scholarly journals KASP Genotyping as a Molecular Tool for Diagnosis of Cassava-Colonizing Bemisia tabaci

Insects ◽  
2020 ◽  
Vol 11 (5) ◽  
pp. 305
Author(s):  
Everlyne N. Wosula ◽  
Wenbo Chen ◽  
Massoud Amour ◽  
Zhangjun Fei ◽  
James P. Legg
Keyword(s):  
Bemisia Tabaci ◽  
Sub Saharan Africa ◽  
Specific Pcr ◽  
Kasp Assay ◽  
Insect Identification ◽  
Gene Coi ◽  
Cryptic Species Complex ◽  
Allele Specific ◽  
Sub Saharan ◽  
Primer Sets

Bemisia tabaci is a cryptic species complex that requires the use of molecular tools for identification. The most widely used approach for achieving this is the partial sequencing of the mitochondrial DNA cytochrome oxidase I gene (COI). A more reliable single nucleotide polymorphism (SNP)-based genotyping approach, using Nextera restriction-site-associated DNA (NextRAD) sequencing, has demonstrated the existence of six major haplogroups of B. tabaci on cassava in Africa. However, NextRAD sequencing is costly and time-consuming. We, therefore, developed a cheaper and more rapid diagnostic using the Kompetitive Allele-Specific PCR (KASP) approach. Seven sets of primers were designed to distinguish the six B. tabaci haplogroups based on the NextRAD data. Out of the 152 whitefly samples that were tested using these primer sets, 151 (99.3%) produced genotyping results consistent with NextRAD. The KASP assay was designed using NextRAD data on whiteflies from cassava in 18 countries across sub-Saharan Africa. This assay can, therefore, be routinely used to rapidly diagnose cassava B. tabaci by laboratories that are researching or monitoring this pest in Africa. This is the first study to develop an SNP-based assay to distinguish B. tabaci whiteflies on cassava in Africa, and the first application of the KASP technique for insect identification.

scholarly journals Leucine rich repeat kinase 2 (LRRK2) gly2019ser mutation is absent in a second cohort of nigerian africans with parkinson disease

2018 ◽  
Author(s):  
Njideka U Okubadejo ◽  
Mie Rizig ◽  
Oluwadamilola O Ojo ◽  
Hallgeir Jonvik ◽  
Olajumoke Oshinaike ◽  
...  
Keyword(s):  
Parkinson Disease ◽  
Kinase Inhibitors ◽  
Sub Saharan Africa ◽  
Attractive Potential ◽  
Ashkenazi Jews ◽  
Black African ◽  
Specific Pcr ◽  
Kasp Assay ◽  
Sub Saharan ◽  
Black Populations

ABSTRACTTo date the LRRK2 p.G2019S mutation remains the most common genetic cause of Parkinson disease (PD) worldwide. It accounts for up to 6% of familial and approximately 1.5% of sporadic cases. LRRK2 has a kinase enzymatic domain which provides an attractive potential target for drug therapies and LRRK2 kinase inhibitors are in development. Prevalence of the p.G2019S has a variable ethnic and geographic distribution, the highest was reported among Ashkenazi Jews (30% in patients with familial PD, 14% in sporadic PD, 2.0% in controls) and North African Berbers (37% in patients with familial PD, 41% in sporadic PD, and 1% in controls). Little is known about the frequency of the LRRK2 p.G2019S among populations in Sub Saharan Africa. Our group and others previously reported that the p.G2019S is absent in a small cohort from Nigerian PD patients and controls. Here we used Kompetitive Allele Specific PCR (KASP) assay to screen for the p.G2019S in a larger cohort of Black African PD patients (n =126) and healthy controls (n = 55) from Nigeria. Our analysis confirmed that all patients and controls are negative for the p.G2019S mutation. This report provides further evidence that the LRRK2 p.G2019S is not implicated in PD in black populations from Nigeria and support the notion that p.G2019S mutation originated after the early human dispersal from sub-Saharan Africa. Further studies using larger cohorts and advance sequencing technology are required to underpin the genetic causes of PD in this region.

scholarly journals Is High Whitefly Abundance on Cassava in Sub-Saharan Africa Driven by Biological Traits of a Specific, Cryptic Bemisia tabaci Species?

