Genetic Distance Matrix Research Articles

The Cytochrome Oxidase I gene confirms the presence of the nemertine Carcinonemertes conanobrieni, a parasite of the Caribbean spiny lobster (Panulirus argus) in Colombia

Morphological identifications complemented with molecular analysis are important for the delimitation of cryptic species. This document contains annotations on the molecular identification of the parasitic nemertine Carcinonemertes conanobrieni in the Caribbean spiny lobsters Panulirus argus. The collected nemerteans were found parasitizing ovigerous lobsters from the Gulf of Salamanca (Puebloviejo), Colombia. DNA was extracted from a specimen and a fragment of the mitochondrial gene Cytochrome Oxidase I (COI) was amplified using Folmer’s universal primers, the sequence was edited with ProSeq 3.5 and aligned with all the C. conanobrienisequences available in GenBank. A sequence of 488 base pairs corresponding to the section of the genetic barcode of the COI gene was obtained, the matrix of genetic distances showed little variation when comparing the obtained sequence with those available in the GenBank database. These results confirm the presence of this nemertean in the Panulirus argus lobsters in Colombia providing valuable information for the correct identification and detection of this parasitic species in the country, thus facilitating its monitoring

The Cytochrome Oxidase I gene confirms the presence of the nemertine Carcinonemertes conanobrieni, a parasite of the Caribbean spiny lobster (Panulirus argus) in Colombia

Morphological identifications complemented with molecular analysis are important for the delimitation of cryptic species. This document contains annotations on the molecular identification of the parasitic nemertine Carcinonemertes conanobrieni in the Caribbean spiny lobsters Panulirus argus. The collected nemerteans were found parasitizing ovigerous lobsters from the Gulf of Salamanca (Puebloviejo), Colombia. DNA was extracted from a specimen and a fragment of the mitochondrial gene Cytochrome Oxidase I (COI) was amplified using Folmer’s universal primers, the sequence was edited with ProSeq 3.5 and aligned with all the C. conanobrienisequences available in GenBank. A sequence of 488 base pairs corresponding to the section of the genetic barcode of the COI gene was obtained, the matrix of genetic distances showed little variation when comparing the obtained sequence with those available in the GenBank database. These results confirm the presence of this nemertean in the Panulirus argus lobsters in Colombia providing valuable information for the correct identification and detection of this parasitic species in the country, thus facilitating its monitoring

Genetic diversity of seagrass Cymodocea species as an ecological indicator on the Palk Bay Coast, India

Seagrass meadows are rapidly vanishing due to coastal development and climate change. In seagrass research, omics and molecular profiling tools are timely, allowing for new prospects to worldwide concerns. Hence, the present study tested the eight SCoT primers on Cymodocea serrulata and Cymodocea rotundata, which showed 591 polymorphic bands (90.92%), indicating that the individuals are from different populations from the Palk Bay Coast. The Nei-based genetic distance matrix of eight populations of C. serrulata and C. rotundata showed high genetic distance at the intraspecies level in 0.325–0.506. The Nei genetic diversity (h), Shannon information index (I), and allelic number (Ne) of C. serrulata and C. rotundata were low to moderate. C. serrulata had a higher Shannon index (0.54) and genetic diversity (0.36) than the other seven populations, whereas C. rotundata had a higher Shannon index (0.5) and genetic diversity (0.33) in Kattumavadi. The study concludes that the genetic diversity of C. serrulata and C. rotundata shows moderate levels across the study. The Cymodoacea species showed low genetic diversity and heterozygosity due to habitat degradation. These restricted gene flow and fragmented populations are typically exposed to increase their risk of extinction. The population genetics of Cymodoacea species from the Palk Bay region is the first to use SCoT markers to provide insight on seagrass genetics as an ecological indicator for conservation and coastal management.

