Exploring the Genetic Diversity and Population Structure of Wheat Landrace Population Conserved at ICARDA Genebank.

Landraces are considered a valuable source of potential genetic diversity that could be used in the selection process in any plant breeding program. Here, we assembled a population of 600 bread wheat landraces collected from eight different countries, conserved at the ICARDA's genebank, and evaluated the genetic diversity and the population structure of the landraces using single nucleotide polymorphism (SNP) markers. A total of 11,830 high-quality SNPs distributed across the genomes A (40.5%), B (45.9%), and D (13.6%) were used for the final analysis. The population structure analysis was evaluated using the model-based method (STRUCTURE) and distance-based methods [discriminant analysis of principal components (DAPC) and principal component analysis (PCA)]. The STRUCTURE method grouped the landraces into two major clusters, with the landraces from Syria and Turkey forming two clusters with high proportions of admixture, whereas the DAPC and PCA analysis grouped the population into three subpopulations mostly according to the geographical information of the landraces, i.e., Syria, Iran, and Turkey with admixture. The analysis of molecular variance revealed that the majority of the variation was due to genetic differences within the populations as compared with between subpopulations, and it was the same for both the cluster-based and distance-based methods. Genetic distance analysis was also studied to estimate the differences between the landraces from different countries, and it was observed that the maximum genetic distance (0.389) was between the landraces from Spain and Palestine, whereas the minimum genetic distance (0.013) was observed between the landraces from Syria and Turkey. It was concluded from the study that the model-based methods (DAPC and PCA) could dissect the population structure more precisely when compared with the STRUCTURE method. The population structure and genetic diversity analysis of the bread wheat landraces presented here highlight the complex genetic architecture of the landraces native to the Fertile Crescent region. The results of this study provide useful information for the genetic improvement of hexaploid wheat and facilitate the use of landraces in wheat breeding programs.

Genome-Wide Assessment of Population Structure and Genetic Diversity of the Global Finger Millet Germplasm Panel Conserved at the ICRISAT Genebank.

Finger millet [Eleusine coracana (L.) Gaertn.] is an important climate-resilient nutrient-dense crop grown as a staple food grain in Asia and Africa. Utilizing the full potential of the crop mainly depends on an in-depth exploration of the vast diversity in its germplasm. In this study, the global finger millet germplasm diversity panel of 314 accessions was genotyped, using the DArTseq approach to assess genetic diversity and population structure. We obtained 33,884 high-quality single nucleotide polymorphism (SNP) markers on 306 accessions after filtering. Finger millet germplasm showed considerable genetic diversity, and the mean polymorphic information content, gene diversity, and Shannon Index were 0.110, 0.114, and 0.194, respectively. The average genetic distance of the entire set was 0.301 (range 0.040 - 0.450). The accessions of the race elongata (0.326) showed the highest average genetic distance, and the least was in the race plana (0.275); and higher genetic divergence was observed between elongata and vulgaris (0.320), while the least was between compacta and plana (0.281). An average, landrace accessions had higher gene diversity (0.144) and genetic distance (0.299) than the breeding lines (0.117 and 0.267, respectively). A similar average gene diversity was observed in the accessions of Asia (0.132) and Africa (0.129), but Asia had slightly higher genetic distance (0.286) than African accessions (0.276), and the distance between these two regions was 0.327. This was also confirmed by a model-based STRUCTURE analysis, genetic distance-based clustering, and principal coordinate analysis, which revealed two major populations representing Asia and Africa. Analysis of molecular variance suggests that the significant population differentiation was mainly due to within individuals between regions or between populations while races had a negligible impact on population structure. Finger millet diversity is structured based on a geographical region of origin, while the racial structure made negligible contribution to population structure. The information generated from this study can provide greater insights into the population structure and genetic diversity within and among regions and races, and an understanding of genomic-assisted finger millet improvement.

Elucidating SNP-based genetic diversity and population structure of advanced breeding lines of bread wheat (Triticum aestivum L.).

