scholarly journals GWAS provides biological insights into mechanisms of the parasitic plant (Striga) resistance in sorghum

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Jacinta Kavuluko ◽  
Magdaline Kibe ◽  
Irine Sugut ◽  
Willy Kibet ◽  
Joel Masanga ◽  
...  
Keyword(s):  
Smallholder Farmers ◽  
Association Studies ◽  
Resistance Mechanisms ◽  
Hypersensitive Reaction ◽  
Sub Saharan Africa ◽  
Parasite Development ◽  
Genome Wide Association Studies ◽  
Sources Of Resistance ◽  
Response Factors ◽  
Resistance Response

Abstract Background Sorghum yields in sub-Saharan Africa (SSA) are greatly reduced by parasitic plants of the genus Striga (witchweed). Vast global sorghum genetic diversity collections, as well as the availability of modern sequencing technologies, can be potentially harnessed to effectively manage the parasite. Results We used laboratory assays – rhizotrons to screen a global sorghum diversity panel to identify new sources of resistance to Striga; determine mechanisms of resistance, and elucidate genetic loci underlying the resistance using genome-wide association studies (GWAS). New Striga resistant sorghum determined by the number, size and biomass of parasite attachments were identified. Resistance was by; i) mechanical barriers that blocked parasite entry, ii) elicitation of a hypersensitive reaction that interfered with parasite development, and iii) the inability of the parasite to develop vascular connections with hosts. Resistance genes underpinning the resistance corresponded with the resistance mechanisms and included pleiotropic drug resistance proteins that transport resistance molecules; xylanase inhibitors involved in cell wall fortification and hormonal regulators of resistance response, Ethylene Response Factors. Conclusions Our findings are of fundamental importance to developing durable and broad-spectrum resistance against Striga and have far-reaching applications in many SSA countries where Striga threatens the livelihoods of millions of smallholder farmers that rely on sorghum as a food staple.

scholarly journals GWAS Provides Biological Insights into Mechanisms of the Parasitic Plant (Striga) Resistance in Sorghum

2020 ◽  
Author(s):  
Jacinta Kavuluko ◽  
Magdaline Kibe ◽  
Irine Sugut ◽  
Willy Kibet ◽  
Joel Masanga ◽  
...  
Keyword(s):  
Smallholder Farmers ◽  
Association Studies ◽  
Resistance Mechanisms ◽  
Hypersensitive Reaction ◽  
Sub Saharan Africa ◽  
Parasite Development ◽  
Genome Wide Association Studies ◽  
Sources Of Resistance ◽  
Response Factors ◽  
Resistance Response

Abstract Background: Sorghum yields in sub-Saharan Africa (SSA) are greatly reduced by parasitic plants of the genus Striga (witchweed). Vast global sorghum genetic diversity collections, as well as the availability of modern sequencing technologies, can be potentially harnessed to effectively manage the parasite. Results: We used laboratory assays – rhizotrons to screen a global sorghum diversity panel to identify new sources of resistance to Striga; determine mechanisms of resistance, and elucidate genetic loci underlying the resistance using genome-wide association studies (GWAS). New Striga resistant sorghum determined by the number, size and biomass of parasite attahements were identified. In total 13 sorghum genotypes had higher or comparable resistance levels as IS9830 and N13 used as resistance checks. Resistance was by; i) mechanical barriers that blocked parasite entry, ii) elicitation of a hypersensitive reaction that interfered with parasite development, and iii) the inability of the parasite to develop vascular connections with hosts. Resistance genes underpinning the resistance corresponded with the resistance mechanisms and included pleiotropic drug resistance proteins that transport resistance molecules; xylanase inhibitors involved in cell wall fortification and hormonal regulators of resistance response, Ethylene Response Factors. Conclusions: Our findings are of fundamental importance to developing durable and broad-spectrum resistance against Striga and have far-reaching applications in many SSA countries where Striga threatens the livelihoods of millions of smallholder farmers that rely on sorghum as a food staple.

scholarly journals Fine scale human genetic structure in three regions of Cameroon reveals episodic diversifying selection

