Genetic diversity in pigeonpea [Cajanus cajan (L.) Millsp.] Landraces as revealed by simple sequence repeat markers

Genetic relationships among 88 pigeonpea accessions from a presumed centre of origin and diversity, India and a presumed secondary centre of diversity in East Africa were evaluated using six microsatellite markers. Forty-seven (47) alleles were detected in the populations studied, with a mean of eight alleles per locus. Populations were defined by region (India and East Africa) and sub-populations by country in the case of East Africa and State in the case of India. Substantial differentiation among regions was evident from Roger’s modified distance and Wright’s F statistic. Greatest genetic diversity in terms of number of alleles, number of rare alleles and Nei’s unbiased estimate of gene diversity (H) was found in India as opposed to East Africa. This supports the hypothesis that India is the centre of diversity and East Africa is a secondary centre of diversity. Within East Africa, germplasm from Tanzania had the highest diversity according to Nei’s unbiased estimate of gene diversity, followed byKenya and Uganda. Germplasm from Kenya and Tanzania were more closely related than that of Uganda according to Roger’s modified distance. Within India, results did not indicate a clear centre of diversity. Values of genetic distance indicated that genetic relationships followed geographicalproximity

Genetic diversity in pigeonpea [Cajanus cajan (L.) Millsp.] Landraces as revealed by simple sequence repeat markers

Open Access JournalGenetic relationships among 88 pigeonpea accessions from a presumed centre of origin and diversity, India and a presumed secondary centre of diversity in East Africa were evaluated using six microsatellite markers. Forty-seven (47) alleles were detected in the populations studied, with a mean of eight alleles per locus. Populations were defined by region (India and East Africa) and sub-populations by country in the case of East Africa and State in the case of India. Substantial differentiation among regions was evident from Roger’s modified distance and Wright’s F statistic. Greatest genetic diversity in terms of number of alleles, number of rare alleles and Nei’s unbiased estimate of gene diversity (H) was found in India as opposed to East Africa. This supports the hypothesis that India is the centre of diversity and East Africa is a secondary centre of diversity. Within East Africa, germplasm from Tanzania had the highest diversity according to Nei’s unbiased estimate of gene diversity, followed by Kenya and Uganda. Germplasm from Kenya and Tanzania were more closely related than that of Uganda according to Roger’s modified distance. Within India, results did not indicate a clear centre of diversity. Values of genetic distance indicated that genetic relationships followed geographical proximity

Genetic diversity in pigeonpea [Cajanus cajan (L.) Millsp.] Landraces as revealed by simple sequence repeat markers

Genetic relationships among 88 pigeonpea accessions from a presumed centre of origin and diversity, India and a presumed secondary centre of diversity in East Africa were evaluated using six microsatellite markers. Forty-seven (47) alleles were detected in the populations studied, with a mean of eight alleles per locus. Populations were defined by region (India and East Africa) and sub-populations by country in the case of East Africa and State in the case of India. Substantial differentiation among regions was evident from Roger’s modified distance and Wright’s F statistic. Greatest genetic diversity in terms of number of alleles, number of rare alleles and Nei’s unbiased estimate of gene diversity (H) was found in India as opposed to East Africa. This supports the hypothesis that India is the centre of diversity and East Africa is a secondary centre of diversity. Within East Africa, germplasm from Tanzania had the highest diversity according to Nei’s unbiased estimate of gene diversity, followed by Kenya and Uganda. Germplasm from Kenya and Tanzania were more closely related than that of Uganda according to Roger’s modified distance. Within India, results did not indicate a clear centre of diversity. Values of genetic distance indicated that genetic relationships followed geographical proximity

Genetic diversity and demographic history of Cajanus spp. illustrated from genome-wide SNPs

