scholarly journals Genetic relationships between interspecific lines derived from Oryza glaberrima and Oryza sativa crosses using microsatellites and agro-morphological markers

2015 ◽  
Vol 13 (2) ◽  
pp. e0701 ◽  
Author(s):  
Yonnelle D. Moukoumbi ◽  
Olufisayo Kolade ◽  
Khady N. Drame ◽  
Moussa Sie ◽  
Marie Noelle Ndjiondjop
Keyword(s):  
Genetic Relationships ◽  
Rice Genome ◽  
Growth Conditions ◽  
Leaf Length ◽  
Sub Saharan Africa ◽  
Morphological Data ◽  
Oryza Glaberrima ◽  
Recurrent Parent ◽  
Rice Varieties ◽  
Sub Saharan

<p>New Rice(s) for Africa (NERICA) are high yielding rice varieties mostly cultivated in Sub-Saharan Africa and developed by the Africa Rice Center. This study is aimed at investigating the proportion of introgression of parental genomic contribution of 60 lowland NERICA varieties and establishment of molecular profiling. Agro-morphological data from 17 characteristics was recorded and significant (<em>p</em>&lt;0.05) to high significant (<em>p</em>&lt;0.0001) differences were obtained with leaf length and width, plant height at maturity, days to heading, maturity, primary and secondary branching of panicles, and grain width and grain thickness. A total of 114 microsatellite polymorphic markers covering 2183.13 cM of the rice genome showed the proportions of alleles introgressed from the donor parent (<em>Oryza glaberrima</em>) into 52 lowland NERICA lines (TOG5681 and IR64)<em> </em>as follows: 11% for BC<sub>2</sub>, 6.07% for BC<sub>3, </sub>and 7.55% for BC<sub>4</sub>. The introgression proportions for the eight remaining lowland NERICA lines derived from other crosses ranged from 5.5 to 11.3%. The proportion recorded with the recurrent parent was 83.99%. The highest introgression proportions of the <em>O. glaberrima </em>allele for all 60 lowland NERICA lines were found on chromosomes 2, 6 and 12 (TOG5681/IR64) and on chromosome 3 with NERIC-L-29 (TOG5681/IR1529-680-3-2). Multivariate analyses performed using an association of agro-morphological and molecular data revealed two major groups according to the distribution of the lowland NERICAs including the lowland NERICAs released were found in cluster 1 of the dendrogram. Genetic and genomic studies, QTL identification and analysis using agro-morphologically significant traits revealed should be used to develop mega-varieties adapted in rice growth conditions in Sub-Saharan Africa.</p>

scholarly journals Mechanistic understanding of iron toxicity tolerance in contrasting rice varieties from Africa: 2. Root oxidation ability and oxidative stress control

2020 ◽  
Vol 47 (2) ◽  
pp. 145
Author(s):  
Dorothy A. Onyango ◽  
Fredrickson Entila ◽  
James Egdane ◽  
Myrish Pacleb ◽  
Meggy Lou Katimbang ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Sub Saharan Africa ◽  
Rice Varieties ◽  
Excess Iron ◽  
Improvement Programs ◽  
Sub Saharan ◽  
Breeding Efficiency ◽  
Biochemical Analyses ◽  
Fe Toxicity ◽  
And Control

To enhance breeding efficiency for iron (Fe) toxicity tolerance and boost lowland rice production in sub-Saharan Africa, we have characterised the morphological, physiological and biochemical responses of contrasting rice varieties to excess iron. Here, we report the capacity of four varieties (CK801 and Suakoko8 (tolerant), Supa and IR64 (sensitive)) to oxidise iron in the rhizosphere and control iron-induced oxidative stress. The experiments were conducted in hydroponic conditions using modified Magnavaca nutrient solution and 300 ppm of ferrous iron (Fe2+) supplied in the form of FeSO4. Severe oxidative stress was observed in sensitive varieties as revealed by their high levels of lipid peroxidation. Histochemical and biochemical analyses showed that tolerant varieties exhibited a better development of the aerenchyma and greater oxygen release than the sensitive varieties in response to excess Fe. Both suberin and lignin deposits were observed in the root, stem and leaf tissues but with varying intensities depending on the variety. Under iron toxic conditions, tolerant varieties displayed increased superoxide dismutase (SOD), glutathione reductase (GR), peroxidase (POX) and ascorbate peroxidase (APX) activities in both the roots and shoots, whereas sensitive varieties showed increased APX and catalase (CAT) activities in the roots. This study had revealed also that Suakoko8 mainly uses root oxidation to exclude Fe2+ from its rhizosphere, and CK801 possesses a strong reactive oxygen species scavenging system, in addition to root oxidation ability. Key traits associated with these tolerance mechanisms such as a well-developed aerenchyma, radial oxygen loss restricted to the root cap as well as strong activation of antioxidative enzymes (SOD, GR, POX and APX) could be useful selection criteria in rice varietal improvement programs for enhanced Fe toxicity tolerance.