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kevin K. Esoh ◽  
Tobias O. Apinjoh ◽  
Steven G. Nyanjom ◽  
Ambroise Wonkam ◽  
Emile R. Chimusa ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Ethnic Groups ◽  
Genetic Association ◽  
Association Studies ◽  
Genetic Association Studies ◽  
Genomic Region ◽  
Sub Saharan Africa ◽  
Genome Wide Association Studies ◽  
Fine Scale ◽  
Sub Saharan

AbstractInferences from genetic association studies rely largely on the definition and description of the underlying populations that highlight their genetic similarities and differences. The clustering of human populations into subgroups (population structure) can significantly confound disease associations. This study investigated the fine-scale genetic structure within Cameroon that may underlie disparities observed with Cameroonian ethnicities in malaria genome-wide association studies in sub-Saharan Africa. Genotype data of 1073 individuals from three regions and three ethnic groups in Cameroon were analyzed using measures of genetic proximity to ascertain fine-scale genetic structure. Model-based clustering revealed distinct ancestral proportions among the Bantu, Semi-Bantu and Foulbe ethnic groups, while haplotype-based coancestry estimation revealed possible longstanding and ongoing sympatric differentiation among individuals of the Foulbe ethnic group, and their Bantu and Semi-Bantu counterparts. A genome scan found strong selection signatures in the HLA gene region, confirming longstanding knowledge of natural selection on this genomic region in African populations following immense disease pressure. Signatures of selection were also observed in the HBB gene cluster, a genomic region known to be under strong balancing selection in sub-Saharan Africa due to its co-evolution with malaria. This study further supports the role of evolution in shaping genomes of Cameroonian populations and reveals fine-scale hierarchical structure among and within Cameroonian ethnicities that may impact genetic association studies in the country.

scholarly journals Genotypic Variation in Cultivated and Wild Sorghum Genotypes in Response to Striga hermonthica Infestation

2021 ◽  
Vol 12 ◽  
Author(s):  
Nicoleta Muchira ◽  
Kahiu Ngugi ◽  
Lydia N. Wamalwa ◽  
Millicent Avosa ◽  
Wiliter Chepkorir ◽  
...  
Keyword(s):  
Field Trial ◽  
Smallholder Farmers ◽  
Genotypic Variation ◽  
Sub Saharan Africa ◽  
Striga Hermonthica ◽  
Sources Of Resistance ◽  
Factors Affecting ◽  
Progress Curve ◽  
Pot Trial ◽  
Sorghum Genotypes

Striga hermonthica is the most important parasitic weed in sub-Saharan Africa and remains one of the most devastating biotic factors affecting sorghum production in the western regions of Kenya. Farmers have traditionally managed Striga using cultural methods, but the most effective and practical solution to poor smallholder farmers is to develop Striga-resistant varieties. This study was undertaken with the aim of identifying new sources of resistance to Striga in comparison with the conventional sources as standard checks. We evaluated 64 sorghum genotypes consisting of wild relatives, landraces, improved varieties, and fourth filial generation (F4) progenies in both a field trial and a pot trial. Data were collected for days to 50% flowering (DTF), dry panicle weight (DPW, g), plant height (PH, cm), yield (YLD, t ha−1), 100-grain weight (HGW, g), overall disease score (ODS), overall pest score (OPS), area under Striga number progress curve (ASNPC), maximum above-ground Striga (NSmax), and number of Striga-forming capsules (NSFC) at relevant stages. Genetic diversity and hybridity confirmation was determined using Diversity Arrays Technology sequencing (DArT-seq). Residual heterosis for HGW and NSmax was calculated as the percent increase or decrease in performance of F4 crossover midparent (MP). The top 10 best yielding genotypes were predominantly F4 crosses in both experiments, all of which yielded better than resistant checks, except FRAMIDA in the field trial and HAKIKA in the pot trial. Five F4 progenies (ICSVIII IN × E36-1, LANDIWHITE × B35, B35 × E36-1, F6YQ212 × B35, and ICSVIII IN × LODOKA) recorded some of the highest HGW in both trials revealing their stability in good performance. Three genotypes (F6YQ212, GBK045827, and F6YQ212xB35) and one check (SRN39) were among the most resistant to Striga in both trials. SNPs generated from DArT-seq grouped the genotypes into three major clusters, with all resistant checks grouping in the same cluster except N13. We identified more resistant and high-yielding genotypes than the conventional checks, especially among the F4 crosses, which should be promoted for adoption by farmers. Future studies will need to look for more diverse sources of Striga resistance and pyramid different mechanisms of resistance into farmer-preferred varieties to enhance the durability of Striga resistance in the fields of farmers.

