Analysis Of Molecular Variance Research Articles

Genetic diversity and population structure of Uganda cassava germplasm.

Cassava (Manihot esculenta Crantz) holds significant economic importance globally. Evaluating a diverse range of germplasm based on molecular characteristics not only enhances its preservation but also supports its utilization in breeding programs. In this study, we assessed genetic diversity and population structure among 155 cassava genotypes from Uganda using 5247 single nucleotide polymorphism (SNP) markers. Genotyping by sequencing (GBS) was employed for SNP discovery and to evaluate genetic diversity and population structure using the ADMIXTURE software. The cassava accessions comprised two populations: 49 accessions from Ugandan lines and 106 accessions resulting from crosses between South American and Ugandan lines. The average call rate of 96% was utilized to assess marker polymorphism. Polymorphic information content values of the markers ranged from 0.1 to 0.5 with an average of 0.4 which was moderately high. The principal component analysis (PCA) showed that the first two components captured ~ 24.2% of the genetic variation. The average genetic diversity was 0.3. The analysis of molecular variance (AMOVA) indicated that 66.02% and 33.98% of the total genetic variation occurred within accessions and between sub-populations, respectively. Five sub-populations were identified based on ADMIXTURE structure analysis (K = 5). Neighbor-joining tree and hierarchical clustering tree revealed the presence of three different groups which were primarily based on the source of the genotypes. The results suggested that there was considerable genetic variation among the cassava genotypes which is useful in cassava improvement and conservation efforts.

Genetic diversity and population genetics of Schistosoma haematobium isolated from children in Lusaka and Siavonga districts, Zambia.

Urogenital schistosomiasis remains a pervasive health challenge in rural Zambian communities. This study explores the molecular epidemiology and genetic diversity of Schistosoma haematobium using mitochondrial genes (cox1 and nadh1). Urine samples from 421 children in Siavonga and Lusaka districts, Zambia, were collected between December 2020 and February 2022. Microscopy and DNA extraction facilitated the identification of S. haematobium, followed by amplification, sequencing, and phylogenetic analysis of cox1 and nadh1 genes. Phylogenetic analysis revealed clustering with samples from mainland African countries, emphasizing shared haplotypes. Both mitochondrial genes exhibited substantial diversity, with 5 haplotypes from 37 cox1 sequences and 12 haplotypes from 23 nadh1 sequences. High haplotype diversity (0.621-0.808) and low nucleotide diversity (0.00181-0.03288) were observed. Siavonga and Lusaka districts shared the majority of S. haematobium haplotypes. Molecular variance and genetic differentiation analysis indicated variations within populations rather than between populations (cox1: -0.025, nadh1: 0.01646). These findings suggest a limited differentiation between S. haematobium populations in Siavonga and Lusaka, potentially indicating gene flow. Tajima's test revealed negative values, indicating a departure from neutrality, introduction of rare alleles, and recent population expansion. This study contributes essential insights into S. haematobium population genetics, crucial for effective urogenital schistosomiasis control in Zambia.

Population Genetics of the Endemic Hemiculterella wui (Wang, 1935) in the Poyang Lake Basin (China)

The Yangtze River floodplain is an area with an extremely rich diversity of fish species. Poyang Lake, as an important part of this river–floodplain system, is a crucial habitat for the survival of fish. However, prolonged human activities, such as environmental pollution and hydroelectric development, have degraded the habitat in the Poyang Lake Basin, posing threats to fish populations. Understanding genetic diversity is crucial for maintaining fish populations and understanding their dynamics. The genetic diversity of Hemiculterella wui, an economically endemic species in China of subfamily Cultrinae (Cypriniformes: Cyprinidae), has been understudied. This study investigated the genetic diversity and structure of H. wui populations from the Ganjiang, Xinjiang, Fuhe, and Raohe rivers in the Poyang Lake Basin using mitochondrial Cytb gene analysis. Results showed high haplotype diversity but low nucleotide diversity in H. wui’s Cytb sequences. Analysis of molecular variance (AMOVA) showed no significant geographic genetic structure among populations. Haplotype network analysis revealed no clear geographical clustering. Neutrality tests and haplotype nucleotide mismatch distribution indicated that all populations had experienced expansion events. These findings suggest that H. wui in Poyang Lake does not show a distinct geographic structure. However, it is still necessary to monitor the genetic characteristics of H. wui to maintain the genetic diversity of fishes in Poyang Basin, considering the threat of habitat loss and fragmentation to the population.