Information-entropy approach to the analysis of genetic diversity of populations (analytical review)

The application of information-entropy analysis on real data is shown: 84 bulls of Jersey (n = 10), Ayrshire (n = 10), red Danish (n = 10), red Swedish (n = 9) breeds and Holstein ecotypes of German (n = 13), Dutch (n = 17) and North American (n = 15) breeding genotyped by 11 microsatellite loci. The Shannon information index for the combined breed samples was 1.695, the weighted average for the samples was 1.325, the inter-sample component (SHAP) was 0.370 nits or 21.8 % (all calculations according to GenAlEx 6.502). The total absolute diversity of Shannon was 5.45, averaged by samples – 3.76 effective alleles per locus, between breeds – 1.45 effective samples. The relative estimate of the differentiation of breed samples (D'β) was 36.2 % and was close to the «traditional» estimates for Hedrick, Jost and Ciao. The influence of within samples heterozygosity on SHAP estimates has not been established, but a positive trend of D'β-estimates has been noted. The matrix of paired genetic distances by breeds (D'β) and its 2D projection had a high correspondence with those by GST(NEI)-, FST(W&C)-, G"ST(HED)-, F'ST(W&C)-, DJOST-, DCHAO-measures (RMantel ≥ 0,94). Fixation indices (GST(NEI) and FST(W&C)) should be used to study the evolutionary stories of subdivided populations. To analyze the current structure of the genetic diversity of (sub)populations with an emphasis on dominant allele measures based on heterozygosity (G'ST(HED), F'ST(W&C), DJOST and DCHAO), if necessary, take into account all alleles – the Shannon measure (D'β). In conclusion, a family of Hill power measures of order q = 0, 1, 2 is considered for constructing diversity profiles containing all information about the distribution of alleles in a population.

CDDP and ISSR markers-assisted diversity and structure analysis in Iraqi Mazu (Quercus infectoria Oliv.) accessions

Mazu, or oak gall (Quercus infectoria Oliv.), a member of the Fabaceae family, is an abundant tree species in Iraq. Because of ongoing habitat damage, this species is on the verge of extinction. However, the genetic diversity of wild oak populations has yet to be measured. Semi-arbitrary [Inter-simple sequence repeat (ISSR)] and gene-targeted [Conserved DNA derived polymorphism (CDDP)] markers were employed separately or in combination to investigate genetic diversity within and among 85 Iraqi Mazu (Q. infectoria) accessions based on geographic origin. A total of 88 polymorphic alleles were produced in this investigation utilizing nine CDDP primers, with an average of 9.78 alleles per primer. The mean values for the major allele frequency (MAF), polymorphism information content (PIC), and marker index were 0.23, 0.29, and 2.79, respectively. Twenty ISSR primers were used to amplify 195 alleles (9.75 bands per primer), with MAF, PIC, and MI values of 0.21, 0.28, and 2.72, respectively. All accessions were divided into two major groups with multiple sub-groups based on Ward clustering and structure analysis. Within-population variance was calculated to be 94.17% using CDDP markers and 92.97% using ISSR markers. As per the fixation index values derived from the STRUCTURE analysis, there was a significant difference within the population. Increased gene flow was found among populations. The correlation (r) between the CDDP-based genetic distance matrix and the ISSR-based genetic distance matrix was 0.54, with a p-value of 0.001. The genetic dissimilarity calculated by CDDP and ISSR data revealed a wide range of diversity, demonstrating substantial genetic variation across accessions originating from various populations. This investigation’s findings could aid in the conservation and further utilization of oak germplasm.

Genetic diversity study of Chrysoperla carnea (Neuroptera: Chrysopidae) populations via molecular markers