Understanding genetic structure of Cajanus spp. is essential for achieving genetic improvement by quantitative trait loci (QTL) mapping or association studies and use of selected markers through genomic assisted breeding and genomic selection. After developing a comprehensive set of 1,616 single nucleotide polymorphism (SNPs) and their conversion into cost effective KASPar assays for pigeonpea (Cajanus cajan), we studied levels of genetic variability both within and between diverse set of Cajanus lines including 56 breeding lines, 21 landraces and 107 accessions from 18 wild species. These results revealed a high frequency of polymorphic SNPs and relatively high level of cross-species transferability. Indeed, 75.8% of successful SNP assays revealed polymorphism, and more than 95% of these assays could be successfully transferred to related wild species. To show regional patterns of variation, we used STRUCTURE and Analysis of Molecular Variance (AMOVA) to partition variance among hierarchical sets of landraces and wild species at either the continental scale or within India. STRUCTURE separated most of the domesticated germplasm from wild ecotypes, and separates Australian and Asian wild species as has been found previously. Among Indian regions and states within regions, we found 36% of the variation between regions, and 64% within landraces or wilds within states. The highest level of polymorphism in wild relatives and landraces was found in Madhya Pradesh and Andhra Pradesh provinces of India representing the centre of origin and domestication of pigeonpea respectively. © 2014 Saxena et al

Morbidity and mortality in HIV - infected children admitted at Moi Teaching and Referral Hospital in Western Kenya

Background: HIV-infected children are at higher risk of opportunistic infections that could result in hospitalisation. The outcomes of hospitalisation are variable and depend on the admission diagnosis, the patients’ immune status and whether or not the patient is on anti-retroviral drugs.Objective: To describe the characteristics and causes of hospitalisation and mortality for HIV infected children admitted to Moi Teaching and Referral hospital in western Kenya.Design: a retrospective study of prospectively collected data.Setting: The paediatric wards of Moi Teaching and Referral Hospital (MTRH). A Kenyan National Referral Hospital.Subjects: HIV-infected children admitted the paediatric wards.Interventions: Treatment with combination anti-retroviral therapy (cART), treatment of common opportunistic infections.Main outcome measures: Demographic and clinical data, including diagnosis, immune status, and treatment with combination anti-retroviral therapy (cART), were extracted from hospital admission records of HIV-infected children registered with the USAIDAcademic Model Providing Access to Healthcare (AMPATH) partnership. We conducted descriptive statistical analyses and used chi-square and fisher’s exact tests to assess for associations between categorical variables and each of the independent variables.Results: Between December 2006 and May 2009, 396 HIV-infected children were admitted to MTRH. Median age at admission was 2.0 years (range 0-15); 236 (59%) were male; 36 (15%) of available 236 orphan status entries were orphaned; 198 (73%) were in CDC categories B and C and 61 (16%) of available 386 had been on ART. Among 108 patients with documented immunologic status, the mean CD4 cell percentage was 16% (SD 10.8). Among the 396 children, 104 (15%) were diagnosed with pneumonia, 92 (14%) with gastroenteritis, 36 (9%) with tuberculosis and 37 (9%) with malaria. Deaths occurred in 28(7%) of the patients. The median duration of hospitalisation was seven days (range 1- 516) for discharged patients and six days (range 0-72) for those who died. A significantly higher percentage of the children who were not previously enrolled in AMPATH died, signifying 14 (15%) mortality among this population of admitted patients, p = 0.0017. Of those who died, (17%) were diagnosed with pneumonia and 22 (79%) of them were not on cART.Conclusion: The common diagnoses at hospitalisation included pneumonia, gastroenteritis, malaria and tuberculosis. Higher mortality occurred among those diagnosed with pneumonia and those not previously enrolled in the HIV care programme. Aggressive treatment and prevention of the most prevalent diseases and early enrollment into HIV care are recommended for HIV-infected children. A follow-up study to investigate the pathological causes of death in this population is recommended

Risk factors of virologic failure and slow response to art among HIV-infected children and adolescents in Nairobi