Genetic diversity and population structure information are crucial for enhancing traits of interest and the development of superlative varieties for commercialization. The present study elucidated the population structure and genetic diversity of 141 advanced wheat breeding lines using single nucleotide polymorphism markers. A total of 14,563 high-quality identified genotyping-by-sequencing (GBS) markers were distributed covering 13.9 GB wheat genome, with a minimum of 1,026 SNPs on the homoeologous group four and a maximum of 2,838 SNPs on group seven. The average minor allele frequency was found 0.233, although the average polymorphism information content (PIC) and heterozygosity were 0.201 and 0.015, respectively. Principal component analyses (PCA) and population structure identified two major groups (sub-populations) based on SNPs information. The results indicated a substantial gene flow/exchange with many migrants (Nm = 86.428) and a considerable genetic diversity (number of different alleles, Na = 1.977; the number of effective alleles, Ne = 1.519; and Shannon's information index, I = 0.477) within the population, illustrating a good source for wheat improvement. The average PIC of 0.201 demonstrates moderate genetic diversity of the present evaluated advanced breeding panel. Analysis of molecular variance (AMOVA) detected 1% and 99% variance between and within subgroups. It is indicative of excessive gene traffic (less genetic differentiation) among the populations. These conclusions deliver important information with the potential to contribute new beneficial alleles using genome-wide association studies (GWAS) and marker-assisted selection to enhance genetic gain in South Asian wheat breeding programs.

AlleleShift: an R package to predict and visualize population-level changes in allele frequencies in response to climate change.

BACKGROUND: At any particular location, frequencies of alleles that are associated with adaptive traits are expected to change in future climates through local adaption and migration, including assisted migration (human-implemented when climate change is more rapid than natural migration rates). Making the assumption that the baseline frequencies of alleles across environmental gradients can act as a predictor of patterns in changed climates (typically future but possibly paleo-climates), a methodology is provided by AlleleShift of predicting changes in allele frequencies at the population level. METHODS: The prediction procedure involves a first calibration and prediction step through redundancy analysis (RDA), and a second calibration and prediction step through a generalized additive model (GAM) with a binomial family. As such, the procedure is fundamentally different to an alternative approach recently proposed to predict changes in allele frequencies from canonical correspondence analysis (CCA). The RDA step is based on the Euclidean distance that is also the typical distance used in Analysis of Molecular Variance (AMOVA). Because the RDA step or CCA approach sometimes predict negative allele frequencies, the GAM step ensures that allele frequencies are in the range of 0 to 1. RESULTS: AlleleShift provides data sets with predicted frequencies and several visualization methods to depict the predicted shifts in allele frequencies from baseline to changed climates. These visualizations include 'dot plot' graphics (function shift.dot.ggplot), pie diagrams (shift.pie.ggplot), moon diagrams (shift.moon.ggplot), 'waffle' diagrams (shift.waffle.ggplot) and smoothed surface diagrams of allele frequencies of baseline or future patterns in geographical space (shift.surf.ggplot). As these visualizations were generated through the ggplot2 package, methods of generating animations for a climate change time series are straightforward, as shown in the documentation of AlleleShift and in the supplemental videos. AVAILABILITY: AlleleShift is available as an open-source R package from https://cran.r-project.org/package=AlleleShift and https://github.com/RoelandKindt/AlleleShift. Genetic input data is expected to be in the adegenet::genpop format, which can be generated from the adegenet::genind format. Climate data is available from various resources such as WorldClim and Envirem.

A generalized framework for AMOVA with multiple hierarchies and ploidies.

