Validation of KASP markers associated with cassava mosaic disease resistance, storage root dry matter and provitamin A carotenoid contents in Ugandan cassava germplasm

INTRODUCTION

The intrinsic high heterozygosity of cassava makes conventional breeding ineffective for rapid genetic improvement. However, recent advances in next generation sequencing technologies have enabled the use of high-density markers for genome-wide association studies, aimed at identifying single nucleotide polymorphisms (SNPs) linked to major traits such as cassava mosaic disease (CMD) resistance, dry matter content (DMC) and total carotenoids content (TCC). A number of these trait-linked SNPs have been converted to Kompetitive allele-specific polymerase chain reaction (KASP) markers for downstream application of marker assisted selection.

METHODS

We assayed 13 KASP markers to evaluate their effectiveness in selecting for CMD, DMC and TCC in 1,677 diverse cassava genotypes representing two independent breeding populations in Uganda.

RESULTS

Five KASP markers had significant co-segregation with phenotypes; CMD resistance (2), DMC (1) and TCC (2), with each marker accounting for at least 30% of the phenotypic variation. Markers located within the chromosomal regions for which strong marker-trait association loci have been characterised (chromosome 12 markers for CMD, chromosome 1 markers for DMC and TCC) had consistently superior ability to discriminate the respective phenotypes.

DISCUSSION

The results indicate varying discriminatory abilities of the KASP markers assayed and the need for their context-based use for MAS, with PSY2_572 particularly effective in selecting for high TCC. Availing the effective KASP markers on cost-effective genotyping platforms could facilitate practical implementation of marker-assisted cassava breeding for accelerated genetic gains for CMD, DMC and provitamin A carotenoids.

Comparing cardiac MRI and lung PET/CT after completion of tuberculosis treatment – preliminary findings of participants co-enrolled into the StatinTB trial and Cardiac Imaging After TB (CIA-TB) study

Introduction

Mortality rates after successful tuberculosis (TB) treatment remain elevated and healthy survival is impaired by chronic pulmonary disease and persistent inflammation. Inflammation leads to a complex cascade of events and has been associated with cardiovascular disease (CVD). Recent epidemiological work described an increased risk of CVD in persons with history of TB.

Aims and objectives

In our ongoing StatinTB trial (NCT04147286), we evaluate safety and efficacy of 40 mg atorvastatin to reduce persistent lung inflammation (PLI) after TB treatment in HIV−/HIV+ adults measured by 18F-FDG-PET/CT. Participants are co-enrolled into the Cardiac Imaging After Tuberculosis (CIA-TB) study. Here we report preliminary findings of participants enrolled into the StatinTB trial and CIA-TB study with the aim to correlate PLI with cardiac magnetic resonance imaging (CMR) parameters.

Methods

Participants with clinical response to TB treatment and a negative sputum culture at 16 weeks were screened at the end of a 24-week course of treatment for drug-sensitive TB. PET/CT was performed on a Philips Gemini TF scanner and analysed using MIM®Software. PLI was defined as total lung glycolysis (TLG) ≥50 SUV·mL (Figure 1). CMR was performed using a 3T Siemens Magnetom Skyra scanner and parameters were derived from the following acquisitions: SSFP cine imaging of the short and long axes, T1 mapping (MOLLI, 5 (3) 3), T2 mapping and late gadolinium enhancement (LGE) imaging. StatinTB trial is conducted according to ICH-GCP.

Results

26 participants (mean age 37.8±13.8 years, 38.5% women) underwent PET/CT and CMR. 23.1% were infected with HIV, 34.6% smokers, and 26.9% had a previous history of TB. Median BMI was 21.3 (IQR 19.7; 24.3). One participant reported hypertension. Common symptoms at enrollment were cough (26.9%), shortness of breath (11.5%), and chest pain (3.9%). On CT scan, 73.1% had pulmonary nodules, 57.7% scarring, 50.0% cavities, 42.3% bronchiectasis, 19.2% centrilobular disease, 19.2% distorted lung architecture, and 11.5% consolidations. On PET/CT, PLI was detected among 11 (42.3%) participants with a mean TLG of 216.0 (IQR 78.2; 384.0). In a multivariable regression analysis, left ventricular end systolic volume (LVESV) (−1.46; 95% CI: −2.89, −0.23; p=0.047) and distorted lung architecture (2.84; 95% CI: 1.17, 4.52; p=0.003) were significantly associated with TLG. Native T1 relaxation time showed a strong, but not significant association with TLG (15.01; 95% CI: −8.08, 38.10; p=184).

