First products of DNA marker-assisted selection in sorghum released for cultivation by farmers in sub-saharan Africa

Striga hermonthica (Del.) Benth. is the major biotic constraint to sorghum production. Its control is difficult and can only be achieved through integrated management strategies that depend mainly on host plant resistance and enhanced soil fertility. However, breeding for resistance is hampered by the complexity of host parasite interactions and lack of reliable screening methods. The invention of molecular markers has enhanced the effectiveness of breeding for resistance. Five genomic regions (QTLs) with linked markers associated with Striga resistance were mapped in sorghum variety N13 by [10]. In this study, to increase the efficiency of marker-assisted selection (MAS), 27 EST-SSR markers in close association with Striga resistance QTLs were also identified and mapped. Populations of backcross (BC3S4) derived from N13 (Striga resistant) X three farmer preferred sorghum cultivars: Tabat, Wad Ahmed and AG-8 (Striga susceptible) were generated. Thirty-one lines (BC3S4) with confirmed Striga field resistance were genotyped with foreground and background selection makers. Twenty resistant lines, with two or more major QTLs were selected for regional evaluation. Of these 10 lines were selected and advanced for multi-location testing, together with Wad Ahmed, Tabat, AG-8, N13, SRN39 and IS9830 as checks. Standard variety trials were conducted in Striga sick plots over three seasons (2009-2011) in Sudan, Gezira Research Station, Damazine, Sinnar, and Gedarif. Results revealed that four lines (T1BC3S4, AG6BC3S4, AG2BC3S4 and W2BC3S4) were Striga resistant and agronomically superior with yields ranging from 180% to 298% higher relative to their recurrent parents. This Striga resistance coupled with superior attributes of the recurrent parent (including very high yield potentials, high grain quality and drought tolerance) will provide adaptation and stability across a wide range of environments. These are the first products of DNA markerassisted selection (MAS) in sorghum released for cultivation by farmers in sub-Saharan Africa

Towards an optimal design of target for tsetse control: comparisons of novel targets for the control of palpalis group tsetse in West Africa

Background: Tsetse flies of the Palpalis group are the main vectors of sleeping sickness in Africa. Insecticide impregnated targets are one of the most effective tools for control. However, the cost of these devices still represents a constraint to their wider use. The objective was therefore to improve the cost effectiveness of currently used devices. Methodology/Principal Findings: Experiments were performed on three tsetse species, namely Glossina palpalis gambiensis and G. tachinoides in Burkina Faso and G. p. palpalis in Côte d'Ivoire. The 1×1 m2 black blue black target commonly used in W. Africa was used as the standard, and effects of changes in target size, shape, and the use of netting instead of black cloth were measured. Regarding overall target shape, we observed that horizontal targets (i.e. wider than they were high) killed 1.6-5x more G. p. gambiensis and G. tachinoides than vertical ones (i.e. higher than they were wide) (P<0.001). For the three tsetse species including G. p. palpalis, catches were highly correlated with the size of the target. However, beyond the size of 0.75 m, there was no increase in catches. Replacing the black cloth of the target by netting was the most cost efficient for all three species. Conclusion/Significance: Reducing the size of the current 1*1 m black-blue-black target to horizontal designs of around 50 cm and replacing black cloth by netting will improve cost effectiveness six-fold for both G. p. gambiensis and G. tachinoides. Studying the visual responses of tsetse to different designs of target has allowed us to design more cost-effective devices for the effective control of sleeping sickness and animal trypanosomiasis in Africa

Marker-assisted introgression improves Striga resistance in an Eritrean Farmer-Preferred Sorghum Variety

