Association Studies and Legume Synteny Reveal Haplotypes Determining Seed Size in Vigna unguiculata.

Highly specific seed market classes for cowpea and other grain legumes exist because grain is most commonly cooked and consumed whole. Size, shape, color, and texture are critical features of these market classes and breeders target development of cultivars for market acceptance. Resistance to biotic and abiotic stresses that are absent from elite breeding material are often introgressed through crosses to landraces or wild relatives. When crosses are made between parents with different grain quality characteristics, recovery of progeny with acceptable or enhanced grain quality is problematic. Thus genetic markers for grain quality traits can help in pyramiding genes needed for specific market classes. Allelic variation dictating the inheritance of seed size can be tagged and used to assist the selection of large seeded lines. In this work we applied 1,536-plex SNP genotyping and knowledge of legume synteny to characterize regions of the cowpea genome associated with seed size. These marker-trait associations will enable breeders to use marker-based selection approaches to increase the frequency of progeny with large seed. For 804 individuals derived from eight bi-parental populations, QTL analysis was used to identify markers linked to 10 trait determinants. In addition, the population structure of 171 samples from the USDA core collection was identified and incorporated into a genome-wide association study which supported more than half of the trait-associated regions important in the bi-parental populations. Seven of the total 10 QTLs were supported based on synteny to seed size associated regions identified in the related legume soybean. In addition to delivering markers linked to major trait determinants in the context of modern breeding, we provide an analysis of the diversity of the USDA core collection of cowpea to identify genepools, migrants, admixture, and duplicates

Intestinal parasite infections and associated risk factors in communities exposed to wastewater in urban and peri-urban transition zones in Hanoi, Vietnam

BACKGROUND: Infections with intestinal parasites (helminths and intestinal protozoa) are endemic in Southeast Asia and inappropriate management and reuse of wastewater might exacerbate the risk of human infections. In rapidly growing urban settings, little is known about the extent of intestinal parasite infections. We assessed the point-prevalence and risk factors of intestinal parasite infections in population groups differently exposed to wastewater in urban and peri-urban transition zones in Hanoi, the capital of Vietnam. METHODS: A cross-sectional survey was carried out between April and June 2014 in people aged ≥ 18 years at risk of wastewater exposure from To Lich River: workers maintaining wastewater treatment facilities; urban farmers reusing wastewater; and urban dwellers at risk of flooding events. For comparison, two peri-urban population groups living in close proximity to the Red River were chosen: farmers using river water for irrigation purposes; and people living in the same communities. A single stool sample was subjected to Kato-Katz and formalin-ether concentration methods for the diagnosis of helminth and intestinal protozoa infections. A questionnaire was administered to determine risk factors and self-reported signs and symptoms. RESULTS: A total of 681 individuals had complete data records. Highest point-prevalence rates of intestinal parasite infections were observed for peri-urban farmers (30 %). Hookworm and Trichuris trichiura were the predominant helminth species (25 % and 5 %, respectively). Peri-urban farmers were at higher odds of infection with intestinal parasites than any other groups (adjusted odds ratio 5.8, 95 % confidence interval 2.5 to 13.7). Lack of access to improved sanitation and not receiving deworming within the past 12 months were associated with higher infection risk, while higher educational attainment and socioeconomic status were negatively associated with intestinal parasite infections. CONCLUSIONS: Our results suggest that exposure to wastewater was not directly associated with infection with helminths and intestinal protozoa in different population groups in Hanoi. These findings might be explained by a high level of awareness of health risks and access to safe sanitary infrastructure in urban areas. The high prevalence rates observed in peri-urban farmers call for specific interventions targeting this population group

Phosphorus recovery: a need for an integrated approach

Increasing cost of phosphate fertilizer, a scarcity of high quality phosphate rock (PR)and increasing surface water pollution are driving aneed to accelerate the recovery and re-use ofphosphorus (P) from various waste sectors. Options to recover P occur all along the open P cycle from mining to households to oceans. However, P recovery as a regional and global strategy towards P sustainability and future food, bio energy and water security is in its infancy because of a number of technological, socio-economic and institutional constraints. There is no single solution and resolving these constraints requires concerted collaboration betweenrelevant stakeholders and an integrated approach combiningsuccessful business models withsocio-economic and institutional change. We suggest that an operational framework is developed for fast tracking cost-effective recovery options