The analysis of molecular variance (AMOVA) is a widely used statistical method in population genetics and molecular ecology. The classic framework of AMOVA only supports haploid and diploid data, in which the number of hierarchies ranges from two to four. In practice, natural populations can be classified into more hierarchies, and polyploidy is frequently observed in extant species. The ploidy level may even vary within the same species, and/or within the same individual. We generalized the framework of AMOVA such that it can be used for any number of hierarchies and any level of ploidy. Based on this framework, we present four methods to account for data that are multilocus genotypic and allelic phenotypic (with unknown allele dosage). We use simulated datasets and an empirical dataset to evaluate the performance of our framework. We make freely available our methods in a new software package, polygene, which is freely available at https://github.com/huangkang1987/polygene.

Genetic diversity and population structure of Camellia huana (Theaceae), a limestone species with narrow geographic range, based on chloroplast DNA sequence and microsatellite markers.

Camellia huana is an endangered species with a narrow distribution in limestone hills of northern Guangxi and southern Guizhou provinces, China. We used one chloroplast DNA (cpDNA) fragment and 12 pairs of microsatellite (simple sequence repeat; SSR) markers to assess the genetic diversity and structure of 12 C. huana populations. A total of 99 alleles were detected for 12 polymorphic loci, and eight haplotypes and nine polymorphic sites were detected within 5200 bp of cpDNA. C. huana populations showed a low level of genetic diversity (n = 8, Hd = 0.759, Pi = 0.00042 for cpDNA, N A  = 3.931, H E  = 0.466 for SSRs), but high genetic differentiation between populations (F ST  = 0.2159 for SSRs, F ST  = 0.9318 for cpDNA). This can be attributed to the narrow distribution and limestone habitat of C. huana. STRUCTURE analysis divided natural C. huana populations into two groups, consistent with their geographical distribution. Thus, we suggest that five natural C. huana populations should be split into two units to be managed effectively.

Molecular genetic analysis of spring wheat core collection using genetic diversity, population structure, and linkage disequilibrium.

BACKGROUND: Wheat (Triticum aestivium L.) is an important crop globally which has a complex genome. To identify the parents with useful agronomic characteristics that could be used in the various breeding programs, it is very important to understand the genetic diversity among global wheat genotypes. Also, understanding the genetic diversity is useful in breeding studies such as marker-assisted selection (MAS), genome-wide association studies (GWAS), and genomic selection. RESULTS: To understand the genetic diversity in wheat, a set of 103 spring wheat genotypes which represented five different continents were used. These genotypes were genotyped using 36,720 genotyping-by-sequencing derived SNPs (GBS-SNPs) which were well distributed across wheat chromosomes. The tested 103-wheat genotypes contained three different subpopulations based on population structure, principle coordinate, and kinship analyses. A significant variation was found within and among the subpopulations based on the AMOVA. Subpopulation 1 was found to be the more diverse subpopulation based on the different allelic patterns (Na, Ne, I, h, and uh). No high linkage disequilibrium was found between the 36,720 SNPs. However, based on the genomic level, D genome was found to have the highest LD compared with the two other genomes A and B. The ratio between the number of significant LD/number of non-significant LD suggested that chromosomes 2D, 5A, and 7B are the highest LD chromosomes in their genomes with a value of 0.08, 0.07, and 0.05, respectively. Based on the LD decay, the D genome was found to be the lowest genome with the highest number of haplotype blocks on chromosome 2D. CONCLUSION: The recent study concluded that the 103-spring wheat genotypes and their GBS-SNP markers are very appropriate for GWAS studies and QTL-mapping. The core collection comprises three different subpopulations. Genotypes in subpopulation 1 are the most diverse genotypes and could be used in future breeding programs if they have desired traits. The distribution of LD hotspots across the genome was investigated which provides useful information on the genomic regions that includes interesting genes.

Genetic diversity and population structure analysis of synthetic and bread wheat accessions in Western Siberia.