Exploring genetic diversity and population structure in Cinnamomum cassia (L.) J.Presl germplasm in China through phenotypic, chemical component, and molecular marker analyses

Cinnamomum cassia (L.) J.Presl, a tropical aromatic evergreen tree belonging to the Lauraceae family, is commonly used in traditional Chinese medicine. It is also a traditional spice used worldwide. However, little is currently known about the extent of the genetic variability and population structure of C. cassia. In this study, 71 individuals were collected from seven populations across two geographical provinces in China. Nine morphological features, three chemical components, and single nucleotide polymorphism (SNP) markers were used in an integrated study of C. cassia germplasm variations. Remarkable genetic variation exists in both phenotypic and chemical compositions, and certain traits, such as leaf length, leaf width, volatile oil content, and geographic distribution, are correlated with each other. One-year-old C. cassia seedling leaf length, leaf width, elevation, and volatile oil content were found to be the main contributors to diversity, according to principal component analysis (PCA). Three major groupings were identified by cluster analysis based on the phenotypic and volatile oil data. This was in line with the findings of related research using 1,387,213 SNP markers; crucially, they all demonstrated a substantial link with geographic origin. However, there was little similarity between the results of the two clusters. Analysis of molecular variance (AMOVA) revealed that the genetic diversity of C. Cassia populations was low, primarily among individuals within populations, accounting for 95.87% of the total. Shannon’s information index (I) varied from 0.418 to 0.513, with a mean of 0.478 (Na=1.860, Ne =1.584, Ho =0.481, He =0.325, and PPB =86.04%). Genetic differentiation across populations was not significant because natural adaptation or extensive exchange of seeds among farmers between environments, thus maintaining the relationship. Following a population structure analysis using the STRUCTURE software, 71 accessions were found to be clustered into three groups, with 38% of them being of the pure type, a finding that was further supported by PCA. Future breeding strategies and our understanding of the evolutionary relationships within the C. cassia population would benefit greatly from a thorough investigation of phenotypic, chemical, and molecular markers.

Genetic diversity and population structure of wheat landraces in Southern Winter Wheat Region of China

BackgroundWheat landraces are considered a valuable source of genetic diversity for breeding programs. It is useful to evaluate the genetic diversity in breeding studies such as marker-assisted selection (MAS), genome-wide association studies (GWAS), and genomic selection. In addition, constructing a core germplasm set that represents the genetic diversity of the entire variety set is of great significance for the efficient conservation and utilization of wheat landrace germplasms.ResultsTo understand the genetic diversity in wheat landrace, 2,023 accessions in the Jiangsu Provincial Crop Germplasm Resource Bank were used to explore the molecular diversity and population structure using the Illumina 15 K single nucleotide polymorphism (SNP) chip. These accessions were divided into five subpopulations based on population structure, principal coordinate and kinship analysis. A significant variation was found within and among the subpopulations based on the molecular variance analysis (AMOVA). Subpopulation 3 showed more genetic variability based on the different allelic patterns (Na, Ne and I). The M strategy as implemented in MStratv 4.1 software was used to construct the representative core collection. A core collection with a total of 311 accessions (15.37%) was selected from the entire landrace germplasm based on genotype and 12 different phenotypic traits. Compared to the initial landrace collections, the core collection displayed higher gene diversity (0.31) and polymorphism information content (PIC) (0.25), and represented almost all phenotypic variation.ConclusionsA core collection comprising 311 accessions containing 100% of the genetic variation in the initial population was developed. This collection provides a germplasm base for effective management, conservation, and utilization of the variation in the original set.