D 5.5.2. Report on near-market consumer testing of new improved products and substitutes in Africa. Project AFTER “African Food Tradition rEvisited by Research”

In this deliverable, the reengineered products relating to groups 1 to 3 are tested by consumers in Africa in order to test whether the acceptance meets consumer needs. The summaries are by group. These products were widely different and tested in differing cultures and situations. A common feature, however, is that all products are already commonly consumed by the communities and accepted, particularly with respect to the baseline products. Some products were found to be more acceptable (Gowe and Akpan in Benin, Kenkey in Ghana, Kong and Lanhouin in Senegal, Bissap and Baobab in Senegal), some of similar acceptance (Kitoza in Madagascar) and some were less acceptable (Kishk Sa'eedi in Egypt and Jaabi in Cameroon). Ways forward are discussed in all cases. Group 1: The reengineered group 1 products had mixed acceptance to consumers. Ones that were highly accepted were the reengineered Akpan which was highly accepted regardless of age, gender, socio- professional category and possessions (goods) and the majority (84.9%) expressed an interest for purchasing the reengineered Akpan and the reengineered gowe (n=100 consumers) in Benin, which was strongly accepted and more so than the traditional gowe. However, the reengineered Kenkey in Ghana while being comparable acceptance to the traditional white kenkey this would only meet a niche market. However, for the reengineered Kishk Sa'eedi, it was less acceptable and the difference was due to sour taste and spicy flavour. Group 2:The group 2 products had mixed acceptance among consumers. In the case of Kong in and Lanhouin in Senegal, the reengineered products had improved acceptance while for kitoza in Madagascar, there was no improvement in acceptance apart from those in terms of quality and safety. More specifically, Kong made using liquid smoke novel technique (RLK) had by far the highest acceptance and could easily be integrated as part of the Senegalese cuisine. This shows that there is a potential for RLK on the Senegalese market. Two types of reengineered Lanhouin types (Lanhouin dry powder, Lanhouin dry fillet) were greatly acceptable and the powdered form more than the fillet. In the case of Kitoza, consumer acceptance studies showed that there was no significant difference between all samples tested. Group 3: Group 3 reengineered products had mixed acceptance among consumers. Re-engineered bissap (hibiscus drinks) in Senegal were positively appreciated by consumers in Senegal and better accepted than the traditional commercial infusion used as baseline comparison. However, the new drinks were not perceivably different from the baseline drink to consumers concerning both the traditional character and the nutritional and healthy attributes. The reengineered baobab drinks were positively appreciated by consumers in Senegal and significantly better appreciated than the traditional commercial ones earlier tested. Jaabi (Ziziphus mauritiana). The result is the proposition of a reengineered Yaabande presenting fine texture well appreciated by consumers. However, particle size was critical and this needed to be lower than 125μm. Due to this limit, processors have adopted the manual production of flour of particle size 250μm>Ø>125μm, which is less tiresome, though it appears in second rank in the preference of consumers. The detailed methodology for each product is given for Groups I, II and III respectively. Common to all of the methodologies is the Ethical assessment and consent which is listed as follows: Ethical assessment and consent. The studies have been assessed and approved by the University of Greenwich Research Ethics Committee and the Ethics Committee at CIRAD. Consent was sought from sensory panellists and from adult consumers participating in this study. Enumerators informed participants about the study and explained that their participation was entirely voluntary, that they could stop the interview at any point and that the responses would be anonymous

Genome Resources for Climate‐Resilient Cowpea, an Essential Crop for Food Security

