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Diversity analysis using molecular markers serves as a powerful tool in unravelling the intricacies of inclusivity within various populations and is an initial step in the assessment of populations and the development of inbred lines for host plant resistance in maize. This study was conducted to assess the genetic diversity and population structure of 242 newly developed S3 inbred lines using 3,305 single nucleotide polymorphism (SNP) markers and to also assess the level of homozygosity achieved in each of the inbred lines. A total of 1,184 SNP markers were found highly informative, with a mean polymorphic information content (PIC) of 0.23. Gene diversity was high among the inbred lines, ranging from 0.04 to 0.50, with an average of 0.27. The residual heterozygosity of the 242 S3 inbred lines averaged 8.8%, indicating moderately low heterozygosity levels among the inbred lines. Eighty-four percent of the 58,322 pairwise kinship coefficients among the inbred lines were near zero (0.00–0.05), with only 0.3% of them above 0.50. These results revealed that many of the inbred lines were distantly related, but none were redundant, suggesting each inbred line had a unique genetic makeup with great potential to provide novel alleles for maize improvement. The admixture-based structure analysis, principal coordinate analysis, and neighbour-joining clustering were concordant in dividing the 242 inbred lines into three subgroups based on the pedigree and selection history of the inbred lines. These findings could guide the effective use of the newly developed inbred lines and their evaluation in quantitative genetics and molecular studies to identify candidate lines for breeding locally adapted fall armyworm tolerant varieties in Ghana and other countries in West and Central Africa. [ABSTRACT FROM AUTHOR]

Genetic resources of tepary bean (Phaseolus acutifolius A. Gray) germplasm collections are not well characterized due to a lack of dedicated genomic resources. There is a need to assemble genomic resources specific to tepary bean for germplasm characterization, heterotic grouping, and breeding. Therefore, the objectives of this study were to deduce the genetic groups in tepary bean germplasm collection using high-density Diversity Array Technology (DArT) based single nucleotide polymorphism (SNP) markers and select contrasting genotypes for breeding. Seventy-eight tepary bean accessions were genotyped using 10527 SNPs markers, and genetic parameters were estimated. Population structure was delineated using principal component and admixture analyses. A mean polymorphic information content (PIC) of 0.27 was recorded, indicating a relatively low genetic resolution of the developed SNPs markers. Low genetic variation (with a genetic distance [GD] = 0.32) existed in the assessed tepary bean germplasm collection. Population structure analysis identified five sub-populations through sparse non-negative matrix factorization (snmf) with high admixtures. Analysis of molecular variance indicated high genetic differentiation within populations (61.88%) and low between populations (38.12%), indicating high gene exchange. The five sub-populations exhibited variable fixation index (FST). The following genetically distant accessions were selected: Cluster 1:Tars-Tep 112, Tars-Tep 10, Tars-Tep 23, Tars-Tep-86, Tars-Tep-83, and Tars-Tep 85; Cluster 3: G40022, Tars-Tep-93, and Tars-Tep-100; Cluster 5: Zimbabwe landrace, G40017, G40143, and G40150. The distantly related and contrasting accessions are useful to initiate crosses to enhance genetic variation and for the selection of economic traits in tepary bean. [ABSTRACT FROM AUTHOR]

The Human Leukocyte Antigen (HLA) region plays an important role in autoimmune and infectious diseases. HLA is a highly polymorphic region and thus difficult to impute. We, therefore, sought to evaluate HLA imputation accuracy, specifically in a West African population, since they are understudied and are known to harbor high genetic diversity. The study sets were selected from 315 Gambian individuals within the Gambian Genome Variation Project (GGVP) Whole Genome Sequence datasets. Two different arrays, Illumina Omni 2.5 and Human Hereditary and Health in Africa (H3Africa), were assessed for the appropriateness of their markers, and these were used to test several imputation panels and tools. The reference panels were chosen from the 1000 Genomes (1kg-All), 1000 Genomes African (1kg-Afr), 1000 Genomes Gambian (1kg-Gwd), H3Africa, and the HLA Multi-ethnic datasets. HLA-A, HLA-B, and HLA-C alleles were imputed using HIBAG, SNP2HLA, CookHLA, and Minimac4, and concordance rate was used as an assessment metric. The best performing tool was found to be HIBAG, with a concordance rate of 0.84, while the best performing reference panel was the H3Africa panel, with a concordance rate of 0.62. Minimac4 (0.75) was shown to increase HLA-B allele imputation accuracy compared to HIBAG (0.71), SNP2HLA (0.51) and CookHLA (0.17). The H3Africa and Illumina Omni 2.5 array performances were comparable, showing that genotyping arrays have less influence on HLA imputation in West African populations. The findings show that using a larger population-specific reference panel and the HIBAG tool improves the accuracy of HLA imputation in a West African population. [ABSTRACT FROM AUTHOR]