scholarly journals Adding function to the genome of AfricanSalmonellaST313

2018 ◽  
Author(s):  
Rocío Canals ◽  
Disa L. Hammarlöf ◽  
Carsten Kröger ◽  
Siân V. Owen ◽  
Wai Yee Fong ◽  
...  
Keyword(s):  
Large Scale ◽  
Global Gene Expression ◽  
Growth Conditions ◽  
Trna Synthetase ◽  
Sub Saharan Africa ◽  
Phenotypic Differences ◽  
Metabolic Genes ◽  
Lineage 2 ◽  
Global Gene Expression Analysis ◽  
Sub Saharan

AbstractSalmonellaTyphimurium ST313 causes invasive nontyphoidalSalmonella(iNTS) disease in sub-Saharan Africa, targeting susceptible HIV+, malarial or malnourished individuals. An in-depth genomic comparison between the ST313 isolate D23580, and the well-characterized ST19 isolate 4/74 that causes gastroenteritis across the globe, revealed extensive synteny. To understand how the 856 nucleotide variations generated phenotypic differences, we devised a large-scale experimental approach that involved the global gene expression analysis of strains D23580 and 4/74 grown in sixteen infection-relevant growth conditions. Comparison of transcriptional patterns identified virulence and metabolic genes that were differentially expressed between D23580 versus 4/74, many of which were validated by proteomics. We also uncovered theS.Typhimurium D23580 and 4/74 genes that showed expression differences during infection of murine macrophages. Our comparative transcriptomic data are presented in a new enhanced version of theSalmonellaexpression compendium SalComD23580:bioinf.gen.tcd.ie/cgi-bin/salcom_v2.pl. We discovered that the ablation of melibiose utilization was caused by 3 independent SNP mutations in D23580 that are shared across ST313 lineage 2, suggesting that the ability to catabolise this carbon source has been negatively selected during ST313 evolution. The data revealed a novel plasmid maintenance system involving a plasmid-encoded CysS cysteinyl-tRNA synthetase, highlighting the power of large-scale comparative multi-condition analyses to pinpoint key phenotypic differences between bacterial pathovariants.

scholarly journals Frequent infection of Hylobates pileatus (pileated gibbon) with species-associated variants of hepatitis B virus in Cambodia

2005 ◽  
Vol 86 (2) ◽  
pp. 333-337 ◽  
Author(s):  
A. A. Sall ◽  
S. Starkman ◽  
J. M. Reynes ◽  
S. Lay ◽  
T. Nhim ◽  
...  
Keyword(s):  
Hepatitis B Virus ◽  
Hepatitis B ◽  
East Asia ◽  
Genetic Relationships ◽  
Sub Saharan Africa ◽  
Human Populations ◽  
South East Asia ◽  
B Virus ◽  
Hylobates Pileatus ◽  
Sub Saharan

As well as being distributed widely in human populations, hepatitis B virus (HBV) infections occur frequently in chimpanzee, gibbon and other ape populations in sub-Saharan Africa and South-East Asia. To investigate the frequency and genetic relationships of HBV infecting gibbons in Cambodia, pileated gibbons (Hylobates pileatus) that were originally wild-caught were screened for surface antigen. Twelve of 26 (46 %) were positive, of which 11 were positive for HBV DNA. Phylogenetic analysis of complete genome sequences revealed two distinct genetic groups in the gibbon/orangutan clade. Three were similar to previously described variants infecting H. pileatus in Thailand and eight formed a distinct clade, potentially representing distinct strains of HBV circulating in geographically separated populations in South-East Asia. Because of the ability of HBV to cross species barriers, large reservoirs of infection in gibbons may hamper ongoing attempts at permanent eradication of HBV infection from human populations in South-East Asia through immunization.

