Feasibilty of zein proteins, simple sequence repeats and phenotypic traits for background selection in quality protein maize breeding

Widespread adoption of quality protein maize (QPM), especially among tropical farming systems has been slow mainly due to the slow process of generating varieties with acceptable kernel quality and adaptability to different agroecological contexts. A molecular based foreground selection system for opaque 2 (o2), the cause of enhanced lysine content in maize exists. Background selection systems albeit, are poorly developed in spite of the mapping of putative loci associated with kernel modification and knowledge on causes of modification. The aim of this study was to develop background selection systems for o2 introgression into locally adapted genotypes. Experiments were conducted at Makerere University Agricultural Research Institute, Kabanyolo (MUARIK), in Uganda on backcross progeny (BC1F1) and BC2F2), derived from a locally adapted line 136R and a QPM donor CML176. We tested the use of zein proteins known to influence modification as well as DNA markers and phenotypic descriptors as tools for background selection for recurrent parent genome and modifier loci in locally adapted maize genotypes. Simply inherited traits such as maize streak virus disease resistance were suitable for background selection. Other traits include plant and ear heights. The simple sequence repeats markers mapped to chromosomes 3, 5, 7, respectively and associated with quantitative trait loci (QTL) conditioning resistance in maize to grey leaf spot and anthesis to silking interval were suitable for assay of recurrent parent genome. The 27-kDa g zein protein levels was suitable for background selection for kernel modification. It should, however, be used along with other zeins such as the 22 kDa and 19 kDa zein proteins.L'adoption du ma\uefs de prot\ue9ne de qualit\ue9 (QPM), sp\ue9cialement parmi les syst\ue8mes culturaux tropicaux a \ue9t\ue9 lente principalement due au processus lent de g\ue9n\ue9ration de vari\ue9t\ue9s avec de grains acceptables de qualit\ue9 et d'adaptabilit\ue9 \ue0 diff\ue9rents contextes agro\ue9cologiques. Il existe une cause du contenu am\ue9lior\ue9 de la lysine dans le ma\uefs, un syst\ue8me bas\ue9 sur la s\ue9lection mol\ue9culaire opaque 2 (o2). Malgr\ue9 les syst\ue8mes de s\ue9lection de fond, ceux-ci sont pauvrement d\ue9velopp\ue9s en d\ue9pit du "mapping" du loci associ\ue9 avec la modification du grain et la connaissance sur les causes de modification. L'objet de cette \ue9tude \ue9tait de d\ue9velopper les syst\ue8mes de s\ue9lection de fond pour l'introgression o2 dans les g\ue9notypes localement adapt\ue9s. Des essais \ue9taient conduits sur la prog\ue9nie de "backcross" (BC1F1) et BC2F2), d\ue9riv\ue9s de lign\ue9es adapt\ue9es 136R et un QPM doneur CML176. Nous avons test\ue9 l'usage des prot\ue9ines z\ue9ines capables d'influencer de modifications des marqueurs d'ADN et descripteurs ph\ue9notypiques comme mat\ue9riel de s\ue9lection de fond pour parent de g\ue9nome recurrent et modifiant de loci dans les g\ue9notypes de ma\ubfs localement adapt\ue9s. Des traits simplement h\ue9rit\ue9s dont la r\ue9sistance \ue0 la maladie de virus de m\ue8che \ue9taient appropri\ue9s pour la s\ue9lection de fond. D'autres traits incluaient la hauteur de plants et la taille de l'\ue9pis. Les marqueurs SSR repr\ue9sent\ue9s sur les chromosomes 3,5,7, respectivement et associ\ue9s aux traits quantitatifs loci (QTL) conditionnant la r\ue9sistance dans le ma\ubfs \ue0 la maladie de t\ue2che grise de feuilles ansi que l'intervalle de l'anthesis jusqu'\ue0 la s\ue9cr\ue9tion du "silk" \ue9taient appropri\ue9s pour \ue9valuation du g\ue9nome parent recurrent. Les niveaux de prot\ue9ines z\ue9ines 27-kDa g \ue9taient appropri\ue9s pour la s\ue9lection de fond pour la modification de grains. Ceci pourra \ueatre utilis\ue9 \ue0 c\uf4t\ue9 d'autres z\ue9ines telles que les prot\ue9ines z\ue9ines 22 kDa et 19 kDa

Physiological parameters of seed vigour in ex situ stored sorghum germplasm

Viability and vigour are seed quality parameters that affect the seed chain. Seed vigour is a measure of accumulated damage in seed as viability declines from physiological maturity. This study aimed at determining the seed vigour of various sorghum genotypes stored ex situ for 10 years using the Heat Shock Stress Test (HSST), Cold Test (CT), Standard Germination Test (SGT) and field germination. The samples from the regeneration trial were kept in ex situ storage at 0-4°C and 40% relative humidity from 2003 to 2014. The experiments were arranged in a completely randomised design with four replication and differences in radicle length, shoot length for the 65 genotypes evaluated at 5% level of significance. An unpaired T- test was used to compare the accuracy of the quality methods in predicting field emergence. All the evaluated genotypes responded differentially to all the vigour test methods. There were significant differences (P<0.01) in the performance of genotypes with respect to radical and shoot length in response to the CT, HSST and the SGT. The results of CT and HSST predicted field emergence better than the standard germination test. None of the quality test methods and a strong and significant correlation with field emergence. Genotypes IS 30260 and IS 34637 were vigourous as they had the highest shoot length of 43.75 and 42.38 mm and IS 30063 had 45.52 mm in root length after 48 h of incubation. Overall, this study showed that field emergence of sorghum cannot be accurately predicted from a standard germination, HSST and CT