Recurrent selection and intercrossing between best of the best parents in each generation of breeding cycle resulted in a narrower genetic diversity in elite wheat (Triticum aestivum L.) germplasm. Therefore, we investigated diverse source of 143 synthetic and bread wheat accessions for identifying potentially rich genetic resources for improving the genetic diversity in wheat. This study identified 47,526 genotyping-by-sequencing-derived SNP markers that were nearly evenly distributed across three genomes of wheat. The population structure analysis identified three distinct clusters (Japan synthetics, CIMMYT synthetics, and bread wheat) of wheat genotypes on the basis of type and geographical origin of wheat accessions. Population differentiation using analysis of molecular variance indicated 21% of the total genetic variance among subgroups and the remainder within subgroups. This study also identified that the Japan synthetic group was the most divergent group compared with other subgroups. The genetic diversity comparisons between synthetic and bread wheat lines showed that the gene diversity of synthetic wheat was 33% higher than bread wheat accessions, indicating the potential use of these lines for broadening the genetic diversity of modern wheat cultivars. The results from this study will be helpful in further understanding genomic features of wheat and facilitate their use in wheat breeding programs.

Genetic Diversity and Population Structure of a Camelina sativa Spring Panel.

There is a need to explore renewable alternatives (e.g., biofuels) that can produce energy sources to help reduce the reliance on fossil oils. In addition, the consumption of fossil oils adversely affects the environment and human health via the generation of waste water, greenhouse gases, and waste solids. Camelina sativa, originated from southeastern Europe and southwestern Asia, is being re-embraced as an industrial oilseed crop due to its high seed oil content (36-47%) and high unsaturated fatty acid composition (>90%), which are suitable for jet fuel, biodiesel, high-value lubricants and animal feed. C. sativa's agronomic advantages include short time to maturation, low water and nutrient requirements, adaptability to adverse environmental conditions and resistance to common pests and pathogens. These characteristics make it an ideal crop for sustainable agricultural systems and regions of marginal land. However, the lack of genetic and genomic resources has slowed the enhancement of this emerging oilseed crop and exploration of its full agronomic and breeding potential. Here, a core of 213 spring C. sativa accessions was collected and genotyped. The genotypic data was used to characterize genetic diversity and population structure to infer how natural selection and plant breeding may have affected the formation and differentiation within the C. sativa natural populations, and how the genetic diversity of this species can be used in future breeding efforts. A total of 6,192 high-quality single nucleotide polymorphisms (SNPs) were identified using genotyping-by-sequencing (GBS) technology. The average polymorphism information content (PIC) value of 0.29 indicate moderate genetic diversity for the C. sativa spring panel evaluated in this report. Population structure and principal coordinates analyses (PCoA) based on SNPs revealed two distinct subpopulations. Sub-population 1 (POP1) contains accessions that mainly originated from Germany while the majority of POP2 accessions (>75%) were collected from Eastern Europe. Analysis of molecular variance (AMOVA) identified 4% variance among and 96% variance within subpopulations, indicating a high gene exchange (or low genetic differentiation) between the two subpopulations. These findings provide important information for future allele/gene identification using genome-wide association studies (GWAS) and marker-assisted selection (MAS) to enhance genetic gain in C. sativa breeding programs.

Genetic diversity and population structure among 133 elite genotypes of sugarcane (Saccharum spp.) for use as parents in sugarcane varietal improvement.