Synthetic Cultivar Development in Cumin: Enhancing Yield and Drought Tolerance

Cumin (Cuminum cyminum L.) is a valuable spice crop with medicinal properties belonging to the Apiaceae family. While farmers often favor the cultivation of cumin, low seed yield, particularly under drought stress, poses challenges to its commercial production. Due to cumin small flowers, self-incompatibility, and cross-pollination attributes, the production of synthetic varieties through polycross breeding can be an effective method for improving seed performance and enhancing drought tolerance in cumin. This study, for the first time, investigates the breeding progress of cumin in three populations over two generations. The first generation resulting from polycross breeding (SYN2 population), along with parental genotypes, was evaluated for agro-morphological traits under normal and low-water irrigation conditions in two locations and compared with the SYN1 population. Additionally, genetic diversity among parental genotypes, SYN1, and SYN2 populations was examined using Start Codon Targeted Polymorphism (SCoT) markers. Low water stress negatively affected all studied traits, except for essential oil content. Improved seed yield, increased drought tolerance, and higher cuminaldehyde content were observed in the SYN2 population compared to parental genotypes. Estimation of genetic parameters indicated a higher heritability and heterosis for traits in the SYN1 population compared to SYN2. Furthermore, trait heritability in the SYN2 population was higher under normal irrigation condition than under water stress. The highest narrow-sense heritability in both SYN1 and SYN2 populations was associated with the thousand-seed weight. Positive and significant phenotypic and genotypic correlations between thousand-seed weight and seed yield were observed in the SYN1 population, while the SYN2 population exhibited the least negative impact of drought stress on this trait. Grouping populations through cluster analysis and principal coordinate analysis based on both molecular and agro-morphological data showed complete concordance, effectively distinguishing cumin populations from one another. The SCoT molecular marker confirmed the homogeneity of the improved populations, demonstrating high efficiency in assessing intra- and inter-population diversity. Molecular variance analysis revealed lower within-population diversity (29%) compared to between-population diversity (71%). Among populations, SYN1, equivalent to F2 generation, exhibited the highest level of molecular diversity based on diversity indices.

Genetic Diversity and Population Structure of a Large USDA Sesame Collection.

Sesame, Sesamum indicum L., is one of the oldest domesticated crops used for its oil and protein in many parts of the world. To build genomic resources for sesame that could be used to improve sesame productivity and responses to stresses, a USDA sesame germplasm collection of 501 accessions originating from 36 countries was used in this study. The panel was genotyped using genotyping-by-sequencing (GBS) technology to explore its genetic diversity and population structure and the relatedness among its accessions. A total of 24,735 high-quality single-nucleotide polymorphism (SNP) markers were identified over the 13 chromosomes. The marker density was 1900 SNP per chromosome, with an average polymorphism information content (PIC) value of 0.267. The marker polymorphisms and heterozygosity estimators indicated the usefulness of the identified SNPs to be used in future genetic studies and breeding activities. The population structure, principal components analysis (PCA), and unrooted neighbor-joining phylogenetic tree analyses classified two distinct subpopulations, indicating a wide genetic diversity within the USDA sesame collection. Analysis of molecular variance (AMOVA) revealed that 29.5% of the variation in this population was due to subpopulations, while 57.5% of the variation was due to variation among the accessions within the subpopulations. These results showed the degree of differentiation between the two subpopulations as well as within each subpopulation. The high fixation index (FST) between the distinguished subpopulations indicates a wide genetic diversity and high genetic differentiation among and within the identified subpopulations. The linkage disequilibrium (LD) pattern averaged 161 Kbp for the whole sesame genome, while the LD decay ranged from 168 Kbp at chromosome LG09 to 123 Kbp in chromosome LG05. These findings could explain the complications of linkage drag among the traits during selections. The selected accessions and genotyped SNPs provide tools to enhance genetic gain in sesame breeding programs through molecular approaches.

Genetic Analysis and Construction of a Fingerprint for Licensed Triadica sebifera Cultivars Using SSR Markers.

Triadica sebifera is an important landscaping tree species because of its colorful autumn leaves. In recent years, some cultivars have been bred and licensed, but it can be difficult to identify them from their morphological traits due to their similar phenotypes. To explore the genetic relationships and construct a fingerprint of the cultivars, the licensed T. sebifera cultivars were analyzed using SSR markers. A total of 179 alleles were identified among the 21 cultivars at 16 SSR loci, and these alleles exhibited a high level of genetic diversity (He = 0.86). The genetic variations mainly occurred among cultivars based on an analysis of molecular variance (AMOVA). According to phylogenetic analysis, principal coordinate analysis (PCoA), and Bayesian clustering analysis, the genetic relationships were independent of geographic distances, which may be mainly due to transplantations between regions. Some cultivars with different leaf colors showed obvious genetic differentiation and may be preliminary candidates for cross-breeding. Finally, the fingerprint for the licensed cultivars was constructed with two SSR markers. The results of this study can provide technical support for the application and legal protection of licensed Triadica sebifera cultivars.