The objective of this study was to determine the genetic diversity among Chrysoperla carnea samples collected from different locations of Iran (including, East-Azerbaijan, West-Azerbaijan, Isfahan, Kerman, Kermanshah, Lorestan, Mazandaran, Gilan, Hormozgan and Hamedan provinces) using the Inter simple sequence repeat (ISSR) and mitochondrial (Cytochrome Oxidase I - COI) molecular markers in 2016-2018. The results showed that a total of 64 bands were produced by ten primers of ISSR markers which among them 43 bands were polymorphic. The highest and lowest polymorphic percentages belonged to primer UBC-809 (88.88%) and primer UBC-886 (33.33%), respectively. The results of cluster analysis based on ISSR marker data divided the samples into three separate clusters. This grouping was also confirmed by analysis of molecular variance. According to the results of the analysis of molecular variance diversity within and among groups was about 84% and 16%, respectively. In the present study five haplotypes were obtained. The first haplotype (H1) was common in all populations which can be considered as the ancestral haplotype, the other haplotypes have been evolved from it. The novelty of this study is that we report the first time genetic diversity analysis of family Chrysopidae using ISSR and CO1 markers covering more than ten provinces and thirty cities of Iran with a full picture of its genetic diversity. Genetic distance matrix based on Jaccard index indicated low genetic distance of populations. The results showed that ISSR and CO1 markers have high efficiency in study of genetic diversity in the family Chrysopidae.

GENETIC VARIABILITY IN Sechium spp. (Cucurbitaceae) EVALUATED WITH AFLP MARKERS

There are few studies in Mexico aimed at evaluating the genetic variability of Sechium spp. Despite certain biological variants are reported with very high potential to develop antineoplastic supplements to treat public health conditions. Using the Amplified Fragment Length Polymorphism (AFLP) technique, the genetic variability of a sample of 95 accessions of three species of Sechium (S. edule, S. chinantlense, S. compositum) was evaluated, with leaf DNA from the Banco Nacional de Germoplasma de Sechium edule en Mexico. Four combinations of AFPL were applied (EcoRI + ACC/MseI + CAC, EcoRI + ACC/MseI + CAT, EcoRI + ACC/MseI + CGC, and EcoRI + ACC/MseI + CGG). DNA samples were classified into three groups based on the flavour of the fruit (sweet, neutral, bitter). An average of 47.91% polymorphism, 0.16 heterozygosity, 32.83 number of polymorphic bands, and a zero Wright fixation index (Fst) was obtained. The evidence showed that the domesticated accessions (sweet, neutral) were separated from the bitter-taste genotypes. A monophyletic tree was generated with the genetic distance matrix and the neighbour-joining methodology. Analyses showed S. edule as the root taxon, deriving S. compositum and S. chinantlense as subgroups, and suggesting that there is not enough differentiation to treat them as separate species. The evaluated sample showed that there is no apparent reproductive barrier for genetic cross breeding. Genotypes behaved as a complex with evolutive dynamism; that genetic complexity would allow the design of new variants.

Impact of Gene Flow and Introgression on the Range Wide Genetic Structure of Quercus robur (L.) in Europe

As for most other temperate broadleaved tree species, large-scale genetic inventories of pedunculate oak (Quercus robur L.) have focused on the plastidial genome, which showed the impact of post-glacial recolonization and manmade seed transfer. However, how have pollen mediated gene flow and introgression impacted the large-scale genetic structure? To answer these questions, we did a genetic inventory on 1970 pedunculate oak trees from 197 locations in 13 European countries. All samples were screened with a targeted sequencing approach on a set of 381 polymorphic loci (356 nuclear SNPs, 3 nuclear InDels, 17 chloroplast SNPs, and 5 mitochondrial SNPs). In a former analysis with additional 1763 putative Quercus petraea trees screened for the same gene markers we obtained estimates on the species admixture of all pedunculate oak trees. We identified 13 plastidial haplotypes, which showed a strong spatial pattern with a highly significant autocorrelation up to a range of 1250 km. Significant spatial genetic structure up to 1250 km was also observed at the nuclear loci. However, the differentiation at the nuclear gene markers was much lower compared to the organelle gene markers. The matrix of genetic distances among locations was partially correlated between nuclear and organelle genomes. Bayesian clustering analysis revealed the best fit to the data for a sub-division into two gene pools. One gene pool is dominating the west and the other is the most abundant in the east. The western gene pool was significantly influenced by introgression from Quercus petraea in the past. In Germany, we identified a contact zone of pedunculate oaks with different introgression intensity, likely resulting from different historical levels of introgression in glacial refugia or during postglacial recolonization. The main directions of postglacial recolonization were south to north and south to northwest in West and Central Europe, and for the eastern haplotypes also east to west in Central Europe. By contrast, the pollen mediated gene flow and introgression from Q. petraea modified the large-scale structure at the nuclear gene markers with significant west–east direction.