A measure of genetic diversity of genotypes to be used as parents is imperative to use them prudently in crop improvement. In this study, genetic diversity and population structure of 133 sugarcane hybrid derivatives were quantified using 20 sequence-tagged microsatellite sites (STMS) primers. The number of alleles ranged from 9 to 27 with the average of 17.95 alleles per primer, while the polymorphism information content values of the primers ranged from 0.29 to 0.78. Cophenetic correlation coefficient value observed as 0.84 by STMS markers revealed that the cluster result was acceptable for the calculation of genetic similarity matrix. Principal component analysis showed that 133 genotypes fell in two groups, first and second components associated 8.34 and 3.22% with eigen values of 5.61 and 2.17, respectively. Similar trend was observed with principal coordinate analysis, wherein, the first and second component accounted to 8.34 and 3.22% with eigen values of 741.29 and 286.11. The similarity index values ranged from 0.50 to 0.87 for the possible 8778 combinations from 133 genotypes, of which 8069 combinations exhibited less/moderate genetic similarity indicating the availability of sufficient genetic diversity in the experimental material and hence their value in the genetic improvement of sugarcane. Dissimilarity analysis using DARwin of 133 genotypes could distinguish two major clusters and into five subclusters and the results matched with those of the population structure which also showed five subpopulations. The bigger group SP1 was predominantly comprised of clones developed at the main sugarcane-breeding place in India, located at Coimbatore. The subpopulation SP4 was formed largely with clones from research stations other than at Coimbatore and interspecific hybrids, while SP5 comprised of clones of early origin. These observations were similar to the radial tree based on the DARwin software in that 81.95% of the genotypes of each cluster were similar in the two analyses. The results thus showed that location and time of origin were two major factors that contributed to diversity. Based on analysis of molecular variance, subpopulations SP2 and SP4 were more variable from the rest. SP2 (comprising of Co 99008, Co 99006, Co 94012, Co 93023, CoC 671, Co 89034, Co 91003, Co 06022, Co 98017, Co 87044, Co 06018, Co 89003, Co 98014, and Co 86032) exhibited maximum genetic variation, the least gene flow, and the lowest heterozygosity value and would serve as the best group for utilization in genetic improvement. Graphical genotyping (GGT) image of each genotype was distinctly different, indicating the genetic uniqueness of sugarcane genotypes under study as revealed through STMS technology. A core set of 40 genotypes was identified using GGT 2.0 software program for the easiness of harnessing the available genetic diversity of 133 genotypes, through hybridization in sugarcane improvement programs.

Evaluation of genetic diversity of Panicum turgidum Forssk from Saudi Arabia.

The genetic diversity of 177 accessions of Panicum turgidum Forssk, representing ten populations collected from four geographical regions in Saudi Arabia, was analyzed using amplified fragment length polymorphism (AFLP) markers. A set of four primer-pairs with two/three selective nucleotides scored 836 AFLP amplified fragments (putative loci/genome landmarks), all of which were polymorphic. Populations collected from the southern region of the country showed the highest genetic diversity parameters, whereas those collected from the central regions showed the lowest values. Analysis of molecular variance (AMOVA) revealed that 78% of the genetic variability was attributable to differences within populations. Pairwise values for population differentiation and genetic structure were statistically significant for all variances. The UPGMA dendrogram, validated by principal coordinate analysis-grouped accessions, corresponded to the geographical origin of the accessions. Mantel's test showed that there was a significant correlation between the genetic and geographical distances (r = 0.35, P < 0.04). In summary, the AFLP assay demonstrated the existence of substantial genetic variation in P. turgidum. The relationship between the genetic diversity and geographical source of P. turgidum populations of Saudi Arabia, as revealed through this comprehensive study, will enable effective resource management and restoration of new areas without compromising adaptation and genetic diversity.

Parallel Patterns of Host-Specific Morphology and Genetic Admixture in Sister Lineages of a Commensal Barnacle.

Symbiotic relationships are often species specific, allowing symbionts to adapt to their host environments. Host generalists, on the other hand, have to cope with diverse environments. One coping strategy is phenotypic plasticity, defined by the presence of host-specific phenotypes in the absence of genetic differentiation. Recent work indicates that such host-specific phenotypic plasticity is present in the West Pacific lineage of the commensal barnacle Chelonibia testudinaria (Linnaeus, 1758). We investigated genetic and morphological host-specific structure in the genetically distinct Atlantic sister lineage of C. testudinaria. We collected adult C. testudinaria from loggerhead sea turtles, horseshoe crabs, and blue crabs along the eastern U.S. coast between Delaware and Florida and in the Gulf of Mexico off Mississippi. We find that shell morphology, especially shell thickness, is host specific and comparable in similar host species between the Atlantic and West Pacific lineages. We did not detect significant genetic differentiation related to host species when analyzing data from 11 nuclear microsatellite loci and mitochondrial sequence data, which is comparable to findings for the Pacific lineage. The most parsimonious explanation for these parallel patterns between distinct lineages of C. testudinaria is that C. testudinaria maintained phenotypic plasticity since the lineages diverged 4-5 mya.