Genetic diversity and population structure of Bellamya purificata in Guangxi.

Bellamya purificata is an important medicinal value and economically farmed species in China. However, because little is known about the genetic characteristics of this species, the utilization of high-quality germplasm resources is hindered. The study examined the genetic differentiation between, and the structure of 12 B. purificata populations in Guangxi using 7 microsatellite DNA markers. High genetic diversity occurred in each population, with mean observed heterozygosity 0.655 and a mean expected heterozygosity 0.832. Analysis of molecular variance reveals genetic diversity to be greater within (95.2%) than among populations (4.8%). Genetic differentiation between populations is weak (Fst = 0.048, P < 0.001), with mixing of genetic clusters prevalent at the level of the individual. Genetic flow exists between populations (Nm = 3.084-11.778), with Longshui and Guilin populations exchanging frequently. A Mantel test reveals a low correlation between geographic and genetic distances (r = 0.2482, P < 0.071), suggesting that dispersal between neighboring populations facilitates population exchange. No significant heterozygosity excess was observed for any population (P > 0.05), indicating a lack of recent genetic bottlenecks. The results provide important genetic information for B. purificata, and data for potential germplasm discovery and aquaculture development.

Population structure and diversification of Gymnospermium kiangnanense, a plant species with extremely small populations endemic to eastern China

Background Gymnospermium kiangnanense is the only species distributed in the subtropical region within the spring ephemeral genus Gymnospermium. Extensive human exploitation and habitat destruction have resulted in a rapid shrink of G. kiangnanense populations. This study utilizes microsatellite markers to analyze the genetic diversity and structure and to deduce historical population events of extant populations of G. kiangnanense. Methods A total of 143 individuals from eight extant populations of G. kiangnanense, including two populations from Anhui Province and six populations from Zhejiang Province, were analyzed with using 21 pairs of microsatellite markers. Genetic diversity indices were calculated using Cervus, GENEPOP, GenALEX. Population structure was assessed using genetic distance (UPGMA), principal coordinate analysis (PCoA), Bayesian clustering method (STRUCTURE), and molecular variation analysis of variance (AMOVA). Population history events were inferred using DIYABC. Results The studied populations of G. kiangnanense exhibited a low level of genetic diversity (He = 0.179, I = 0.286), but a high degree of genetic differentiation (FST = 0.521). The mean value of gene flow (Nm) among populations was 1.082, indicating prevalent gene exchange via pollen dispersal. Phylogeographic analyses suggested that the populations of G. kiangnanense were divided into two lineages, Zhejiang (ZJ) and Anhui (AH). These two lineages were separated by the Huangshan-Tianmu Mountain Range. AMOVA analysis revealed that 36.59% of total genetic variation occurred between the two groups. The ZJ lineage was further divided into the Hangzhou (ZJH) and Zhuji (ZJZ) lineages, separated by the Longmen Mountain and Fuchun River. DIYABC analyses suggested that the ZJ and AH lineages were separated at 5.592 ka, likely due to the impact of Holocene climate change and human activities. Subsequently, the ZJZ lineage diverged from the ZJH lineage around 2.112 ka. Given the limited distribution of G. kiangnanense and the significant genetic differentiation among its lineages, both in-situ and ex-situ conservation strategies should be implemented to protect the germplasm resources of G. kiangnanense.

Characterisation of the Cinnamomumparthenoxylon (Jack) Meisn (Lauraceae) transcriptome using Illumina paired-end sequencing and EST-SSR markers development for population genetics.