Genetic polymorphism of 19 autosomal STR loci in the Yi ethnic minority of Liangshan Yi autonomous prefecture from Sichuan province in China

The Yi is one of fifty-six ethnic populations and one of the most ancient ethnic groups in China. The Liangshan Yi Autonomous Prefecture (LYAP) in Sichuan Province has the single largest Yi community in China. To establish a Yi population database in the LYAP of Sichuan in China, a Goldeneye™ DNA Identification System 20A Kit with 19 autosomal STRs (short tandem repeats) was used. As a result, the total discrimination power (TDP) and the cumulative probability of exclusion (CPE) for these STRs in 1016 unrelated individuals were 0.999999999999999999999897 and 0.9999999597, respectively. Totals of 273 alleles for 19 STRs and 8–22 alleles for each locus were found. The allelic frequencies ranged from 0.0005 to 0.5084. The forensic parameter averages of these STRs were as follows: observed heterozygosity (Hobs) of 78.44%, expected heterozygosity (Hexp) of 79.89%, discrimination power (DP) of 92.66%, and probability of exclusion (PE) of 57.68%. Penta E presented the highest levels of Hobs and DP, whereas TPOX showed the lowest Hobs and DP values. Nei’s standard genetic distance matrix among 31 populations found that the nearest genetic distance to the Yi population was the Sichuan Han (0.0056). Altogether, we first reported the forensic parameters and allele frequencies of 19 autosomal STRs of the Yi group in Liangshan. These 19 STR makers could provide highly informative polymorphisms for individual identification, paternity testing and genetic population analyses.

Genetic polymorphism of myostatin (MSTN) in Nigerian sheep breeds

Myostatin (MSTN) also known as growth differentiation factor 8 (GDF-8) has been implicated to play an important role in growth regulation, and it is a candidate gene in marker assisted selection (MAS). This study was carried out to identify the polymorphism of MSTN gene as a genetic marker for growth traits in Nigerian indigenous sheep. Genomic DNA (gDNA) was extracted from blood samples of Balami, Yankasa, Uda and West African Dwarf (WAD) breeds of sheep. Parts of 5’UTR, intron and exon1 (614bp) was amplified using a primer sequence designed by FastPCR-primer software. The amplicons were digested with restriction enzyme HaeIII and the fragments produced were stained with luminescent dye and run on gel electrophoresis. The genetic structure of the sampled population was investigated after analysis with POPGENE32 software. The HaeIII digested results showed that Myostatin has three polymorphs (AA, AB and BB), controlled by two alleles (A and B), with B having a higher allelic frequency (82.84%) and BB genotype has the highest frequency of 73%. The sampled population showed a deviation from Hardy-Weinberg equilibrium (p<0.05) while the F-statistics results of the Nigerian breeds of sheep showed the breeds are genetically identical (33.40%) within them. The genetic distance matrix established that Uda and Yankasa show the greatest distant (3.00%) while Uda and WAD are almost identical (99.85%). The four breeds of sheep studied showed polymorphism for Myostatin gene in the intron 1 and exon 1. Myostatin, therefore, could be considered a candidate gene for MAS

Can We Compare Effect Size of Spatial Genetic Structure Between Studies and Species Using Moran Eigenvector Maps?