Background: Antiretroviral therapy (ART) in resource-limited settings is effective when backed up with adequate clinical, immunological, and virologic monitoring. Undetected, virologic failure results in increased HIV-1 drug resistance mutations (DRMs), morbidity and mortality, or the need for costly second-line and third-line ART.Objective: To evaluate the prevalence, patterns, and risk factors of virologic failure and slow response to ART, among children and adolescents in resource-limited settings in Nairobi, Kenya.Design: A Retrospective study.Setting: The 8 Lea Toto Programme (LTP) Clinics in Dagoretti, Dandora, Kangemi, Kariobangi, Kawangware, Kibera, Mukuru, and Zimmerman areas of Nairobi. Subjects: One hundred and forty-six HIV-infected children and adolescents aged 1 month to 19 years of the LTP in Nairobi Kenya. Medical and demographic data including, HIV-1 viral loads, information on adherence to ART, HIV-1 DRMs and other key determinants of virologic failure, collected over a period of 2 years, was used for this study.Results: A threshold of 1,000 HIV RNA copies/ml was used to determine treatment outcome. The virologic failure rates in this cohort were 43.8% after 6 months, 32.2% after 12 months, 28.8% after 18 months, and 24.0% after 24 months of first-line ART. Twelve (8.2%) of 146 children showed a slow response to ART: they initially failed ART at 12 months, but had treatment success after 18 to 24 months. The rates of virologic rebound were 4 (2.7%) after 18 months and 3 (2.1%) after 24 months of ART. Multivariate Cox proportional hazards regression revealed that children with suboptimal adherence to ART were 37 times more likely to experience virologic failure (P = 0.000003).Conclusions: This study showed that ART implementation in resource-limited settings is effective when regular virologic monitoring, adherence counselling, and HIV-DR testing are available. Secondly, adherence to ART is a strong predictor of treatment outcome for children and adolescents in resourcelimited settings. Therefore, methods of optimizing adherence levels should be explored and implemented

MATERNAL IMMUNE RESPONSES AND RISK OF INFANT INFECTION WITH HIV-1 AFTER A SHORT COURSE ZIDOVUDINE IN A COHORT OF HIV-1 INFECTED PREGNANT WOMEN IN RURAL KENYA

Objective: To investigate the effects of short-course nucleoside reverse transcriptaseinhibitor (Zidovudine, ZDW/AZT) on maternal immune responses and risk of infantinfection with HIV-1 among rural-based mothers in western Kenya.Design: A prospective cohort study involving HIV-1 seropositive pregnant mothers andtheir infants.Subjects: One hundred and seven HIV-1 seropositive asymptomatic pregnant womenand their infants.Methods: After informed consent, the women were enrolled at gestation age between16-24 weeks. For cultural and economic reasons, all mothers were allowed to breastfeed their infants. Short-course antepartum regime of AZT was administered to allmothers starting at 36 weeks gestation until start of labour. Maternal absolute CD4+T cell subset assays were performed before 3rd trimester (about 36 weeks gestation)and after a 4-week therapy of AZT (at least one month post-nuptially). Infant HIV-1 status was determined by HIV-1 DNA polymerase chain reaction (PCR) on samplessequentially taken at 1, 2, 3, 4, 6 and 9 months and confirmed by serology at 18 monthsof age.Interventions: Antepartum short-course orally administered AZT: 300mg twice-dailystarting at 36 weeks gestation until start of labour, 300mg at labour onset and 300mgevery three hours during labour until delivery.Main Outcome Measures: Maternal CD4+ T cell counts before and after AZT treatment.Determination of infant HIV-1 infection status.Results: Among 107 women sampled, only 59 received full dose of AZT and thus qualifiedfor present analysis. Of these, 12 infected their children with HIV, while 47 did not.Comparison of CD4+ T cells before and after AZT treatment scored a significant risein all mothers (P = 0.01). This increase in CD4+ T cells was not significant amongmothers who infected their infants with HIV-1 (P = 0.474). However, a significant risein CD4+ T cells following AZT therapy was observed only in mothers who did nottransmit HIV-1 to their infants (P=0.014).Conclusion: These data suggest that a rise in the CD4+ T cell counts following shortAZT regimen, now widely in use in resource-weak countries, may be evidence of theactive suppression of the replication of HIV. However, further studies to examine themulti-factorial effect of CD4+ lymphocytes and pregnancy on MTCT of HIV need tobe carried out to help fully explain the effect of AZT on immune response and whetherthe CD4+T cell count can be used as a true test of immunological normalisation duringantiretroviral therapy

HIV-1 subtype and viral tropism determination for evaluating antiretroviral therapy options: an analysis of archived Kenyan blood samples