SLC30A9 encodes a ubiquitously zinc transporter (ZnT9) and has been consistently suggested as a candidate for positive selection in humans. However, no direct adaptive molecular phenotype has been demonstrated. Our results provide evidence for directional selection operating in two major complementary haplotypes in Africa and East Asia. These haplotypes are associated with differential gene expression but also differ in the Met50Val substitution (rs1047626) in ZnT9, which we show is found in homozygosis in the Denisovan genome and displays accompanying signatures suggestive of archaic introgression. Although we found no significant differences in systemic zinc content between individuals with different rs1047626 genotypes, we demonstrate that the expression of the derived isoform (ZnT9 50Val) in HEK293 cells shows a gain of function when compared with the ancestral (ZnT9 50Met) variant. Notably, the ZnT9 50Val variant was found associated with differences in zinc handling by the mitochondria and endoplasmic reticulum, with an impact on mitochondrial metabolism. Given the essential role of the mitochondria in skeletal muscle and since the derived allele at rs1047626 is known to be associated with greater susceptibility to several neuropsychiatric traits, we propose that adaptation to cold may have driven this selection event, while also impacting predisposition to neuropsychiatric disorders in modern humans. Author summary: Contrasting continental signatures of positive natural selection have been previously found in the human SLC30A9 gene encoding the protein ZnT9, which transports zinc across cell membranes. Here we investigate the genetic variants that have been targeted by natural selection in the surrounding region of this gene and which molecular and whole-body changes may have brought about. We found that two major SLC30A9 variant combinations (haplotypes) that are extremely frequent in Africa and East Asia, respectively, are expressed differentially. These two haplotypes also differ at one site that creates an amino acid difference at ZnT9; the version most often found outside Africa avoiding zinc overload in the endoplasmic reticulum and mitochondria and directly influencing mitochondrial activity. Moreover, we found that this substitution, which is known to be associated with greater susceptibility to several neuropsychiatric disorders, is present in the Denisova and displays accompanying patterns of variation that could be suggestive of adaptive introgression. Since mitochondria play an important role in skeletal muscle energy metabolism, we speculate that adaptation to cold may have driven this selection event outside Africa, while also impacting predisposition to neuropsychiatric disorders in modern humans. [ABSTRACT FROM AUTHOR]

In the last decades, illegal logging has posed a serious threat for the integrity of forest ecosystems and for biodiversity conservation in tropical Africa. Although international treaties and regulatory plans have been implemented to reduce illegal logging, much of the total timber volume is harvested and traded illegally from tropical African forest regions. As a result, the development and the application of analytical tools to enhance the traceability and the identification of wood and related products is critical to enforce international regulations. Among available techniques, DNA barcoding is a promising approach for the molecular identification of plant species. However, although it has been used successfully for the discrimination of animal species, no set of genetic markers is available for the universal identification of plant species. In this work, we firstly characterized the genetic diversity of 17 highly-valuable African timber species from five genera (Afzelia, Guibourtia, Leplea, Milicia, Tieghemella) across their distribution ranges in West and Central Africa using the genome skimming approach in order to reconstruct their chloroplast genomes and nuclear ribosomal DNA. Next, we identified single-nucleotide polymorphisms (SNPs) for the discrimination of closely-related species. In this way, we successfully developed and tested novel species-specific genetic barcodes for species identification. [ABSTRACT FROM AUTHOR]