As the field of landscape genetics is progressing toward comparative empirical studies and meta-analysis, it is important to know how best to compare the strength of spatial genetic structure between studies and species. Moran’s Eigenvector Maps are a promising method that does not make an assumption of isolation-by-distance in a homogeneous environment but can discern cryptic structure that may result from multiple processes operating in heterogeneous landscapes. MEMgene uses spatial filters from Moran’s Eigenvector Maps as predictor variables to explain variation in a genetic distance matrix, and it returns adjusted R2 as a measure of the amount of genetic variation that is spatially structured. However, it is unclear whether, and under which conditions, this value can be used to compare the degree of spatial genetic structure (effect size) between studies. This study addresses the fundamental question of comparability at two levels: between independent studies (meta-analysis mode) and between species sampled at the same locations (comparative mode). We used published datasets containing 9,900 haploid, biallelic, neutral loci simulated on a quasi-continuous, square landscape under four demographic scenarios (island model, isolation-by-distance, expansion from one or two refugia). We varied the genetic resolution (number of individuals and loci) and the number of random sampling locations. We considered two measures of effect size, the MEMgene adjusted R2 and multivariate Moran’s I, which is related to Moran’s Eigenvector Maps. Both metrics were highly sensitive to the number of locations, even when using standardized effect sizes, SES, and the number of individuals sampled per location, but not to the number of loci. In comparative mode, using the same Moran Eigenvector Maps for all species, even those with missing values at some sampling locations, reduced bias due to the number of locations under isolation-by-distance (stationary process) but increased it under expansion from one or two refugia (non-stationary process). More robust measures of effect size need to be developed before the strength of spatial genetic structure can be accurately compared, either in a meta-analysis of independent empirical studies or within a comparative, multispecies landscape genetic study.

ВАРИАБЕЛЬНОСТЬ ГЕНОМНЫХ RGA-ЛОКУСОВ СОВРЕМЕННЫХ ОТЕЧЕСТВЕННЫХ СОРТОВ КАРТОФЕЛЯ: ДАННЫЕ NBS-МАРКИРОВАНИЯ

The plant immunity is aimed at protecting against biotic and abiotic stresses and, therefore, at adapting to adverse environmental conditions. At the first protection step, a wide range of phytopathogenic receptors encoded by resistance R-genes is employed. The presence of a conserved NBS-domain in the receptors makes it possible to profile the plant genome by amplification of R-gene analogues. The method of multilocus NBS-profiling makes it possible to efficiently characterize the plant genome in terms of the representativeness and variability of the NBS-domain containing R-genes. This method is used to study the diversity of R-gene loci in crops and related wild species, as well as the introgressive hybridization phenomena and the R-gene evolution in plant species with varying degrees of pathogen resistance. NBS-profiling is also applied for genotyping GenBank collections, developing markers and saturating genetic maps. The requirement for cultivar genotype certification and profiling, along with a limited number of similar studies in Russia, makes research on the molecular profiling of domestic and foreign cultivars farmed in the Russian Federation relevant. In the present work, NBS-profiling was used for genotyping 65 potato Solanum tuberosum cultivars of mainly modern domestic breeding, as well as the related species Solanum stoloniferum (as an outgroup). Using two primer/enzyme combinations (NBS7/MseI and NBS9/MseI), 204 NBS fragments were generated, of which 144 (70.6 %) were polymorphic and one fragment was unique to cv. Gala. For each cultivar, a specific spectrum of NBS fragments was determined. Analysis of genetic distance matrix revealed a high level of polymorphism (GD = 0.18-0.45 with an average value of 0.33) among the studied cultivars. Genetic distances within the analyzed cultivars varied more than between the cultivars and the accession of S. stoloniferum (GD = 0.27-0.40). The most related cultivars were Solnechny/Pamyati Rogacheva (GD = 0.18) and Velikan/Vympel (GD = 0.19) originated from Lorch Potato Research Institute, and the most distant cultivars were Charoito/Red Scarlett (GD = 0.45). Statistical analysis of NBS-profiling data clustered studied potato cultivars in accordance with the pedigree and resistance to phytopathogens. On the dendrogram and graphs generated using the PAST and Structure 2.3.4, a pronounced tendency to group cultivars by traits of resistance to the Potato virus Y (Potyvirus, Potyviridae) and the Potato leafroll virus (Polerovirus, Luteoviridae) was shown. The primer/enzyme systems used in this study for NBS-profiling can be applied to study the mechanisms of potato resistance to biotic stresses.