scholarly journals Structure of genetic diversity and genome-wide association studies of bean fly (Ophiomyia spencerella) resistance in common bean

Euphytica ◽  
2021 ◽  
Vol 217 (12) ◽  
Author(s):  
Pascal P. Okwiri Ojwang ◽  
Tilly Eldridge ◽  
Pilar Corredor-Moreno ◽  
Vincent Njung’e
Keyword(s):  
Genetic Diversity ◽  
Common Bean ◽  
Association Studies ◽  
Sub Saharan Africa ◽  
Genome Wide Association ◽  
Eastern Africa ◽  
Genome Wide Association Studies ◽  
Ophiomyia Spencerella ◽  
Genome Wide ◽  
Bean Fly

AbstractEastern Africa is a significant region of common bean (Phaseolus vulgaris L.) production and genetic diversity. Insect pests are a major biotic constraint in subsistence crop production systems. Bean fly (Ophiomyia spencerella) is a serious pest of beans in eastern Africa highlands. Breeding efforts focus on combining adaptability traits with user preferred seed types. However, lack of information on molecular markers linked to genes modulating bean fly resistance has slowed breeding progress. The objectives were to: (i) characterize genetic diversity and uncover putative bean fly resistant genotypes within diverse seed types and market classes and (ii) identify genomic regions controlling bean fly resistance using genome-wide association analysis (GWAS). A set of 276 diverse genotypes comprising local landraces and varieties from Kenya alongside introductions from International Centre for Tropical Agriculture (CIAT), were assembled. The germplasm represented varied bean production ecologies and seed types. Genetic diversity conforming to Andean and Mesoamerican genepools was established. Out of 276 genotypes evaluated, 150 were Andean, 74 were Mesoamerican and 52 were admixed. Twenty-two genotypes were resistant to bean fly. Association mapping results for stem damage score and plant mortality identified six significant single-nucleotide polymorphisms (SNPs) on chromosomes Pv01 and Pv09. The most significant SNP marker was 12 kilobases downstream of Phvul.001G074900 gene with LOD score > 4.0 hence in linkage disequilibrium with the postulated gene. The identified candidate gene is pleiotropic and modulates both flowering time and plant responses to stress. These findings are a key step towards marker-enabled breeding in common bean for sub-Saharan Africa.

scholarly journals Genome-Wide Association Studies of malaria susceptibility and resistance: progress, pitfalls and prospects

2018 ◽  
Author(s):  
Delesa Damena ◽  
Awany Denis ◽  
Lemu Golassa ◽  
Emile R. Chimusa
Keyword(s):  
Molecular Mechanisms ◽  
Association Studies ◽  
Genetic Correlations ◽  
Sub Saharan Africa ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Malaria Susceptibility ◽  
Endemic Areas ◽  
Susceptibility And Resistance

AbstractP. falciparum malaria is still among the leading causes of child mortality in sub-Saharan Africa; killing hundreds of thousands of children each year. Malaria has been recognized as one of the prominent evolutionary selective forces of human genome that led to the emergence of multiple host protective polymorphisms associated with minimizing the risk of developing severe malaria in endemic areas. A comprehensive understanding of the genetic bases of malaria resistance can shed light to the molecular mechanisms of host-parasite interactions that can potentially pave ways to the development of new therapeutics and vaccines. Genome-wide association studies (GWASs) have recently been implemented in malaria endemic areas and identified a number of novel association genetic variants. Despite this success, only few variants did replicate across the studies and the underlying biology is yet to be understood for the majority of the novel variants. Besides, there are several open questions around heritability, polygenic effects, epistatic interactions, genetic correlations and associated molecular pathways among others. In this review, we first assess the progress and pitfalls of malaria susceptibility GWASs. We then, provide an overview of the current progress in post-GWAS approaches and discuss how these approaches can potentially be implemented in malaria susceptibility GWASs to extract further functional information. We conclude by highlighting the importance of multi-step and multidimensional integrative studies for unravelling the genetic basis of malaria susceptibility and resistance at systems biology level.

