior candidates for further use in hybrid breeding. Conclusions The substantial genetic variation and diversity observed in inter-subspecific derivatives suggest their potential for exploitation in two-line or three-line breeding to enhance the level of heterosis. Implications Diverse breeding lines developed from Inter-subspecific hybridisation with desirable traits can be used to develop hybrids predicted to be heterotic than intra-subspecific hybrids. Multi-trait selection indices facilitate the simultaneous improvement of yield attributes and quality traits.

Tidal marshes at the Paul S. Sarbanes Ecosystem Restoration Project at Poplar Island (PI) are part of a large‐scale restoration project to replace lost island habitat in Chesapeake Bay, United States. However, observations of Spartina alterniflora die‐back prompted questions about the impact on genetic diversity and resilience of restored versus natural marshes, leading to an investigation of genetic diversity and population structure. Transects were established across three distinct restored marshes with different ages and histories of die‐back and across two local, non‐restored native marshes. Plants were genotyped at eight microsatellite markers to examine metrics of genetic diversity, population structure, and clonality. Allelic richness but not heterozygosity was higher in restored marshes compared to reference marshes, which showed significantly higher clonality and spatial genetic autocorrelation. Restored marsh areas experiencing die‐back had slightly lower multilocus diversity indices than non‐die back areas in two third cases, but not a third comparison. Significant genetic differentiation was observed between the native and restored marshes (mean GST approximately 0.06), which reflects the approximately 100 km distance between native marshes and restored seed source in New Jersey. Overall, die‐back in restored marshes did not substantially affect genetic diversity or composition, but substantial differences in diversity were observed between restored and native marshes. Reduced clonal diversity in mature, native marshes may be a function of their greater age, as has been reported elsewhere. Future monitoring of neutral genetic diversity in PI marshes will be useful for understanding longer‐term patterns of genetic change and diversity in planted, restored marshes.

The abundance of butternut (Juglans cinerea L.) trees has severely declined rangewide over the past 50 years. An important factor in the decline is butternut canker, a disease caused by the fungus Ophiognomonia clavigigenti-juglandacearum, which has left the remaining butternuts isolated and sparsely distributed. To manage the remaining populations effectively, information regarding how butternut’s population genetic structure is affected by environmental and historical factors is needed. In this study, we assessed genetic structure and diversity of 161 butternut trees from 19 adjacent watersheds in the southern portion of butternut’s range using 12 microsatellite markers. We assessed the genetic diversity and genetic differentiation among trees grouped at various spatial scales. Our goal was to use historical abundance and land use data for these watersheds, which are now all a part of the Great Smoky Mountains National Park (GSMNP), to understand the ecological and evolutionary forces that challenge the conservation and management of butternut. In general, butternuts within the 19 neighboring watersheds were all part of one continuous population, with gene flow throughout. Significant genetic differentiation was detected between some groups of trees, but the differentiation was quite small and may not represent an ecologically significant distinction. The mean heterozygosity in all watersheds remained high, despite extensive mortality. Overall, genetic diversity and rare alleles were evenly distributed across all watersheds, with some variability in subpopulations containing butternut-Japanese walnut hybrids (Juglans x bixbyi or buarts). These results indicate that management of this species should focus on protection from future hybridization with Japanese walnut, promotion of regeneration, and persistence of all remaining butternut trees, which still retain high levels of genetic diversity.