VARIABILITY OF GENOMIC RGA-LOCI OF MODERN RUSSIAN POTATO CULTIVARS: NBS-PROFILING DATA

The plant immunity is aimed at protecting against biotic and abiotic stresses and, therefore, at adapting to adverse environmental conditions. At the first protection step, a wide range of phytopathogenic receptors encoded by resistance R-genes is employed. The presence of a conserved NBS-domain in the receptors makes it possible to profile the plant genome by amplification of R-gene analogues. The method of multilocus NBS-profiling makes it possible to efficiently characterize the plant genome in terms of the representativeness and variability of the NBS-domain containing R-genes. This method is used to study the diversity of R-gene loci in crops and related wild species, as well as the introgressive hybridization phenomena and the R-gene evolution in plant species with varying degrees of pathogen resistance. NBS-profiling is also applied for genotyping GenBank collections, developing markers and saturating genetic maps. The requirement for cultivar genotype certification and profiling, along with a limited number of similar studies in Russia, makes research on the molecular profiling of domestic and foreign cultivars farmed in the Russian Federation relevant. In the present work, NBS-profiling was used for genotyping 65 potato Solanum tuberosum cultivars of mainly modern domestic breeding, as well as the related species Solanum stoloniferum (as an outgroup). Using two primer/enzyme combinations (NBS7/MseI and NBS9/MseI), 204 NBS fragments were generated, of which 144 (70.6 %) were polymorphic and one fragment was unique to cv. Gala. For each cultivar, a specific spectrum of NBS fragments was determined. Analysis of genetic distance matrix revealed a high level of polymorphism (GD = 0.18-0.45 with an average value of 0.33) among the studied cultivars. Genetic distances within the analyzed cultivars varied more than between the cultivars and the accession of S. stoloniferum (GD = 0.27-0.40). The most related cultivars were Solnechny/Pamyati Rogacheva (GD = 0.18) and Velikan/Vympel (GD = 0.19) originated from Lorch Potato Research Institute, and the most distant cultivars were Charoito/Red Scarlett (GD = 0.45). Statistical analysis of NBS-profiling data clustered studied potato cultivars in accordance with the pedigree and resistance to phytopathogens. On the dendrogram and graphs generated using the PAST and Structure 2.3.4, a pronounced tendency to group cultivars by traits of resistance to the Potato virus Y (Potyvirus, Potyviridae) and the Potato leafroll virus (Polerovirus, Luteoviridae) was shown. The primer/enzyme systems used in this study for NBS-profiling can be applied to study the mechanisms of potato resistance to biotic stresses.

A Geometrical Framework for f-Statistics.

A detailed derivation of the f-statistics formalism is made from a geometrical framework. It is shown that the f-statistics appear when a genetic distance matrix is constrained to describe a four population phylogenetic tree. The choice of genetic metric is crucial and plays an outstanding role as regards the tree-like-ness criterion. The case of lack of treeness is interpreted in the formalism as the presence of population admixture. In this respect, four formulas are given to estimate the admixture proportions. One of them is the so-called [Formula: see text]-ratio estimate and we show that a second one is related to a known result developed in terms of the fixation index [Formula: see text]. An illustrative numerical simulation of admixture proportion estimates is included. Relationships of the formalism with coalescence times and pairwise sequence differences are also provided.

SNP genotyping for fast and consistent clustering of maize inbred lines into heterotic groups

Abstract Advances in genotyping technologies have transformed the way breeding programs manage their genetic resources. The identification of single nucleotide polymorphisms (SNPs) can improve understanding of the genetic diversity of maize (Zea mays) inbred lines and their classification into heterotic groups, which is useful in determining certain crosses to obtain hybrids with higher yield performance. The genetic diversity of 293 inbred lines was investigated with 5252 SNPs with minor allele frequency (MAF)>5%. There was an average of 525 SNPs per chromosome. Polymorphism information content (PIC) averaged 0.297. The unweighted pair group method with arithmetic mean analysis (UPGMA) and principal component analysis (PCA) based on the genetic distance matrix revealed four similar clusters and high cophenetic correlation coefficients (0.953 and 0.863, respectively). The results showed consistency between genetic distance-based grouping and the heterotic groups previously established using pedigree and topcross information for the inbred lines studied.