Cinnamomumparthenoxylon is an endemic and endangered species with significant economic and ecological value in Vietnam. A better understanding of the genetic architecture of the species will be useful when planning management and conservation. We aimed to characterize the transcriptome of C.parthenoxylon, develop novel molecular markers, and assess the genetic variability of the species. First, transcriptome sequencing of five trees (C.parthenoxylon) based on root, leaf, and stem tissues was performed for functional annotation analysis and development of novel molecular markers. The transcriptomes of C.parthenoxylon were analyzed via an Illumina HiSeqTM 4000 sequencing system. A total of 27,363,199 bases were generated for C.parthenoxylon. De novo assembly indicated that a total of 160,435 unigenes were generated (average length = 548.954 bp). The 51,691 unigenes were compared against different databases, i.e. COG, GO, KEGG, KOG, Pfam, Swiss-Prot, and NR for functional annotation. Furthermore, a total of 12,849 EST-SSRs were identified. Of the 134 primer pairs, 54 were randomly selected for testing, with 15 successfully amplified across nine populations of C.parthenoxylon. We uncovered medium levels of genetic diversity (PIC = 0.52, Na = 3.29, Ne = 2.18, P = 94.07%, Ho = 0.56 and He = 0.47) within the studied populations. The molecular variance was 10% among populations and low genetic differentiation (Fst = 0.06) indicated low gene flow (Nm = 2.16). A reduction in the population size of C.parthenoxylon was detected using BOTTLENECK (VP population). The structure analysis suggested two optimal genetic clusters related to gene flow among the populations. Analysis of molecular variance (AMOVA) revealed higher genetic variation within populations (90%) than among populations (10%). The UPGMA approach and DAPC divided the nine populations into three main clusters. Our findings revealed a significant fraction of the transcriptome sequences and these newlydeveloped novel EST-SSR markers are a very efficient tool for germplasm evaluation, genetic diversity and molecular marker-assisted selection in C.parthenoxylon. This study provides comprehensive genetic resources for the breeding and conservation of different varieties of C.parthenoxylon.

Phylogenetic Diversity, Host Specificity, and Distribution of the Wood-Decaying Fungus Phellinotus teixeirae in Western Colombia’s Seasonally Dry Tropical Forest

Phellinotus (Polyporales) is a common genus of wood-decay fungi in tropical and subtropical areas, endemic to the Seasonally Dry Tropical Forest (SDTF) biome. However, Phellinotus diversity remains unexplored, despite being a major threat to living trees. Therefore, this study is aimed at confirming and characterizing through morphological and molecular data the first isolates of Phellinotus teixeirae in Pithecellobium dulce (Fabaceae) trees (locally referred to as ‘Chiminango’) from the endangered Colombian SDTF biome. Fifteen fungal specimens were recovered from living P. dulce trees, in the urban area and at the Universidad del Valle campus, and classified as P. teixeirae based on taxonomical descriptors. Phylogenetic relationships were inferred from a four-loci dataset (ribosomal and gene-coding regions), including 82 taxa covering 3991 nucleotide positions. The analysis recovered seven highly supported (&gt;90% bootstrapping) monophyletic taxa of the ‘Phellinotus Clade’, and confirmed the new distribution range of P. teixeirae (100% bootstrap support), which extends approx. 1000 km north in the Neotropics. Hierarchical stratified Analysis of MOlecular VAriance (AMOVA) provided a clear genetic distinction between species (70% of variation, p-value = 0.001) and low differentiation among country of origin within species (11%, p-value = 0.044). Discriminant Analysis for Principal Components (DAPC) indicated complex clustering including closely related species, probably a signal of recent radiation and weak species boundaries. Median-joining haplotype network analysis identified unique haplotypes, which may correlate with new host colonization and population expansion (Tajima’s D ≤ −0.5). In conclusion, this study provides the first assessment of the genetic diversity of P. teixeirae in a novel geography (SDTP) and host tree (P. dulce). However, increasing the number of isolates remains critical to understand further the genus’ distribution patterns and drivers of genetic diversity.

Exploring cannabidiol variations, investigation of genetic diversity, population structure and unveiling male-specific genetic marker in industrial hemp (Cannabis sativa L.)