Cowpea (Vigna unguiculata L. Walp.) is a legume crop that is resilient to hot and drought‐prone climates, and a primary source of protein in sub‐Saharan Africa and other parts of the developing world. However, genome resources for cowpea have lagged behind most other major crops. Here we describe foundational genome resources and their application to the analysis of germplasm currently in use in West African breeding programs. Resources developed from the African cultivar IT97K‐499‐35 include a whole‐genome shotgun (WGS) assembly, a bacterial artificial chromosome (BAC) physical map, and assembled sequences from 4355 BACs. These resources and WGS sequences of an additional 36 diverse cowpea accessions supported the development of a genotyping assay for 51 128 SNPs, which was then applied to five bi‐parental RIL populations to produce a consensus genetic map containing 37 372 SNPs. This genetic map enabled the anchoring of 100 Mb of WGS and 420 Mb of BAC sequences, an exploration of genetic diversity along each linkage group, and clarification of macrosynteny between cowpea and common bean. The SNP assay enabled a diversity analysis of materials from West African breeding programs. Two major subpopulations exist within those materials, one of which has significant parentage from South and East Africa and more diversity. There are genomic regions of high differentiation between subpopulations, one of which coincides with a cluster of nodulin genes. The new resources and knowledge help to define goals and accelerate the breeding of improved varieties to address food security issues related to limited‐input small‐holder farming and climate stress

D 5.3.2.2. Initial report on sensory and African consumer acceptance for Group 2. Project AFTER “African Food Tradition rEvisited by Research”.

The sensory profile and consumer acceptance of Lanhouin, a traditional salted fermented fish made from two types of fish (king fish and cassava fish) and three different fermentation processes (aerobic, semi aerobic and anaerobic condition) were explored. Traditional Lanhouin were sensorially different, with king fish Lanhouin having the highest smell (score of putrid odour) and cassava fish Lanhouin being the whitish. Three classes of consumers' behaviour essentially, those who like all the Lanhouin samples (Lanhouin likers; 35 % of consumers), those who does not prefer king fish Lanhouin from anaerobic fermentation (Lanhouin KFAN dislikers; 37 %) and those who does not like cassava fish Lanhouin from aerobic fermentation (Lanhouin CFA dislikers; 28 %) were identified. Consumers' acceptance was significantly associated with size of fish, whitish colour, dried fish odour and ammoniacal odour. Considering consumers' preference, Lanhouin from king fish with semi aerobic fermentation and Lanhouin from cassava fish (except for aerobic fermentation) were more accepted and could be interesting for reengineering. The similarity in tasting attributes for cassava fish and king fish when used for cooked rice will be helpful to design the form in which Lanhouin can be marketed for large acceptance Considering Kong, no prior work has explored sensory tasting. Four samples were produced for the sensory test: Kong was smoked with wood only and or with wood/coconut. For the sensory evaluation, smoked kong only and smoked kong in sauce and were scored by a semitrained sensory panel. Then, 109 consumers were interviewed. Acceptability was only evaluated on smoked kong. The results show that all four samples were quite distinctive from each other but not when in sauce. Most of the Kong products were on average acceptable but moist kong had a better acceptability than dried kong samples submitted to the same processes of smoking. Consumers were segmented into two three groups as: “indifferent likers” (27%), “dry kong dislikers” (15%), and “dry Kong less preferred” (59%). Clusters really differed in terms of professional activity in fish sector but did not significantly differ in the frequency of consumption. Therefore it appears that, smoked Kong is a main product of consumption in the Senegalese market. Since more than 50% of consumers consumed smoked Kong at least once a week, it appears that Kong is a main product of consumption with a strong potential for the Senegalese market but also for the international market. (Résumé d'auteur

Direct evidence for sequence-dependent attraction between double-stranded DNA controlled by methylation

Although proteins mediate highly ordered DNA organization in vivo, theoretical studies suggest that homologous DNA duplexes can preferentially associate with one another even in the absence of proteins. Here we combine molecular dynamics simulations with single-molecule fluorescence resonance energy transfer experiments to examine the interactions between duplex DNA in the presence of spermine, a biological polycation. We find that AT-rich DNA duplexes associate more strongly than GC-rich duplexes, regardless of the sequence homology. Methyl groups of thymine acts as a steric block, relocating spermine from major grooves to interhelical regions, thereby increasing DNA-DNA attraction. Indeed, methylation of cytosines makes attraction between GC-rich DNA as strong as that between AT-rich DNA. Recent genome-wide chromosome organization studies showed that remote contact frequencies are higher for AT-rich and methylated DNA, suggesting that direct DNA-DNA interactions that we report here may play a role in the chromosome organization and gene regulationopen