Insects ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 260
Author(s):  
Habibu Mugerwa ◽  
Peter Sseruwagi ◽  
John Colvin ◽  
Susan Seal
Keyword(s):  
Food Security ◽  
Bemisia Tabaci ◽  
Development Time ◽  
Adult Emergence ◽  
Sub Saharan Africa ◽  
Biological Traits ◽  
Population Development ◽  
Species Classification ◽  
First Instar ◽  
Sub Saharan

In East Africa, the prevalent Bemisia tabaci whiteflies on the food security crop cassava are classified as sub-Saharan Africa (SSA) species. Economically damaging cassava whitefly populations were associated with the SSA2 species in the 1990s, but more recently, it has been to SSA1 species. To investigate whether biological traits (number of first instar nymphs, emerged adults, proportion of females in progeny and development time) of the cassava whitefly species are significant drivers of the observed field abundance, our study determined the development of SSA1 sub-group (SG) 1 (5 populations), SG2 (5 populations), SG3 (1 population) and SSA2 (1 population) on cassava and eggplant under laboratory conditions. SSA1-(SG1-SG2) and SSA2 populations’ development traits were similar. Regardless of the host plant, SSA1-SG2 populations had the highest number of first instar nymphs (60.6 ± 3.4) and emerged adults (50.9 ± 3.6), followed by SSA1-SG1 (55.5 ± 3.2 and 44.6 ± 3.3), SSA2 (45.8 ± 5.7 and 32.6 ± 5.1) and the lowest were SSA1-SG3 (34.2 ± 6.1 and 32.0 ± 7.1) populations. SSA1-SG3 population had the shortest egg–adult emergence development time (26.7 days), followed by SSA1-SG1 (29.1 days), SSA1-SG2 (29.6 days) and SSA2 (32.2 days). Regardless of the whitefly population, development time was significantly shorter on eggplant (25.1 ± 0.9 days) than cassava (34.6 ± 1.0 days). These results support that SSA1-(SG1-SG2) and SSA2 B. tabaci can become highly abundant on cassava, with their species classification alone not correlating with observed abundance and prevalence.

First report of the Sub-Saharan Africa 2 species of the Bemisia tabaci complex in the Southern France

2015 ◽  
Vol 43 (5) ◽  
pp. 679-687 ◽  
Author(s):  
Margarita Hadjistylli ◽  
George K. Roderick ◽  
Nathalie Gauthier
Keyword(s):  
Bemisia Tabaci ◽  
Sub Saharan Africa ◽  
Southern France ◽  
First Report ◽  
Sub Saharan

scholarly journals A rep-based hairpin inhibits replication of diverse maize streak virus isolates in a transient assay

2011 ◽  
Vol 92 (10) ◽  
pp. 2458-2465 ◽  
Author(s):  
Betty E. Owor ◽  
Darren P. Martin ◽  
Edward P. Rybicki ◽  
Jennifer A. Thomson ◽  
Marion E. Bezuidenhout ◽  
...  
Keyword(s):  
Virus Replication ◽  
Inverted Repeat ◽  
Virus Genome ◽  
Sub Saharan Africa ◽  
Transcriptional Gene Silencing ◽  
Streak Virus ◽  
Transient Expression Assay ◽  
Specific Pcr ◽  
Post Transcriptional Gene Silencing ◽  
Sub Saharan