scholarly journals Genome wide association mapping of Pyrenophora teres f. maculata and Pyrenophora teres f. teres resistance loci utilizing natural Turkish wild and landrace barley populations

2021 ◽  
Author(s):  
Shaun James Clare ◽  
Arzu Çelik Oğuz ◽  
Karl Effertz ◽  
Roshan Sharma Poudel ◽  
Deven See ◽  
...  
Keyword(s):  
Fungal Pathogens ◽  
Genome Wide Association Study ◽  
Association Studies ◽  
Hordeum Spontaneum ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Pyrenophora Teres ◽  
Net Blotch ◽  
Sources Of Resistance ◽  
Genome Wide

Unimproved landraces and wild relatives of crops are sources of genetic diversity that were lost post domestication in modern breeding programs. To tap into this rich resource, genome wide association studies in large plant genomes have enabled the rapid genetic characterization of desired traits from natural landrace and wild populations. Wild barley (Hordeum spontaneum), the progenitor of domesticated barley (H. vulgare), is dispersed across Asia and North Africa, and has co-evolved with the ascomycetous fungal pathogens Pyrenophora teres f. teres and P. teres f. maculata, the casual agents of the diseases net form of net blotch and spot form of net blotch, respectively. Thus, these wild and local adapted barley landraces from the region of origin of both the host and pathogen represent a diverse gene pool to identify new sources of resistance, due to millions of years of co-evolution. The barley - P. teres pathosystem is governed by complex genetic interactions with dominant, recessive, and incomplete resistances and susceptibilities, with many isolate-specific interactions. Here we provide the first genome wide association study of wild and landrace barley from the Fertile Crescent for resistance to both forms of P. teres. A total of 14 loci, four against P. teres f. maculata and ten against Pyrenophora teres f. teres, were identified in both wild and landrace populations, showing that both are genetic reservoirs for novel sources of resistance. We also highlight the importance of using multiple algorithms to both identify and validate additional loci.

scholarly journals A custom genotyping array reveals population-level heterogeneity for the genetic risks of prostate cancer and other cancers in Africa

2019 ◽  
Author(s):  
Maxine Harlemon ◽  
Olabode Ajayi ◽  
Paidamoyo Kachambwa ◽  
Michelle S. Kim ◽  
Corinne N. Simonti ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Association Studies ◽  
Genomic Medicine ◽  
Sub Saharan Africa ◽  
Risk Scores ◽  
Genome Wide Association Studies ◽  
Genotyping Array ◽  
Common Genetic Variants ◽  
African Populations ◽  
Disease Associations

AbstractAlthough prostate cancer is the leading cause of cancer mortality for African men, the vast majority of known disease associations have been detected in European study cohorts. Furthermore, most genome-wide association studies have used genotyping arrays that are hindered by SNP ascertainment bias. To overcome these disparities in genomic medicine, the Men of African Descent and Carcinoma of the Prostate (MADCaP) Network has developed a genotyping array that is optimized for African populations. The MADCaP Array contains more than 1.5 million markers and an imputation backbone that successfully tags over 94% of common genetic variants in African populations. This array also has a high density of markers in genomic regions associated with cancer susceptibility, including 8q24. We assessed the effectiveness of the MADCaP Array by genotyping 399 prostate cancer cases and 403 controls from seven urban study sites in sub-Saharan Africa. We find that samples from Ghana and Nigeria cluster together, while samples from Senegal and South Africa yield distinct ancestry clusters. Using the MADCaP array, we identified cancer-associated loci that have large allele frequency differences across African populations. Polygenic risk scores were also generated for each genome in the MADCaP pilot dataset, and we found that predicted risks of CaP are lower in Senegal and higher in Nigeria.SignificanceWe have developed an Africa-specific genotyping array which enables investigators to identify novel disease associations and to fine-map genetic loci that are associated with prostate and other cancers.

scholarly journals Contrasting approaches to genome-wide association studies impact the detection of resistance mechanisms in Staphylococcus aureus