Plasmodium ovale curtisi and P. ovale wallikeri are both endemic in sub-Saharan Africa, the Middle East and Southeast Asia. Molecular surveillance data for drug resistance in P. ovale spp. is limited at present. We analysed polymorphisms in the podhfr, pocrt and pocytb genes of P. ovale spp. in 147 samples collected from travelers returning to China from Africa. Two podhfr mutations, S58R and S113N/T were detected in P. ovale curtisi with high/moderate frequencies of 52.17% and 17.39%, respectively. Evidence of positive selection (dN/dS = 2.41) was found for podhfr in P. ovale curtisi and decreased diversity (He) of microsatellite markers flanking the mutant alleles suggests that selective sweeps have occurred for both. Mutations E34G (1.50%) and L43V (1.50%) in pocrt of P. ovale curtisi, and E34G (3.70%), I102M (1.80%) and V111F (1.80%) of P. ovale wallikeri were found at low frequencies. Mutations R66K (6.20%), R75K (11.63%) and R95K (3.88%) of pocytb were found in both P. ovale curtisi and P. ovale wallikeri. These results suggest that the podhfr gene of P. ovale curtisi may be subject to drug selection in Africa, warranting further attention. We observed significant differences in the prevalence and distribution of podhfr mutations between the two P. ovale species, suggestive of fundamental biological differences between them. Author summary: The importance of the hitherto neglected malaria parasites Plasmodium ovale curtisi, Plasmodium ovale wallikeri and Plasmodium malariae is now becoming apparent. It is clear that these species are prevalent in Africa at much higher rates than previously thought, and that they are responsible for a significant amount of malaria-related morbidity. There is very little currently known about the epidemiology of these parasites, despite their importance. Of particular importance is understanding whether these parasites undergo selection for drug resistance in similar ways as Plasmodium falciparum and Plasmodium vivax. The fact that little is known regarding the molecular epidemiology of these parasites is due to difficulties in identifying them in the field, the fact that they are often present at low parasite densities in the blood, are often masked by co-infection with P. falciparum, and that there is no in vitro culture system available for them. We were able to utilise a unique and priceless resource–P. ovale spp. samples, mostly in mono-infections, from non-immune Chinese travellers to Africa–to sequence orthologues of several genes known to be linked to drug resistance in other malaria parasite species. This resource enabled us to sample a number of parasites from a widespread geographical area; something that has never before been possible. Through sequencing of the orthologues of several genes known to be linked to drug resistance in other malaria parasite species, high frequencies of S58R and S113N/T mutations were observed in podhfr in P. ovale curtisi isolates from Africa. Furthermore, by surveying the genetic diversity around these loci using microsatellite markers, we were able to show that the podhfr gene of African P. ovale curtisi has undergone selection for particular mutations, probably due to drug pressure, and this warrants further attention. [ABSTRACT FROM AUTHOR]

Rift Valley fever (RVF) is an arboviral disease of humans and livestock responsible for severe economic and human health impacts. In humans, RVF spans a variety of clinical manifestations, ranging from an acute flu-like illness to severe forms of disease, including late-onset encephalitis. The large variations in human RVF disease are inadequately represented by current murine models, which overwhelmingly die of early-onset hepatitis. Existing mouse models of RVF encephalitis are either immunosuppressed, display an inconsistent phenotype, or develop encephalitis only when challenged via intranasal or aerosol exposure. In this study, the genetically defined recombinant inbred mouse resource known as the Collaborative Cross (CC) was used to identify mice with additional RVF disease phenotypes when challenged via a peripheral foot-pad route to mimic mosquito-bite exposure. Wild-type Rift Valley fever virus (RVFV) challenge of 20 CC strains revealed three distinct disease phenotypes: early-onset hepatitis, mixed phenotype, and late-onset encephalitis. Strain CC057/Unc, with the most divergent phenotype, which died of late-onset encephalitis at a median of 11 days post-infection, is the first mouse strain to develop consistent encephalitis following peripheral challenge. CC057/Unc mice were directly compared to C57BL/6 mice, which uniformly succumb to hepatitis within 2–4 days of infection. Encephalitic disease in CC057/Unc mice was characterized by high viral RNA loads in brain tissue, accompanied by clearance of viral RNA from the periphery, low ALT levels, lymphopenia, and neutrophilia. In contrast, C57BL/6 mice succumbed from hepatitis at 3 days post-infection with high viral RNA loads in the liver, viremia, high ALT levels, lymphopenia, and thrombocytopenia. The identification of a strain of CC mice as an RVFV encephalitis model will allow for future investigation into the pathogenesis and treatment of RVF encephalitic disease and indicates that genetic background makes a major contribution to RVF disease variation. Author summary: Rift Valley fever virus (RVFV) is a negative sense RNA arbovirus of clinical relevance found throughout Africa and into the Middle East. In humans, RVF disease exhibits various clinical manifestations including acute febrile illness, hepatitis, hemorrhagic fever, and encephalitis. Unfortunately, existing murine models have been limited to studies of acute lethal hepatitis. Here, we identify a mouse model in which all animals survive acute hepatitis and go on to succumb to late onset encephalitis. A key feature of this new experimental system is administration of the virus in the footpad (to mimic mosquito bite), to model a natural route of infection. Importantly in this work, we used the Collaborative Cross recombinant inbred mouse resource to identify this RVFV CNS model. Therefore, our study demonstrates that host genetics can modulate RVF disease manifestations. The identification of this model also enables the field for high throughput, in vivo studies of central nervous system pathogenesis as well as in vivo evaluation of vaccines and therapeutics targeted against RVF encephalitis. [ABSTRACT FROM AUTHOR]