The parasitic weed Striga hermonthica hampers the production of sorghum, the most important cereal crop in Eritrea. This weed has a complex mode of infestation that adapts to many hosts and environments, complicating conventional breeding for resistance, which is the only form of crop improvement available to Eritrean breeders, but has failed. This study aimed at improving resistance against this parasite by transferring 5 Striga resistant Quantitative Trait Loci (QTLs) from resistance donor N13 to Striga susceptible Farmer-Preferred Sorghum Variety (FPSV) Hugurtay from Eritrea. The method involved backcrossing using marker-assisted selection (MAS) and evaluation of the best introgressed lines for Striga resistance in artificially infested fields. Foreground selection was performed with up to 11 polymorphic simple sequence repeat (SSR) markers linked to Striga resistance QTLs, while background selection was conducted in the BC3F2 generation with 27 polymorphic unlinked SSR markers to identify the best recovery of the recurrent parent (RP) genetic background. Out of 84 BC3F3 lines, L2P3-B, L1P5-A and L2P5P35 performed best with respect to both grain yield and reduced Striga infestation. These lines were more resistant to Striga than Hugurtay, but less resistant than N13. The three lines yielded twice as much as N13, with Area Under Striga Number Progression Curve (AUSNPC) values on average 18% higher than that of N13 and 38% lower than that of Hugurtay. This suggests that the introgressed QTLs conferred significant Striga resistance and yield advantage to these BC3F3 backcross progenies under Striga pressure. These lines have good potential for future release and demonstrate that when MAS is available to conventional breeders, even in countries with no genotyping facilities, it is a useful tool for enhancement, expediency and precision in crop improvement

Population genetics of trypanosoma brucei rhodesiense: clonality and diversity within and between foci

African trypanosomes are unusual among pathogenic protozoa in that they can undergo their complete morphological life cycle in the tsetse fly vector with mating as a non-obligatory part of this development. Trypanosoma brucei rhodesiense, which infects humans and livestock in East and Southern Africa, has classically been described as a host-range variant of the non-human infective Trypanosoma brucei that occurs as stable clonal lineages. We have examined T. b. rhodesiense populations from East (Uganda) and Southern (Malawi) Africa using a panel of microsatellite markers, incorporating both spatial and temporal analyses. Our data demonstrate that Ugandan T. b. rhodesiense existed as clonal populations, with a small number of highly related genotypes and substantial linkage disequilibrium between pairs of loci. However, these populations were not stable as the dominant genotypes changed and the genetic diversity also reduced over time. Thus these populations do not conform to one of the criteria for strict clonality, namely stability of predominant genotypes over time, and our results show that, in a period in the mid 1990s, the previously predominant genotypes were not detected but were replaced by a novel clonal population with limited genetic relationship to the original population present between 1970 and 1990. In contrast, the Malawi T. b. rhodesiense population demonstrated significantly greater diversity and evidence for frequent genetic exchange. Therefore, the population genetics of T. b. rhodesiense is more complex than previously described. This has important implications for the spread of the single copy T. b. rhodesiense gene that allows human infectivity, and therefore the epidemiology of the human disease, as well as suggesting that these parasites represent an important organism to study the influence of optional recombination upon population genetic dynamics

Discovery of mating in the major African livestock pathogen Trypanosoma congolense

The protozoan parasite, Trypanosoma congolense, is one of the most economically important pathogens of livestock in Africa and, through its impact on cattle health and productivity, has a significant effect on human health and well being. Despite the importance of this parasite our knowledge of some of the fundamental biological processes is limited. For example, it is unknown whether mating takes place. In this paper we have taken a population genetics based approach to address this question. The availability of genome sequence of the parasite allowed us to identify polymorphic microsatellite markers, which were used to genotype T. congolense isolates from livestock in a discrete geographical area of The Gambia. The data showed a high level of diversity with a large number of distinct genotypes, but a deficit in heterozygotes. Further analysis identified cryptic genetic subdivision into four sub-populations. In one of these, parasite genotypic diversity could only be explained by the occurrence of frequent mating in T. congolense. These data are completely inconsistent with previous suggestions that the parasite expands asexually in the absence of mating. The discovery of mating in this species of trypanosome has significant consequences for the spread of critical traits, such as drug resistance, as well as for fundamental aspects of the biology and epidemiology of this neglected but economically important pathogen

Plasmodium-associated changes in human odor attract mosquitoes.

Malaria parasites (Plasmodium) can change the attractiveness of their vertebrate hosts to Anopheles vectors, leading to a greater number of vector-host contacts and increased transmission. Indeed, naturally Plasmodium-infected children have been shown to attract more mosquitoes than parasite-free children. Here, we demonstrate Plasmodium-induced increases in the attractiveness of skin odor in Kenyan children and reveal quantitative differences in the production of specific odor components in infected vs. parasite-free individuals. We found the aldehydes heptanal, octanal, and nonanal to be produced in greater amounts by infected individuals and detected by mosquito antennae. In behavioral experiments, we demonstrated that these, and other, Plasmodium-induced aldehydes enhanced the attractiveness of a synthetic odor blend mimicking "healthy" human odor. Heptanal alone increased the attractiveness of "parasite-free" natural human odor. Should the increased production of these aldehydes by Plasmodium-infected humans lead to increased mosquito biting in a natural setting, this would likely affect the transmission of malaria