The state of African cattle genetic resources II. Geographical distribution, characteristics and uses of present-day breeds and strains

1999 ◽  
Vol 26 ◽  
pp. 1-25 ◽  
Author(s):  
J.E.O. Rege ◽  
C.L. Tawah
Keyword(s):  
Genetic Resources ◽  
Genetic Relationships ◽  
Sub Saharan Africa ◽  
East African ◽  
African Cattle ◽  
The Status ◽  
Quantitative Indication ◽  
Sub Saharan ◽  
Large Effort ◽  
Further Development

SummaryThis paper summarises preliminary results of a survey conducted as part of a large effort to systematically collate information aimed at assessing the status of cattle genetic resources of sub-Saharan Africa. The 146 indigenous breeds/strains identified from the survey are classified into nine broad groups (Humpless Longhorns, Humpless Shorthorns, Large East African Zebu, Small East African Zebu, West African Zebu, Sanga, Zenga, Recently Derived Breeds and Commercial Composites) some of which are further subdivided into several groups (based on possible genetic relationships) and clusters (based on eco-geographical locations). Each breed is then described in terms of location, physical characteristics, adaptive attributes, if known, current main uses and status in terms of qualitative or quantitative indication of trends, where available, and presence or absence of programmes for its management or further development.

scholarly journals Mozambican genetic variation provides new insights into the Bantu expansion

2019 ◽  
Author(s):  
Armando Semo ◽  
Magdalena Gayà-Vidal ◽  
Cesar Fortes-Lima ◽  
Bérénice Alard ◽  
Sandra Oliveira ◽  
...  
Keyword(s):  
Iron Age ◽  
Genetic Relationships ◽  
Central Africa ◽  
Sub Saharan Africa ◽  
Eastern Africa ◽  
Nucleotide Polymorphisms ◽  
Wide Range ◽  
The Rich ◽  
Sub Saharan ◽  
Genetic Substructure

AbstractThe Bantu expansion, which started in West Central Africa around 5,000 BP, constitutes a major migratory movement involving the joint spread of peoples and languages across sub-Saharan Africa. Despite the rich linguistic and archaeological evidence available, the genetic relationships between different Bantu-speaking populations and the migratory routes they followed during various phases of the expansion remain poorly understood. Here, we analyze the genetic profiles of southwestern and southeastern Bantu-speaking peoples located at the edges of the Bantu expansion by generating genome-wide data for 200 individuals from 12 Mozambican and 3 Angolan populations using ∼1.9 million autosomal single nucleotide polymorphisms. Incorporating a wide range of available genetic data, our analyses confirm previous results favoring a “late split” between West and East Bantu speakers, following a joint passage through the rainforest. In addition, we find that Bantu speakers from eastern Africa display genetic substructure, with Mozambican populations forming a gradient of relatedness along a North-South cline stretching from the coastal border between Kenya and Tanzania to South Africa. This gradient is further associated with a southward increase in genetic homogeneity, and involved minimum admixture with resident populations. Together, our results provide the first genetic evidence in support of a rapid North-South dispersal of Bantu peoples along the Indian Ocean Coast, as inferred from the distribution and antiquity of Early Iron Age assemblages associated with the Kwale archaeological tradition.

Linking root traits and grain yield for rainfed rice in sub-Saharan Africa: Response of Oryza sativa×Oryza glaberrima introgression lines under drought

2014 ◽  
Vol 165 ◽  
pp. 25-35 ◽  
Author(s):  
Abubakary A. Kijoji ◽  
Susan Nchimbi-Msolla ◽  
Zakaria L. Kanyeka ◽  
Rachid Serraj ◽  
Amelia Henry
Keyword(s):  
Oryza Sativa ◽  
Grain Yield ◽  
Root Traits ◽  
Introgression Lines ◽  
Sub Saharan Africa ◽  
Oryza Glaberrima ◽  
Rainfed Rice ◽  
Sub Saharan

scholarly journals Closing Gender Gaps in Climate-Smart Agriculture through Strengthening Women Rice Seed Farmer’s Capacities and Access to Quality Stress-tolerant Seed in Benin