Maize streak disease, caused by the A strain of the African endemic geminivirus, maize streak mastrevirus (MSV-A), threatens the food security and livelihoods of subsistence farmers throughout sub-Saharan Africa. Using a well-established transient expression assay, this study investigated the potential of a spliceable-intron hairpin RNA (hpRNA) approach to interfere with MSV replication. Two strategies were explored: (i) an inverted repeat of a 662 bp region of the MSV replication-associated protein gene (rep), which is essential for virus replication and is therefore a good target for post-transcriptional gene silencing; and (ii) an inverted repeat of the viral long intergenic region (LIR), considered for its potential to trigger transcriptional silencing of the viral promoter region. After co-bombardment of cultured maize cells with each construct and an infectious partial dimer of the cognate virus genome (MSV-Kom), followed by viral replicative-form-specific PCR, it was clear that, whilst the hairpin rep construct (pHPrepΔI662) completely inhibited MSV replication, the LIR hairpin construct was ineffective in this regard. In addition, pHPrepΔI662 inhibited or reduced replication of six MSV-A genotypes representing the entire breadth of known MSV-A diversity. Further investigation by real-time PCR revealed that the pHPrepΔI662 inverted repeat was 22-fold more effective at reducing virus replication than a construct containing the sense copy, whilst the antisense copy had no effect on replication when compared with the wild type. This is the first indication that an hpRNA strategy targeting MSV rep has the potential to protect transgenic maize against diverse MSV-A genotypes found throughout sub-Saharan Africa.

scholarly journals Genetic Diversity of Mitochondrial DNA of Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) Associated with Cassava and the Occurrence of Cassava Mosaic Disease in Zambia

Insects ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 761
Author(s):  
Patrick Chiza Chikoti ◽  
Mathias Tembo ◽  
James Peter Legg ◽  
Rudolph Rufini Shirima ◽  
Habibu Mugerwa ◽  
...  
Keyword(s):  
Bemisia Tabaci ◽  
Control Strategies ◽  
Mosaic Disease ◽  
Sub Saharan Africa ◽  
Cassava Mosaic Disease ◽  
Northern Province ◽  
Western Province ◽  
Key Factor ◽  
Sub Saharan ◽  
Brown Streak

Bemisia tabaci is an important vector of cassava brown streak viruses and cassava mosaic begomoviruses, the causal agents of cassava brown streak disease and cassava mosaic disease (CMD), respectively. A study was carried out to determine the genetic variability of B. tabaci associated with cassava and the occurrence of CMD in Zambia in 2013 and 2015. Phylogenetic analysis showed the presence of only the sub-Saharan Africa 1 (SSA1) genetic group in Zambia. The SSA1 population had three population subgroups (SGs): SSA1-SG1, SSA1-SG2 and SSA1-SG3. All three SSA1 population subgroups occurred in Western Province. However, only SSA1-SG3 occurred in Eastern Province, while only SSA1-SG1 occurred in North Western and Luapula Provinces. Adult B. tabaci were most abundant in Western Province in 2013 (11.1/plant) and 2015 (10.8/plant), and least abundant (0.2/plant) in Northern Province in both 2013 and 2015. CMD was prevalent in all seven provinces surveyed, with the highest incidence recorded in Lusaka Province in both 2013 (78%) and 2015 (83.6%), and the lowest in Northern Province in both 2013 (26.6%) and 2015 (29.3%). Although SSA1-SG1 occurred at greater abundances than the other subgroups, there was no direct association demonstrated between whitefly subgroup and incidence of CMD. Establishing which B. tabaci genetic groups and populations are associated with CMD and their distribution in the country is a key factor in guiding the development of CMD control strategies for cassava-dependent households.

scholarly journals Presence of the HPPD Inhibitor Sensitive 1 Gene and ALSS653N Mutation in Weedy Oryza sativa Sensitive to Benzobicyclon

Plants ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 1576
Author(s):  
Chad Brabham ◽  
Jason K. Norsworthy ◽  
Fidel González-Torralva
Keyword(s):  
Weedy Rice ◽  
Japonica Rice ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Herbicide Resistant ◽  
Rice Plants ◽  
Specific Pcr ◽  
Kasp Assay ◽  
Allele Specific ◽  
Allele Specific Pcr