Genetic and Morphological Differentiation of the Semiterrestrial Crab Armases angustipes (Brachyura: Sesarmidae) along the Brazilian Coast.

The genetic and morphometric population structures of the semiterrestrial crab Armases angustipes from along the Brazilian coast were examined. The influence of the Central South Equatorial Current on larval dispersal of A. angustipes also was evaluated. Six populations were sampled from estuarine areas in São Luis do Maranhão, Maranhão; Natal, Rio Grande do Norte; Maceió, Alagoas; Ilhéus, Bahia; Aracruz, Espírito Santo; and Guaratuba, Paraná. Patterns of genetic differentiation were assessed using DNA sequence data corresponding to parts of the mitochondrial cytochrome c oxidase subunit 1. Geometric morphometric techniques were used to evaluate morphological variation in shape and size of the carapace and right cheliped propodus. Our results revealed low genetic variability and lack of phylogeographic structure; geometric morphometrics showed statistically significant morphological differentiation and geographic structuring. Our data indicate the absence of possible barriers to gene flow for this mobile species, and no clear correlation of morphological or genetic variation with ocean currents and/or geographic distance. Our results also suggest that historical geological and climatological events and/or possible bottleneck effects influenced the current low genetic variability among the populations of A. angustipes.

Molecular Characterizations of Kenyan Brachiaria Grass Ecotypes with Microsatellite (SSR) Markers.

Brachiaria grass is an emerging forage option for livestock production in Kenya. Kenya lies within the center of diversity for Brachiaria species, thus a high genetic variation in natural populations of Brachiaria is expected. Overgrazing and clearing of natural vegetation for crop production and nonagricultural uses and climate change continue to threaten the natural biodiversity. In this study, we collected 79 Brachiaria ecotypes from different parts of Kenya and examined them for genetic variations and their relatedness with 8 commercial varieties. A total of 120 different alleles were detected by 22 markers in the 79 ecotypes. Markers were highly informative in differentiating ecotypes with average diversity and polymorphic information content of 0.623 and 0.583, respectively. Five subpopulations: International Livestock Research Institute (ILRI), Kitui, Kisii, Alupe, and Kiminini differed in sample size, number of alleles, number of private alleles, diversity index, and percentage polymorphic loci. The contribution of within-the-individual difference to total genetic variation of Kenyan ecotype population was 81%, and the fixation index (F ST = 0.021) and number of migrant per generation (Nm = 11.58) showed low genetic differentiation among the populations. The genetic distance was highest between Alupe and Kisii populations (0.510) and the lowest between ILRI and Kiminini populations (0.307). The unweighted neighbor-joining (NJ) tree showed test ecotypes grouped into three major clusters: ILRI ecotypes were present in all clusters; Kisii and Alupe ecotypes and improved varieties grouped in clusters I and II; and ecotypes from Kitui and Kiminini grouped in cluster I. This study confirms higher genetic diversity in Kenyan ecotypes than eight commercial varieties (Basilisk, Humidicola, Llanero, Marandú, MG4, Mulato II, Piatá and Xaraés) that represent three species and one three-way cross-hybrid Mulato II. There is a need for further collection of local ecotypes and their morphological, agronomical, and genetic characterizations to support Brachiaria grass breeding and conservation programs.

Chemokine (C-C Motif) Receptor 2 Mediates Dendritic Cell Recruitment to the Human Colon but Is Not Responsible for Differences Observed in Dendritic Cell Subsets, Phenotype, and Function Between the Proximal and Distal Colon.