2021 ◽  
Vol 10 (3) ◽  
pp. 41
Author(s):  
Espérance Zossou ◽  
Afiavi R. Agboh-Noameshie ◽  
Alidou Assouma-Imorou
Keyword(s):  
Seed Production ◽  
Division Of Labour ◽  
Sub Saharan Africa ◽  
Rice Seed ◽  
Design Strategies ◽  
Rice Varieties ◽  
New Varieties ◽  
Sub Saharan ◽  
Smart Agriculture ◽  
And Control

Climate change and stress conditions (drought; submergence, salinity, iron toxicity, and cold) disproportionately affect the poorest and most disadvantaged rice farmers, forcing them deeper into poverty. Recent advances in genetics and breeding enable the development of rice varieties tolerant of these abiotic stresses and their cultivation can substantially contribute to poverty alleviation in unfavourable environments and for poor rice consumers globally. Through the program Stress-Tolerant Rice for Africa and South Asia (STRASA), fourteen new stress-tolerant varieties were released, produced and distributed in Sub-Saharan Africa to reach millions of poor farmers. However, ignoring women&rsquo;s contributions to agriculture and particular in seed production and failing to design strategies to reach them with new varieties miss significant opportunities to reduce poverty. This study investigates on gender issues in rice seed production in Benin through a gender analysis of the division of labour, access and control of resources, livelihood, and constraints and opportunities faced. Both qualitative and quantitative data were collected with 29 women and 29 men seeds producers using both the Harvard Analytical and the Sustainable Livelihoods Frameworks. Data showed that women are central in rice seed production; but are marginalized in their access and control of resources. Given to women resources property rights as well as improving their control on resources will help them to be more performant as seed producers. These areas for action are important in designing and implementing activities in gender-responsive ways for sustainable Stress-Tolerant Rice seed multiplication, dissemination and out scaling in Africa.

scholarly journals The population genetics of Trypanosoma brucei and the origin of human infectivity

2001 ◽  
Vol 356 (1411) ◽  
pp. 1035-1044 ◽  
Author(s):  
Annette MacLeod ◽  
Andy Tait ◽  
C. Michel R. Turner
Keyword(s):  
Trypanosoma Brucei ◽  
Genetic Relationships ◽  
Genetic Exchange ◽  
Sub Saharan Africa ◽  
Tsetse Flies ◽  
Implicit Assumption ◽  
Mixed Genotype ◽  
Disease Biology ◽  
Zoonotic Parasite ◽  
Sub Saharan

The African trypanosome, Trypanosoma brucei , is a zoonotic parasite transmitted by tsetse flies. Two of the three subspecies, T. brucei gambiense and T.b. rhodesiense , cause sleeping sickness in humans whereas the third subspecies, T.b. brucei , is not infective to humans. We propose that the key to understanding genetic relationships within this species is the analysis of gene flow to determine the importance of genetic exchange within populations and the relatedness of populations. T.brucei parasites undergo genetic exchange when present in infections of mixed genotypes in tsetse flies in the laboratory, although this is not an obligatory process. Infections of mixed genotype are surprisingly common in field isolates from tsetse flies such that there is opportunity for genetic exchange to occur. Population genetic analyses, taking into account geographical and host species of origin, show that genetic exchange occurs sufficiently frequently in the field to be an important determinant of genetic diversity, except where particular clones have acquired the ability to infect humans. Thus, T. brucei populations have an ‘epidemic’ genetic structure, but the better-characterized human-infective populations have a ‘clonal’ structure. Remarkably, the ability to infect humans appears to have arisen on multiple occasions in different geographical locations in sub-Saharan Africa. Our data indicate that the classical subspecies terminology for T. brucei is genetically inappropriate. It is an implicit assumption in most infectious disease biology that when a zoonotic pathogen acquires the capability to infect humans, it does so once and then spreads through the human population from that single-source event. For at least one major pathogen in tropical medicine, T. brucei , this assumption is invalid.

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