AbstractCannabis sativa played a pivotal role across different industries. Recently, industrial hemp, particularly in the case of Cannabidiol (CBD), gained attention for its therapeutic potential. This study evaluated cannabinoid variability and genetic diversity within 43 industrial hemp individuals, primarily Turkish, across various plant parts and growth stages, and inflorescences of females showed significant CBD content. The highest contents were observed in Turkish landraces (0.55–8.05% with an average of 3.26%), making them valuable genetic resources for high CBD. Genetic structure revealed distinct populations based on gender and influenced by geographical origin. Analysis of Molecular Variance showed 92% of genetic variation observed within populations and indicated a promising source of novel allelic diversity in the Turkish gene pool. Turkish females showed significant genetic diversity [No. of Different Alleles (Na) 1.507, No. of Effective Alleles (Ne) 1.226, Shannon’s Information Index (I) 0.258, and Percentage of Polymorphic Loc (%P) 74.91], exhibiting richer genetic variation than their international peers. Principal Coordinate Analysis unveiled gender-specific genetic differences, and admixture clusters shed light on genetic interactions and historical connections among diverse populations. Unweighted Pair-Group Method with Arithmetic Averaging highlighted unique genetic profiles and distinct genetic lineages. Genome-wide association study revealed a highly significant male-specific genetic marker explained 50% of the phenotypic variation. These findings inform future breeding strategies and conservation efforts and contribute to varietal identification methods, Marker-Assisted Selection, and efficient cultivar development in upcoming programs.

Genetic connectivity of the common octopus (Octopus insularis) along the southwestern Caribbean

AbstractOctopus insularis is a shallow‐water octopus distributed throughout the western Atlantic, the Gulf of Mexico and the Caribbean. To evaluate its phylogeographic pattern, mitochondrial markers (16S rRNA and COIII) and genome‐wide nuclear markers (SNP's) were analyzed in individuals from artisanal fishing in different locations of the Colombian Caribbean coast. Mitochondrial analyzes displayed novel haplotypes (16S = H2, H3 and H4; COIII = H2–H7) and haplotypes shared with distant geographic areas (16S = H1 COIII = H1). The COIII gene did not show genetic differentiation between the analyzed localities, while the 16S gene showed significant differences between Santa Marta and Isla Fuerte. COIII's demographic analysis indicated that the species' effective population size has remained constant. Inferences were made from next‐generation genomic data with restriction site‐associated DNA (ddRAD‐seq) and 6769 polymorphic loci. The pairwise FST test indicated that there are low but significant differences between localities; however, the general molecular analysis of variance (AMOVA) and the principal coordinate analysis showed a lack of spatial structure in the populations analyzed. The Mantel test found no correlation between genetic distance and geographic distance, and the genetic structure analyses showed the presence of one genetic stock. The information obtained in this study indicates the genetic connectivity of O. insularis in the southwestern Caribbean, the absence of putative biogeographic barriers that affect its gene flow, and the crucial role played by life history strategies (planktonic paralarvae) and oceanographic factors to define the current distribution of its genetic diversity in this region.

Morphological and genetic characterization of jackfruit (Artocarpus heterophyllus) in the Kayunga and Luwero districts of Uganda

BackgroundJackfruit (Artocarpus heterophyllus) is an economically valuable fruit tree in Uganda. However, the production of jackfruit in Uganda is low. Additionally, because of deforestation, genetic erosion of the resource is predicted before its exploitation for crop improvement and conservation. As a prerequisite for crop improvement and conservation, 100 A. heterophyllus tree isolates from the Kayunga and Luwero districts in Uganda were characterized using 16 morphological and 10 microsatellite markers.ResultsThe results from the morphological analysis revealed variations in tree height, diameter at breast height (DBH), and crown diameter, with coefficient of variation (CV) values of 20%, 41%, and 33%, respectively. Apart from the pulp taste, variation was also observed in qualitative traits, including tree vigor, trunk surface, branching density, tree growth habit, crown shape, leaf blade shape, fruit shape, fruit surface, flake shape, flake color, flake flavor and pulp consistency/texture. Genotyping revealed that the number of alleles amplified per microsatellite locus ranged from 2 to 5, with an average of 2.90 and a total of 29. The mean observed (Ho) and expected (He) heterozygosity were 0.71 and 0.57, respectively. Analysis of molecular variance (AMOVA) indicated that 81% of the variation occurred within individual trees, 19% among trees within populations and 0% between the two populations. The gene flow (Nm) in the two populations was 88.72. The results from the ‘partitioning around medoids’ (PAM), principal coordinate analysis (PCoA) and genetic cluster analysis further revealed no differentiation of the jackfruit populations. The Mantel test revealed a negligible correlation between the morphological and genetic distances.ConclusionsBoth morphological and genetic analyses revealed variation in jackfruit within a single interbreeding population. This diversity can be exploited to establish breeding and conservation strategies to increase the production of jackfruit and hence boost farmers’ incomes. However, selecting germplasm based on morphology alone may be misleading.