Conclusion

We present data of a young cohort at the end of TB treatment without significant cardiac risk factors. Structural lung disease is affecting at least half of participants, and many remain symptomatic. PLI is present in more than one-third of participants and our preliminary findings suggest an association with cardiac impairment. Further enrolment and ongoing laboratory studies will shed more light into post-TB cardio-pulmonary sequelae.

Funding Acknowledgement

Type of funding sources: Public grant(s) – EU funding. Main funding source(s): EDCTP

Artificial microRNA-derived resistance to Cassava brown streak disease

Artificial miRNAs (amiRNA) were generated targeting conserved sequences within the genomes of the two causal agents of Cassava brown streak disease (CBSD): Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV). Transient expression studies on ten amiRNAs targeting 21nt conserved sequences of P1(CBSV and UCBSV), P3(CBSV and UCBSV), CI(UCBSV), NIb(CBSV and UCBSV), CP(UCBSV) and the un-translated region (3'-UTR) were tested in Nicotiana benthamiana. Four out of the ten amiRNAs expressed the corresponding amiRNA at high levels. Transgenic N. benthamiana plants were developed for the four amiRNAs targeting the P1 and NIb genes of CBSV and the P1 and CP genes of UCBSV and shown to accumulate miRNA products. Transgenic plants challenged with CBSV and UCBSV isolates showed resistance levels that ranged between ∼20-60% against CBSV and UCBSV and correlated with expression levels of the transgenically derived miRNAs. MicroRNAs targeting P1 and NIb of CBSV showed protection against CBSV and UCBSV, while amiRNAs targeting the P1 and CP of UCBSV showed protection against UCBSV but were less efficient against CBSV. These results indicate a potential application of amiRNAs for engineering resistance to CBSD-causing viruses in cassava.

Prevalence of occupational exposure to HIV among health workers in Northern Uganda

BACKGROUND

The prevalence of HIV in Gulu district is 10.3%. This poses a high risk of occupational exposure and transmission to health workers in hospitals attending to these patients. The risk of HIV transmission from a patient to a health worker has been shown to be between 0.3% and 0.09% following percutaneous and mucocutaneous exposure respectively.

OBJECTIVES

This research aimed at determining the prevalence of occupational exposure to HIV.

METHOD

A cross sectional study of health workers in Gulu Regional Referral Hospital and St. Mary's Hospital Lacor, in northern Uganda was conducted to establish the frequency of occupational exposures to human immunodeficiency virus (HIV)-infected body fluids.

RESULTS

108 (46%) respondents were found to have been exposed to potentially infectious body fluids. Needle stick injuries was the commonest route of exposure, with a prevalence of 27.7%, followed by mucosal exposure 19.1%, contact with broken skin (5.5%) and lastly by a cut with sharp objects (5.1%). There is therefore need for more sensitization of health workers on infection control and post exposure prophylaxis for health workers.

Utilization of a basic care and prevention package by HIV-infected persons in Uganda

Opportunistic infections are the leading cause of mortality among HIV-infected people. Several simple interventions prevent illness, prolong life, or prevent HIV transmission from HIV-infected people in Africa. These include: cotrimoxazole prophylaxis; insecticide-treated bed nets; supplies for household water treatment and safe storage; materials promoting family voluntary counselling and testing (VCT); and condoms. We provided these interventions to adults and children with HIV who were members of the AIDS Support Organization in Uganda. To evaluate use of this basic care and prevention package, we surveyed a representative sample of 112 clients of TASO in their homes. Among respondents, 95% reported taking cotrimoxazole everyday, 89% said they had slept under a bednet the night before, 65% reported current treatment of household drinking water, 89% of sexually active respondents reported using condoms, and 96% reported family use of VCT. Household observations verified that use of cotrimoxazole, bednets, and water treatment products were consistent with reported use. This evaluation suggests successful distribution and use of basic care and prevention services at an AIDS organization in Uganda.