BACKGROUND & AIMS: Most knowledge about gastrointestinal (GI)-tract dendritic cells (DC) relies on murine studies where CD103+ DC specialize in generating immune tolerance with the functionality of CD11b+/- subsets being unclear. Information about human GI-DC is scarce, especially regarding regional specifications. Here, we characterized human DC properties throughout the human colon. METHODS: Paired proximal (right/ascending) and distal (left/descending) human colonic biopsies from 95 healthy subjects were taken; DC were assessed by flow cytometry and microbiota composition assessed by 16S rRNA gene sequencing. RESULTS: Colonic DC identified were myeloid (mDC, CD11c+CD123-) and further divided based on CD103 and SIRPα (human analog of murine CD11b) expression. CD103-SIRPα+ DC were the major population and with CD103+SIRPα+ DC were CD1c+ILT3+CCR2+ (although CCR2 was not expressed on all CD103+SIRPα+ DC). CD103+SIRPα- DC constituted a minor subset that were CD141+ILT3-CCR2-. Proximal colon samples had higher total DC counts and fewer CD103+SIRPα+ cells. Proximal colon DC were more mature than distal DC with higher stimulatory capacity for CD4+CD45RA+ T-cells. However, DC and DC-invoked T-cell expression of mucosal homing markers (ß7, CCR9) was lower for proximal DC. CCR2 was expressed on circulating CD1c+, but not CD141+ mDC, and mediated DC recruitment by colonic culture supernatants in transwell assays. Proximal colon DC produced higher levels of cytokines. Mucosal microbiota profiling showed a lower microbiota load in the proximal colon, but with no differences in microbiota composition between compartments. CONCLUSIONS: Proximal colonic DC subsets differ from those in distal colon and are more mature. Targeted immunotherapy using DC in T-cell mediated GI tract inflammation may therefore need to reflect this immune compartmentalization.

Conservation genetics of endangered medicinal plant Commiphora wightii in Indian Thar Desert.

To ascertain the conservation priorities and strategies for Commiphora wightii, an endangered medicinal plant of Indian Thar Desert, genetic diversity was estimated within and among different populations. The total of 155 amplification products were scored using ten each of RAPD and ISSR primers, exhibiting an overall 86.72% polymorphism across 45 individuals representing eight populations. The cumulative data of two markers were used to compute pair-wise distances. The Neighbor-Joining tree revealed high genetic differentiation among populations except Kiradu population. Nei's gene diversity (h) ranged between 0.082 and 0.193 with total diversity at species level is 0.294. Shannon's information index (I) ranged between 0.118 and 0.275 with an overall diversity of 0.439. Analysis of molecular variance showed more diversity among population level (56.65%) than at within population level (43.35%). The low gene flow value (Nm=0.349) and high coefficient of genetic differentiation (GST=0.589) and high fixation index (FST=0.566) demonstrated elevated genetic differentiation among the population and can be predicted that these populations are not in Hardy-Weinberg proportions. Principal Co-ordinate Analysis confirms that Akal population has become phylogenetically more distinct and less diverse than the rest of the samples. Mantel's test revealed no correlation between genetic and geographical distances of populations (R(2)=0.122). Overall highest diversity was observed in the population of Machiya Safari Park and Kiradu, while lowest in Akal population, later may constitute an evolutionary significant unit, having merit for special management.

Start Codon Targeted (SCoT) marker reveals genetic diversity of Dendrobium nobile Lindl., an endangered medicinal orchid species.