2019 ◽  
Author(s):  
Nicole E. Wheeler ◽  
Sandra Reuter ◽  
Claire Chewapreecha ◽  
John A. Lees ◽  
Beth Blane ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Genome Wide Association Study ◽  
Association Studies ◽  
Resistance Mechanisms ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Phenotypic Resistance ◽  
Resistance Determinants ◽  
Genome Wide ◽  
Resistance Prediction

AbstractRapid detection of antibiotic resistance using whole-genome sequencing (WGS) could improve clinical outcomes and limit the spread of resistance. For this to succeed, we need an accurate way of linking genotype to phenotype, that identifies new resistance mechanisms as they appear. To assess how close we are to this goal, we characterized antimicrobial resistance determinants in >4,000 Staphylococcus aureus genomes of isolates associated with bloodstream infection in the United Kingdom and Ireland. We sought to answer three questions: 1) how well did known resistance mechanisms explain phenotypic resistance in our collection, 2) how many previously identified resistance mechanisms appeared in our collection, and 3) how many of these were detectable using four contrasting genome-wide association study (GWAS) methods. Resistance prediction based on the detection of known resistance determinants was 98.8% accurate. We identified challenges in correcting for population structure, clustering orthologous genes, and identifying causal mechanisms in rare or common phenotypes, which reduced the recovery of known mechanisms. Limited sensitivity and specificity of these methods made prediction using GWAS-discovered hits alone less accurate than using literature-derived genetic determinants. However, GWAS methods identified novel mutations associated with resistance, including five mutations in rpsJ, which improved tetracycline resistance prediction for 28 isolates, and a T118I substitution in fusA which resulted in better fusidic acid resistance prediction for 5 isolates. Thus, GWAS approaches in conjunction with phenotypic testing data can support the development of comprehensive databases to enable real-time use of WGS for patient management.

scholarly journals Genetic Improvement for Resistance to Black Sigatoka in Bananas: A Systematic Review

2021 ◽  
Vol 12 ◽  
Author(s):  
Julianna M. S. Soares ◽  
Anelita J. Rocha ◽  
Fernanda S. Nascimento ◽  
Adriadna S. Santos ◽  
Robert N. G. Miller ◽  
...  
Keyword(s):  
Genetic Improvement ◽  
Sub Saharan Africa ◽  
Black Sigatoka ◽  
Sources Of Resistance ◽  
Resistance Response ◽  
Pathogenesis Related ◽  
Improvement Programs ◽  
Sub Saharan ◽  
Related Proteins

Bananas are an important staple food crop in tropical and subtropical regions in Asia, sub-Saharan Africa, and Central and South America. The plant is affected by numerous diseases, with the fungal leaf disease black Sigatoka, caused by Mycosphaerella fijiensis Morelet [anamorph: Pseudocercospora fijiensis (Morelet) Deighton], considered one of the most economically important phytosanitary problem. Although the development of resistant cultivars is recognized as most effective method for long term control of the disease, the majority of today's cultivars are susceptible. In order to gain insights into this pathosystem, this first systematic literature review on the topic is presented. Utilizing six databases (PubMed Central, Web of Science, Google Academic, Springer, CAPES and Scopus Journals) searches were performed using pre-established inclusion and exclusion criteria. From a total of 3,070 published studies examined, 24 were relevant with regard to the Musa-P. fijiensis pathosystem. Relevant papers highlighted that resistant and susceptible cultivars clearly respond differently to infection by this pathogen. M. acuminata wild diploids such as Calcutta 4 and other diploid cultivars can harbor sources of resistance genes, serving as parentals for the generation of improved diploids and subsequent gene introgression in new cultivars. From the sequenced reference genome of Musa acuminata, although the function of many genes in the genome still require validation, on the basis of transcriptome, proteome and biochemical data, numerous candidate genes and molecules have been identified for further evaluation through genetic transformation and gene editing approaches. Genes identified in the resistance response have included those associated with jasmonic acid and ethylene signaling, transcription factors, phenylpropanoid pathways, antioxidants and pathogenesis-related proteins. Papers in this study also revealed gene-derived markers in Musa applicable for downstream application in marker assisted selection. The information gathered in this review furthers understanding of the immune response in Musa to the pathogen P. fijiensis and is relevant for genetic improvement programs for bananas and plantains for control of black Sigatoka.

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