Ten Simple Rules for Organizing a Virtual Conference—Anywhere

1 International Institute of Tropical Agriculture, Nairobi, Kenya, 2 Faculty of Life Sciences, The University of Manchester, Manchester, United Kingdom, 3 Department of Computer and Information Sciences, Covenant University, Ota, Nigeria, 4 Institute of Bioinformatics, Johannes Kepler University, Linz, Austria, 5 Moroccan Society for Bioinformatics Institute, Morocco, 6 South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa, 7 University of Cape Town, Cape Town, South Africa, 8 University of Notre Dame, South Bend, Indiana, United States of America, 9 Biotechnology Unit, University of Buea, Buea, South West Region, Cameroon, 10 International Livestock Research Institute, Nairobi, Kenya, 11 Biosciences Eastern and Central Africa, Nairobi, Kenya, 12 International Center of Insect Physiology and Ecology, Nairobi, Kenya, 13 Bioinformatics Organization, Hudson, Massachusetts, United States of America, 14 Bioinformatics Team, Center for Development of Advanced Computing, Pune University Campus, Pune, India, 15 Harvard School of Public Health, Boston, Massachusetts, United States of Americ

VarGoats project: a dataset of 1159 whole-genome sequences to dissect Capra hircus global diversity

Background: Since their domestication 10,500&nbsp;years ago, goat populations with distinctive genetic backgrounds have adapted to a broad variety of environments and breeding conditions. The VarGoats project is an international 1000-genome resequencing program designed to understand the consequences of domestication and breeding on the genetic diversity of domestic goats and to elucidate how speciation and hybridization have modeled the genomes of a set of species representative of the genus Capra. Findings: A dataset comprising 652 sequenced goats and 507 public goat sequences, including 35 animals representing eight wild species, has been collected worldwide. We identified 74,274,427 single nucleotide polymorphisms (SNPs) and 13,607,850 insertion-deletions (InDels) by aligning these sequences to the latest version of the goat reference genome (ARS1). A Neighbor-joining tree based on Reynolds genetic distances showed that goats from Africa, Asia and Europe tend to group into independent clusters. Because goat breeds from Oceania and Caribbean (Creole) all derive from imported animals, they are distributed along the tree according to their ancestral geographic origin. Conclusions: We report on an unprecedented international effort to characterize the genome-wide diversity of domestic goats. This large range of sequenced individuals represents a unique opportunity to ascertain how the demographic and selection processes associated with post-domestication history have shaped the diversity of this species. Data generated for the project will also be extremely useful to identify deleterious mutations and polymorphisms with causal effects on complex traits, and thus will contribute to new knowledge that could be used in genomic prediction and genome-wide association studies

LAMP for Human African Trypanosomiasis: A Comparative Study of Detection Formats

Loop-mediated isothermal amplification (LAMP) is at the forefront of the search for innovative diagnostics for human African trypanosomiasis (HAT). Several simple endpoint detection methods have been developed for LAMP and here we compare four of these: (i) visualization of turbidity; (ii) addition of hydroxynaphthol blue before incubation; (iii) addition of calcein with MnCl2 before incubation and (iv) addition of Quant-iT PicoGreen after incubation. These four methods were applied to four LAMP assays for the detection of human African trypanosomiasis, including two Trypanozoon specific and two Trypanosoma brucei rhodesiense specific reactions using DNA extracted from cryo-preserved procyclic form T. b. rhodesiense. A multi-observer study was performed to assess inter-observer reliability of two of these methods: hydroxynapthol blue and calcein with MnCl2, using DNA prepared from blood samples stored on Whatman FTA cards. Results showed that hydroxynaphthol blue was the best of the compared methods for easy, inexpensive, accurate and reliable interpretation of LAMP assays for HAT. Hydroxynapthol blue generates a violet to sky blue colour change that was easy to see and was consistently interpreted by independent observers. Visible turbidity detection is not possible for all currently available HAT LAMP reactions; Quant-iT PicoGreen is expensive and addition of calcein with MnCl2 adversely affects reaction sensitivity and was unpopular with several observers