An attempt to validate molecular and field level screening results for the Corynospora leaf fall disease in rubber (<em>Hevea brasiliensis</em>)

Corynespora Leaf Fall (CLF) disease is one of the serious diseases, caused by Corynespora cassiicola, affecting rubber (Hevea brasiliensis L) plantations. Clones rated as resistant to the disease under the polybag nurseries became susceptible at the field level causing major problems in clone recommendations. Therefore, it is of utmost importance to add new CLF resistant genotypes to the breeding pool. Therefore, the present study was carried out to attempt to validate the molecular screening by field screening results. The molecular screening was carried out using 35 genotypes from 2005 hand-pollinated progeny, their grandparents (RRIC 100 and RRIC 103), grate grandparents (RRIC 52 and PB 86), and two check clones (RRISL 201 and RRISL 208). The 2005 hand-pollinated progeny which has comprised with self progenies, raised at 1978 hand pollination by selfing at CLF susceptible clone RRIC 103 and CLF resistant clone RRIC 100. Four SSR Primers (HB 1, HB 11, HB 29, hmct 5) were selected based on polymorphism between the CLF free clone RRIC 100 and susceptible clone RRIC 103 for molecular screening. Field screening was done at polybag nursery, budwood nursery, and at field level in three locations viz., Nivithigalakale, Monaragala, and Gallewatta. Completely randomized design (CRD) was used with five to ten replicates. Disease assessment was carried out allowing plants for the natural infection based on the index developed for scoring of disease severity. Observations were taken three times during peak and off seasons of CLF disease occurrence and were assessed along with control clones. All primers generated two fragments for Hevea and built the genetic distance matrix using a power maker (V 3.0) computer program and a tree diagram was drawn using the Tree view computer program. Cluster analyses revealed four distinct clusters. Two primary clones, PB 86 and RRIC 52, and the clones RRIC 103 and RRIC 201 were grouped and another cluster was again grouped into three main sub-clusters. Around 40% of field screening results obtained agreed with molecular grouping whereas, 57% were not agreed and around 3% of genotypes did not show a clear correlation. However, further screening at the field level and molecular screening is needed.

Multi-locus genotyping reveals established endemicity of a geographically distinct Plasmodium vivax population in Mauritania, West Africa.

Plasmodium vivax has been recently discovered as a significant cause of malaria in Mauritania, although very rare elsewhere in West Africa. It has not been known if this is a recently introduced or locally remnant parasite population, nor whether the genetic structure reflects epidemic or endemic transmission. To investigate the P. vivax population genetic structure in Mauritania and compare with populations previously analysed elsewhere, multi-locus genotyping was undertaken on 100 clinical isolates, using a genome-wide panel of 38 single nucleotide polymorphisms (SNPs), plus seven SNPs in drug resistance genes. The Mauritanian P. vivax population is shown to be genetically diverse and divergent from populations elsewhere, indicated consistently by genetic distance matrix analysis, principal components analyses, and fixation indices. Only one isolate had a genotype clearly indicating recent importation, from a southeast Asian source. There was no linkage disequilibrium in the local parasite population, and only a small number of infections appeared to be closely genetically related, indicating that there is ongoing genetic recombination consistent with endemic transmission. The P. vivax diversity in a remote mining town was similar to that in the capital Nouakchott, with no indication of local substructure or of epidemic population structure. Drug resistance alleles were virtually absent in Mauritania, in contrast with P. vivax in other areas of the world. The molecular epidemiology indicates that there is long-standing endemic transmission that will be very challenging to eliminate. The virtual absence of drug resistance alleles suggests that most infections have been untreated, and that this endemic infection has been more neglected in comparison to P. vivax elsewhere.

A cautionary note on the use of unsupervised machine learning algorithms to characterise malaria parasite population structure from genetic distance matrices.