Genetic Diversity, Linkage Disequilibrium, and Population Structure in a Common Bean Reference Collection

An in-depth understanding of the extent and pattern of genetic diversity and population structure in crop populations is of paramount importance for any crop improvement program to efficiently promote the translation of genetic diversity into genetic gain. A reference collection of 150 common bean genotypes selected from the International Center for Tropical Agriculture’s global core collection was evaluated using single-nucleotide polymorphism (SNP) markers to quantify the amount of genetic diversity, linkage disequilibrium, and population structure. The cultivars and landraces of the collection were diverse and originated from 14 countries, and wild accessions were used as controls for each gene pool. The collection was genotyped using an SNP array, generating a total of 5398 locus calls distributed across the entire bean genome. The SNP data quality was checked, and two datasets were generated. The first dataset (Dataset_1) comprised a set of 5108 SNPs and 150 genotypes after filtering for 10% missing alleles and an MAF &lt; 0.05. The second dataset (Dataset_2) comprised a set of 2300 SNPs that remained after removing any null-allele SNPs and LD pruning for a criterion of r2 &lt; 0.2. Dataset_1 was used for a principal coordinate analysis (PCoA), phylogenetic relationship determination, an analysis of molecular variance (AMOVA), and a discriminant analysis of principal components. Dataset_2 was used for a population structure analysis using STRUCTURE software and is proposed for a genome-wide association study (GWAS). The population structure analysis split the reference collection into two subpopulations according to an Andean or Mesoamerican gene pool. The Mesoamerican populations displayed higher genetic differentiation and tended to split into more groups that were somewhat aligned with common bean races. Andean beans were characterized by a larger average LD but lower LD percentage, a small average genetic distance between members of the population, and a higher major allele frequency, which suggested narrower genetic diversity compared to the Mesoamerican gene pool. In conclusion, the results indicated the presence of high genetic diversity, which is useful for a GWAS. However, the presence of significant linkage disequilibrium requires that genetic distance be considered as a co-factor for any further genetic studies. Overall, the molecular variation observed in the genotypes shows that this reference collection is valuable as a genebank-derived diversity panel which is useful for marker trait association studies.

Genomic characterization of the Brazilian Crioulo Lageano: Insights for conservation of a Brazilian local bovine breed

Crioulo Lageano (CLAG) is a Brazilian taurine breed traditionally raised in the native fields of mountainous regions in the states of Santa Catarina and Paraná, located in the southern region from Brazil. The present study aimed to analyze the genetic diversity and structure of the breed to provide the basis for the development of strategies for its conservation. Samples from semen and DNA previously stored in the Brazilian Animal Gene Bank (BAGB), and samples collected from eight different farms registered in the Brazilian Association of Crioulo Lageano Cattle Breeders (ABCCL), were genotyped with different panels of SNP markers containing between 50 K and 777 K markers. Obtained estimates of average expected (HE = 0.373) and observed (HO = 0.382) heterozygosities suggest the presence of high levels of genetic variability in the breed. Molecular analysis of variance (AMOVA) revealed that only 2.11 % of the observed genetic variation could be attributed to differences between analyzed populations. Obtained pairwise FST estimates varied between 0.002 and 0.056, corroborating that the degree of differentiation between populations is low. Population structure analyses showed substructures between the studied populations, which could be related to the presence/absence of horns in the animals, in addition to other factors. The estimates obtained for the effective population size (Ne) considering bulls with semen stored in BGAB and the set of samples from the eight studied farms were 6 and 22, respectively, revealing that the Ne of the breed is far below that recommended by FAO for conservation of domestic animal populations. Population structure and admixture analyses comparing CLAG with six other taurine and zebu cattle breeds routinely raised in the region revealed evidence of possible unknown introgressions from animals of indicine origin. Obtained results provide solid insights into the diversity and genetic structure of the Brazilian CLGA breed and offer strategic information for the establishment of effective genetic management strategies for production herds, for the enrichment of the BAGB by collecting germoplasm and for the long-term conservation of this breed.