Genetic variability in the wild genotypes of Dendrobium nobile Lindl. collected from different parts of Northeast India, was analyzed using a Start Codon Targeted (SCoT) marker system. A total of sixty individuals comprising of six natural populations were investigated for the existing natural genetic diversity. One hundred and thirty two (132) amplicons were produced by SCoT marker generating 96.21% polymorphism. The PIC value of the SCoT marker system was 0.78 and the Rp values of the primers ranged between 4.43 and 7.50. The percentage of polymorphic loci (Pp) ranging from 25% to 56.82%, Nei's gene diversity (h) from 0.08 to 0.15 with mean Nei's gene diversity of 0.28, and Shannon's information index (I) values ranging from 0.13 to 0.24 with an average value of 0.43 were recorded. The gene flow value (0.37) and the diversity among populations (0.57) demonstrated higher genetic variation among the populations. Analysis of molecular variance (AMOVA) showed 43.37% of variation within the populations, whereas 56.63% variation was recorded among the populations. Cluster analysis also reveals high genetic variation among the genotypes. Present investigation suggests the effectiveness of SCoT marker system to estimate the genetic diversity of D. nobile and that it can be seen as a preliminary point for future research on the population and evolutionary genetics of this endangered orchid species of medicinal importance.

Indigenous and foreign Y-chromosomes characterize the Lingayat and Vokkaliga populations of Southwest India.

Previous studies have shown that India's vast coastal rim played an important role in the dispersal of modern humans out of Africa but the Karnataka state, which is located on the southwest coast of India, remains poorly characterized genetically. In the present study, two Dravidian populations, namely Lingayat (N=101) and Vokkaliga (N=102), who represent the two major communities of the Karnataka state, were examined using high-resolution analyses of Y-chromosome single nucleotide polymorphisms (Y-SNPs) and seventeen short tandem repeat (Y-STR) loci. Our results revealed that the majority of the Lingayat and Vokkaliga paternal gene pools are composed of four Y-chromosomal haplogroups (H, L, F* and R2) that are frequent in the Indian subcontinent. The high level of L1-M76 chromosomes in the Vokkaligas suggests an agricultural expansion in the region, while the predominance of R1a1a1b2-Z93 and J2a-M410 lineages in the Lingayat indicates gene flow from neighboring south Indian populations and West Asia, respectively. Lingayat (0.9981) also exhibits a relatively high haplotype diversity compared to Vokkaliga (0.9901), supporting the historical record that the Lingayat originated from multiple source populations. In addition, we detected ancient lineages such as F*-M213, H*-M69 and C*-M216 that may be indicative of genetic signatures of the earliest settlers who reached India after their migration out of Africa.

Origin, phylogeny, and spread of Mycobacterium tuberculosis Beijing lineage in the five provinces of northern China / 中华流行病学杂志

Objective Using methodology of molecular genetics to explore the origin,phylogen,and gene flow of Mycobacterium tuberculosis (MTB) Beijing lineage in the five provinces from northern China,including Heilongjiang,Jilin,Liaoning,Neimenggu and Ningxia.Methods 234 MTB Beijing lineage strains were genotyped by 24 Variable Number Tandem Repeat (VNTR),and the h (the allelic diversity) value of each VNTR locus was calculated.On individual level of phylogeny,it was constructed Neighbor-Joining (N-J) tree and minimum spanning tree (MST).Phylogenetic tree was built at the population level,and the most recent common ancestor (TMRCA)was estimated through Bayesian model.Molecular variance (AMOVA) was used to understand the gene flow among strains discovered from the five provinces.Results Allelic diversities of the 24VNTR loci were low (h:0.000-0.744).234 strains of MTB Beijing lineage were dispersed in individual branch of the N-J tree,with 62.0％ (145) of them grouped to the same "colonial complexes" in MST.At the population level,the evolution relationship of 234 strains appeared the closest to Beijing lineage,which was from MIRU-VNTRplus database,and the bootstrap was 100.The TMRCA was 5308 (95％ CI:4263-6470) years.Differences of pairwise Fst values acquired by AMOVA between Jilin and Heilongjiang,Liaoning,Neimenggu and Ningxia,were not statistically significant (P＞0.05).Conclusion The genetic similarity of Beijing lineage MTB from the five provinces of northern China was high.The phylogeny branches had no characteristic dispersal in each province.It was speculated that these strains showed an evolution from a clone of MTB Beijing lineage (about 5000 years ago).The gene flow was taking place between neighboring zones.