Benzobicyclon has shown varying results in controlling weedy rice, including those with imidazolinone (IMI) resistance. Tolerance to benzobicyclon in cultivated japonica rice, but not indica or aus-like cultivars, is conferred by a fully functional HPPD Inhibitor Sensitive 1 (HIS1) gene. Herein, a diagnostic Kompetitive Allele Specific PCR (KASP) assay was developed to predict the HIS1 genotype of weedy rice plants from 37 accessions and correlated to their response to benzobicyclon in the field. Two-thirds of the 693 weedy rice plants screened were tolerant to benzobicyclon (371 g ai ha−1, SC formulation) at 30 days after treatment (DAT). Thirty-four percent of plants were homozygous for the HIS1 allele and 98% of these plants exhibited field tolerance. However, the his1 genotype did not always correlate with field data. Only 52% of his1 plants were considered sensitive, indicating that the single nucleotide polymorphisms (SNPs) chosen in the KASP assay are not a reliable tool in predicting his1 homozygous plants. In an additional experiment, 86% of the 344 plants with at least one copy of the ALSS653N trait harbored a HIS1 allele, suggesting fields infested with IMI herbicide-resistant weedy rice are unlikely to be controlled with benzobicyclon.

scholarly journals Longitudinal Secretion of Paramyxovirus RNA in the Urine of Straw-Coloured Fruit Bats (Eidolon helvum)

2021 ◽  
Author(s):  
Elli Rosa Jolma ◽  
Louise Gibson ◽  
Richard D. Suu-Ire ◽  
Grace Fleischer ◽  
Samuel Asumah ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Environmental Temperature ◽  
Sub Saharan Africa ◽  
Sample Collection ◽  
Rna Sequences ◽  
Sequence Detection ◽  
Specific Pcr ◽  
Fruit Bat ◽  
Sub Saharan ◽  
Eidolon Helvum

The straw-coloured fruit bat (Eidolon helvum) is widespread in sub-Saharan Africa and is widely hunted for bushmeat. It is known to harbour a range of paramyxoviruses, including rubuloviruses and henipaviruses, but the zoonotic potential of these is unknown. We previously found a diversity of paramyxoviruses within a small, captive colony of E. helvum after it had been closed to contact with other bats for five years. In this study, we used under-roost urine collection to further investigate the paramyxovirus diversity and ecology in this colony, which had been closed to the outside for ten years at the time of sampling. By sampling urine weekly throughout an entire year, we investigated possible seasonal patterns of shedding of virus or viral RNA. Using a generic paramyxovirus L-gene PCR, we detected eight distinct paramyxovirus RNA sequences. Six distinct sequences were detected using a Henipavirus-specific PCR which targeted a different region of the L-gene. Sequence detection had a bi-annual pattern, with the greatest peak in July, although different RNA sequences appeared to have different shedding patterns. No significant associations were detected between sequence detection and birthing season, environmental temperature or humidity, and no signs of illness were detected in any of the bats in the colony during the period of sample collection.

scholarly journals Longitudinal Secretion of Paramyxovirus RNA in the Urine of Straw-Coloured Fruit Bats (Eidolon helvum)

Viruses ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 1654
Author(s):  
Elli Rosa Jolma ◽  
Louise Gibson ◽  
Richard D. Suu-Ire ◽  
Grace Fleischer ◽  
Samuel Asumah ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Environmental Temperature ◽  
Sub Saharan Africa ◽  
Sample Collection ◽  
Rna Sequences ◽  
Sequence Detection ◽  
Specific Pcr ◽  
Fruit Bat ◽  
Sub Saharan ◽  
Eidolon Helvum

The straw-coloured fruit bat (Eidolon helvum) is widespread in sub-Saharan Africa and is widely hunted for bushmeat. It is known to harbour a range of paramyxoviruses, including rubuloviruses and henipaviruses, but the zoonotic potential of these is unknown. We previously found a diversity of paramyxoviruses within a small, captive colony of E. helvum after it had been closed to contact with other bats for 5 years. In this study, we used under-roost urine collection to further investigate the paramyxovirus diversity and ecology in this colony, which had been closed to the outside for 10 years at the time of sampling. By sampling urine weekly throughout an entire year, we investigated possible seasonal patterns of shedding of virus or viral RNA. Using a generic paramyxovirus L-gene PCR, we detected eight distinct paramyxovirus RNA sequences. Six distinct sequences were detected using a Henipavirus-specific PCR that targeted a different region of the L-gene. Sequence detection had a bi-annual pattern, with the greatest peak in July, although different RNA sequences appeared to have different shedding patterns. No significant associations were detected between sequence detection and birthing season, environmental temperature or humidity, and no signs of illness were detected in any of the bats in the colony during the period of sample collection.

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