<p>Abstract</p> <p>Background</p> <p>Infection with HIV-1 is characterized by genetic diversity such that specific viral subtypes are predominant in specific geographical areas. The genetic variation in HIV-1 <it>pol </it>and <it>env </it>genes is responsible for rapid development of resistance to current drugs. This variation has influenced disease progression among the infected and necessitated the search for alternative drugs with novel targets. Though successfully used in developed countries, these novel drugs are still limited in resource-poor countries. The aim of this study was to determine HIV-1 subtypes, recombination, dual infections and viral tropism of HIV-1 among Kenyan patients prior to widespread use of antiretroviral drugs.</p> <p>Methods</p> <p>Remnant blood samples from consenting sexually transmitted infection (STI) patients in Nairobi were collected between February and May 2001 and stored. Polymerase chain reaction and cloning of portions of HIV-1 <it>gag</it>, <it>pol </it>and <it>env </it>genes was carried out followed by automated DNA sequencing.</p> <p>Results</p> <p>Twenty HIV-1 positive samples (from 11 females and 9 males) were analyzed. The average age of males (32.5 years) and females (26.5 years) was significantly different (p value < 0.0001). Phylogenetic analysis revealed that 90% (18/20) were concordant HIV-1 subtypes: 12 were subtype A1; 2, A2; 3, D and 1, C. Two samples (10%) were discordant showing different subtypes in the three regions. Of 19 samples checked for co-receptor usage, 14 (73.7%) were chemokine co-receptor 5 (CCR5) variants while three (15.8%) were CXCR4 variants. Two had dual/mixed co-receptor use with X4 variants being minor population.</p> <p>Conclusion</p> <p>HIV-1 subtype A accounted for majority of the infections. Though perceived to be a high risk population, the prevalence of recombination in this sample was low with no dual infections detected. Genotypic co-receptor analysis showed that most patients harbored viruses that are predicted to use CCR5.</p

An overview of chickpea breeding programs in Kenya

Chickpea is a new crop in Kenya and its potential has not been fully utilized. The chickpea grain yields generally range between 1.2 to 3.5 tons/ha at farmers‟ fields, indicating that chickpea has a potential of becoming an important export crop in Kenya. The chickpea breeding program in Kenya is still at infant stage and being established with support from International Crops Research Institute for the Semi-Arid Tropics (ICRISAT). Four chickpea varieties have been recently released from the breeding material supplied by ICRISAT. Efforts are being made on evaluation of germplasm and breeding lines, application of modern molecular breeding tools and techniques in chickpea breeding and establishment of effective seed system for establishing a sustainable chickpea production system in the country

Performance of marker assisted backcross breeding (MABC) elite chickpea lines under drought conditions in Kenya

Drought is the most important constraint affecting production of chickpea and other crops as well. Quantitative traits like drought tolerance are multigenic and their inheritance is difficult to predict hence the need to explore more precise breeding techniques like maker assisted selection. The aim of this study was to introgress the identified root trait QTLs into Kenyan adapted cultivar to enhance drought tolerance through marker assisted backcrossing. Four varieties Chania Desi 1 (ICCV 97105), ICCV10, ICCV 92318, and Saina K1 (ICCV 95423) were selected as a recurrent parents for improvement among ten agronomically superior elite cultivars after exhibiting high polymorphism with SSR markers. Five molecular markers (CaM1903, CaM1502, TAA 170, NCPGR21 and GA11) were validated for use in MABC deployed in this study. Crosses were made between the four parents and ICC 4958 followed by marker screening of the F1 seedling progenies for the QTL of interest. Identified true heterozygotes were used as donors and backcrossed to the recurrent parent to obtain BC1F1 seeds. The process was repeated to obtain BC2F1 and finally BC3F1 with molecular marker identification of seedlings carrying the QTL region at each step. Results of evaluation in one trial site in Kenya semi-arid area (Koibatek ATC) of MABC lines for the four parents ICCV10 (24 lines), ICCV 92318 (8lines), ICCV 97105 (12 lines) and Saina K1-ICCV 95423 (10 lines) showed that the best progenies with higher levels of drought resistance and yield were ICCMABCD-21, 9, 20, 23, 15, 22, 5, 14, 16, 19 and 6 with yields > 2.5 tons/ha. The results indicated that it is possible to transfer QTL that confers drought tolerance using MABC. The best progenies are undergoing further evaluation to validate the contribution of the introgressed QTL in improving drought tolerance and yield