Genetic surveillance of malaria parasites supports malaria control programmes, treatment guidelines and elimination strategies. Surveillance studies often pose questions about malaria parasite ancestry (e.g. how antimalarial resistance has spread) and employ statistical methods that characterise parasite population structure. Many of the methods used to characterise structure are unsupervised machine learning algorithms which depend on a genetic distance matrix, notably principal coordinates analysis (PCoA) and hierarchical agglomerative clustering (HAC). PCoA and HAC are sensitive to both the definition of genetic distance and algorithmic specification. Importantly, neither algorithm infers malaria parasite ancestry. As such, PCoA and HAC can inform (e.g. via exploratory data visualisation and hypothesis generation), but not answer comprehensively, key questions about malaria parasite ancestry. We illustrate the sensitivity of PCoA and HAC using 393 Plasmodium falciparum whole genome sequences collected from Cambodia and neighbouring regions (where antimalarial resistance has emerged and spread recently) and we provide tentative guidance for the use and interpretation of PCoA and HAC in malaria parasite genetic epidemiology. This guidance includes a call for fully transparent and reproducible analysis pipelines that feature (i) a clearly outlined scientific question; (ii) a clear justification of analytical methods used to answer the scientific question along with discussion of any inferential limitations; (iii) publicly available genetic distance matrices when downstream analyses depend on them; and (iv) sensitivity analyses. To bridge the inferential disconnect between the output of non-inferential unsupervised learning algorithms and the scientific questions of interest, tailor-made statistical models are needed to infer malaria parasite ancestry. In the absence of such models speculative reasoning should feature only as discussion but not as results.

Genetic diversity among 435 barley accessions based in morpho-agronomical characteristics under irrigation in the Brazilian savannah

The success of barley (Hordeum vulgare L.) cultivation and its adaptation to cropping systems relies on the knowledge and utilization of existing variability in germplasm banks. The objective of this work was to analyse diversity among pre-selected barley accessions to organize a working collection and to identify genotypes for a breeding program for irrigated barley in the Brazilian Savannah. The field experiment was conducted under irrigation in Planaltina, DF, Brazil. The plant population consisted of 433 accessions plus BRS 180 and BRS 195 as checks. The accessions were evaluated using fifteen morpho agronomic descriptors, in which 11 quantitative and four discrete. The interpolated control design was used for the statistical analysis. A genetic distance matrix was calculated using Gower’s coefficient. From the matrix, a grouping analysis was conducted, using the optimizing Tocher method and the graphic dispersion distance. The genetic distances varied between 0.025 and 0.572, with a mean of 0.256. The accessions were distributed in 18 groups by the Tocher method, which was directly related to the graphic dispersion. The existing genetic divergence in the collection under study helped the definition of accessions in crossing blocks from breeding programs directed to the savannah environment.

Genetic Characterization Based on Rapd-Pcr in Cultured Strains of Clarias gariepinus (Siluriformes: Clariidae)

The genetic polymorphisms of catfish populations collected from four fish farms in four Southwestern states of Nigeria were determined by Randomly Amplified Polymorphic DNA Polymerase Chain Reaction technique. This was to characterize the strains genetically and provide information on the studied catfish. Following standard procedures, polymerase chain reaction was performed by mixing 15 μl reaction mixture containing FIREPOL® Taq DNA polymerase, MgCl2, dNTPs, distilled water, dyes and glycerol, with 1.0 μl DNA sample of 16-week old C. gariepinus strains using OPA03, OPA04, OPC02, OPB08, OPC11, OPG16, OPG19 and OPA19 primers. A sum of 1708 loci having 3072 bands was amplified in all the samples. The RAPD analysis revealed significant genetic variability (P<0.05) among the four sampled populations. The unweighted pair group method with average (UPGMA) dendrogram based on Nei’s unbiased genetic distance matrix separated the Clarias gariepinus populations into two clades. The first clade was made up of populations from Ibadan and Abeokuta while the second clade consisted of populations from Ado-Ekiti and Ile-Ife. Thus, it is imperative to determine the genetic variation and population structure of the stocks of C. gariepinus in advance before commencing on breeding programmes.