The olive fruit fly, specialized to become monophagous during several life stages, remains the most important olive tree pest with high direct production losses, but also affecting the quality, composition, and inherent properties of the olives. Thought to have originated in Africa is nowadays present wherever olive groves are grown. The olive fruit fly evolved to harbor a vertically transmitted and obligate bacterial symbiont -Candidatus Erwinia dacicola- leading thus to a tight evolutionary history between olive tree, fruit fly and obligate, vertical transmitted symbiotic bacterium. Considering this linkage, the genetic diversity (at a 16S fragment) of this obligate symbiont was added in the understanding of the distribution pattern of the holobiont at nine locations throughout four countries in the Mediterranean Basin. This was complemented with mitochondrial (four mtDNA fragments) and nuclear (ten microsatellites) data of the host. We focused on the previously established Iberian cluster for the B. oleae structure and hypothesised that the Tunisian samples would fall into a differentiated cluster. From the host point of view, we were unable to confirm this hypothesis. Looking at the symbiont, however, two new 16S haplotypes were found exclusively in the populations from Tunisia. This finding is discussed in the frame of host-symbiont specificity and transmission mode. To understand olive fruit fly population diversity and dispersion, the dynamics of the symbiont also needs to be taken into consideration, as it enables the fly to, so efficiently and uniquely, exploit the olive fruit resource. [ABSTRACT FROM AUTHOR]

While it is generally accepted that language and speech have genetic foundations, and that the widespread inter-individual variation observed in many of their aspects is partly driven by variation in genes, it is much less clear if differences between languages may also be partly rooted in our genes. One such proposal is that the population frequencies of the so-called "derived" alleles of two genes involved in brain growth and development, ASPM and Microcephalin, are related to the probability of speaking a tone language or not. The original study introducing this proposal used a cross-linguistic statistical approach, showing that these associations are "special" when compared with many other possible relationships between genetic variants and linguistic features. Recent experimental evidence supports strongly a negative effect of the "derived" allele of ASPM on tone perception and/or processing within individuals, but failed to find any effect for Microcephalin. Motivated by these experimental findings, I conduct here a cross-linguistic statistical test, using a larger and updated dataset of 175 samples from 129 unique (meta)populations, and a battery of methods including mixed-effects regression (Bayesian and maximum-likelihood), mediation and path analysis, decision trees and random forests, using permutations and restricted sampling to control for the confounding effects of genealogy (language families) and contact (macroareas). Overall, the results support a negative weak effect of ASPM-D against the presence of tone above and beyond the strong confounding influences of genealogy and contact, but they suggest that the original association between tone and MCPH1 might have been a false positive, explained by differences between populations and languages within and outside Africa. Thus, these cross-linguistic population-scale statistical results are fully consonant with the inter-individual-level experimental results, and suggest that the observed linguistic diversity may be, at least in some cases, partly driven by genetic diversity. [ABSTRACT FROM AUTHOR]