Applicability of SCoT markers in unraveling genetic variation and population structure among sugar beet (Beta vulgaris L.) germplasm.

Sugar beet (Beta vulgaris L.) holds significant importance as a crop globally cultivated for sugar production. The genetic diversity present in sugar beet accessions plays a crucial role in crop improvement programs. During the present study, we collected 96 sugar beet accessions from different regions and extracted DNA from their leaves. Genomic DNA was amplified using SCoT primers, and the resulting fragments were separated by gel electrophoresis. The data were analyzed using various genetic diversity indices, and constructed a population STRUCTURE, applied the unweighted pair-group method with arithmetic mean (UPGMA), and conducted Principle Coordinate Analysis (PCoA). The results revealed a high level of genetic diversity among the sugar beet accessions, with 265 bands produced by the 10 SCoT primers used. The percentage of polymorphic bands was 97.60%, indicating substantial genetic variation. The study uncovered significant genetic variation, leading to higher values for overall gene diversity (0.21), genetic distance (0.517), number of effective alleles (1.36), Shannon's information index (0.33), and polymorphism information contents (0.239). The analysis of molecular variance suggested a considerable amount of genetic variation, with 89% existing within the population. Using STRUCTURE and UPGMA analysis, the sugar beet germplasm was divided into two major populations. Structure analysis partitioned the germplasm based on the origin and domestication history of sugar beet, resulting in neighboring countries clustering together. The utilization of SCoT markers unveiled a noteworthy degree of genetic variation within the sugar beet germplasm in this study. These findings can be used in future breeding programs with the objective of enhancing both sugar beet yield and quality.

Effects of past riverine connectivity on the population structure and species distribution of ‘Geophagus’ brasiliensis (Cichlidae) complex in a Neotropical hotspot

Abstract Once fishes and rivers are intrinsically connected, historical events such as river captures and the reconfiguration of palaeodrainages affect population structure and species distribution. However, direct evidence of these events remains limited. We aimed to directly infer putative connections between adjacent river basins to understand genetic and geographical patterns in populations and species of the ‘Geophagus’ brasiliensis complex. For that, we analysed 174 sequences of the mitochondrial gene cytochrome c oxidase subunit I (COI) from five species along 35 sites within and near a coastal basin in northeastern Brazil. Based on haplotype network, palaeodrainage reconstruction, geological inferences of river captures and analyses of molecular variance (AMOVAs), we tested how the genetic structure could be associated with variable patterns of habitat connectivity through time. In general, high levels of genetic variation were identified, including shared haplotypes among drainages for most species. AMOVA suggested that drainage rearrangements between adjacent basins were the main drivers of genetic diversification in the ‘G.’ brasiliensis complex. Our study refuted dispersal routes via the continental shelf, whereas eight putative river captures suggested historical connections that enabled gene flow among drainages until recent interruption. These results provide novel insights on the role of riverscape evolution on the biogeography of neotropical ichthyofauna.

Does the Artificial Enhancement and Release Activity Affect the Genetic Diversity of Marbled Rockfish Sebastiscus marmoratus in Zhoushan Waters?

Artificial enhancement and release activity is an important method in the restoration of fishery resources. In order to understand the possible genetic effect of hatchery-released populations on wild populations during the artificial enhancement and release activities of Sebastiscus marmoratus in Zhoushan waters, we utilized mitochondrial DNA control region sequences to examine the genetic diversity in four S. marmoratus populations, including one farmed population, one released population and two wild populations. A total of 68 haplotypes from 123 individuals were detected, including 3 shared haplotypes. Haplotype diversity ranged from 0.944 to 0.980, with a mean of 0.966. The nucleotide diversity ranged from 0.020 to 0.025, with a mean of 0.022. Analysis of Molecular Variance (AMOVA) indicated that the primary genetic variation occurs within populations and the index of genetic differentiation between populations (FST) among the four populations showed no differentiation. The results indicate that the current artificial enhancement and release has not impacted the S. marmoratus population in Zhoushan waters. Continued long-term monitoring is essential to protect the high-quality germplasm resources of S. marmoratus.