Impact of a wastewater treatment plant on microbial community composition and function in a hyporheic zone of a eutrophic river

The impact of the installation of a technologically advanced wastewater treatment plant (WWTP) on the benthic microbial community of a vinyl chloride (VC) impacted eutrophic river was examined two years before, and three and four years after installation of the WWTP. Reduced dissolved organic carbon and increased dissolved oxygen concentrations in surface water and reduced total organic carbon and total nitrogen content in the sediment were recorded in the post-WWTP samples. Pyrosequencing of bacterial 16S rRNA gene fragments in sediment cores showed reduced relative abundance of heterotrophs and fermenters such as Chloroflexi and Firmicutes in more oxic and nutrient poor post-WWTP sediments. Similarly, quantitative PCR analysis showed 1-3 orders of magnitude reduction in phylogenetic and functional genes of sulphate reducers, denitrifiers, ammonium oxidizers, methanogens and VC-respiring Dehalococcoides mccartyi. In contrast, members of Proteobacteria adapted to nutrient-poor conditions were enriched in post-WWTP samples. This transition in the trophic state of the hyporheic sediments reduced but did not abolish the VC respiration potential in the post-WWTP sediments as an important hyporheic sediment function. Our results highlight effective nutrient load reduction and parallel microbial ecological state restoration of a human-stressed urban river as a result of installation of a WWTP.Peer reviewe

Meta-omics approaches to understand and improve wastewater treatment systems

Biological treatment of wastewaters depends on microbial processes, usually carried out by mixed microbial communities. Environmental and operational factors can affect microorganisms and/or impact microbial community function, and this has repercussion in bioreactor performance. Novel high-throughput molecular methods (metagenomics, metatranscriptomics, metaproteomics, metabolomics) are providing detailed knowledge on the microorganisms governing wastewater treatment systems and on their metabolic capabilities. The genomes of uncultured microbes with key roles in wastewater treatment plants (WWTP), such as the polyphosphate-accumulating microorganism Candidatus Accumulibacter phosphatis, the nitrite oxidizer Candidatus Nitrospira defluvii or the anammox bacterium Candidatus Kuenenia stuttgartiensis are now available through metagenomic studies. Metagenomics allows to genetically characterize full-scale WWTP and provides information on the lifestyles and physiology of key microorganisms for wastewater treatment. Integrating metagenomic data of microorganisms with metatranscriptomic, metaproteomic and metabolomic information provides a better understanding of the microbial responses to perturbations or environmental variations. Data integration may allow the creation of predictive behavior models of wastewater ecosystems, which could help in an improved exploitation of microbial processes. This review discusses the impact of meta-omic approaches on the understanding of wastewater treatment processes, and the implications of these methods for the optimization and design of wastewater treatment bioreactors.Research was supported by the Spanish Ministry of Education and Science (Contract Project CTQ2007-64324 and CONSOLIDER-CSD 2007-00055) and the Regional Government of Castilla y Leon (Ref. VA038A07). Research of AJMS is supported by the European Research Council (Grant 323009

Paleogene Radiation of a Plant Pathogenic Mushroom

Background: The global movement and speciation of fungal plant pathogens is important, especially because of the economic losses they cause and the ease with which they are able to spread across large areas. Understanding the biogeography and origin of these plant pathogens can provide insights regarding their dispersal and current day distribution. We tested the hypothesis of a Gondwanan origin of the plant pathogenic mushroom genus Armillaria and the currently accepted premise that vicariance accounts for the extant distribution of the species. Methods: The phylogeny of a selection of Armillaria species was reconstructed based on Maximum Parsimony (MP), Maximum Likelihood (ML) and Bayesian Inference (BI). A timeline was then placed on the divergence of lineages using a Bayesian relaxed molecular clock approach. Results: Phylogenetic analyses of sequenced data for three combined nuclear regions provided strong support for three major geographically defined clades: Holarctic, South American-Australasian and African. Molecular dating placed the initial radiation of the genus at 54 million years ago within the Early Paleogene, postdating the tectonic break-up of Gondwana. Conclusions: The distribution of extant Armillaria species is the result of ancient long-distance dispersal rather than vicariance due to continental drift. As these finding are contrary to most prior vicariance hypotheses for fungi, our result

Genetic dissection of the relationships between grain yield components by genome-wide association mapping in a collection of tetraploid wheats

Increasing grain yield potential in wheat has been a major target of most breeding programs. Genetic advance has been frequently hindered by negative correlations among yield components that have been often observed in segregant populations and germplasm collections. A tetraploid wheat collection was evaluated in seven environments and genotyped with a 90K SNP assay to identify major and stable quantitative trait loci (QTL) for grain yield per spike (GYS), kernel number per spike (KNS) and thousand-kernel weight (TKW), and to analyse the genetic relationships between the yield components at QTL level. The genome-wide association analysis detected eight, eleven and ten QTL for KNS, TKW and GYS, respectively, significant in at least three environments or two environments and the mean across environments. Most of the QTL for TKW and KNS were found located in different marker intervals, indicating that they are genetically controlled independently by each other. Out of eight KNS QTL, three were associated to significant increases of GYS, while the increased grain number of five additional QTL was completely or partially compensated by decreases in grain weight, thus producing no or reduced effects on GYS. Similarly, four consistent and five suggestive TKW QTL resulted in visible increase of GYS, while seven additional QTL were associated to reduced effects in grain number and no effects on GYS. Our results showed that QTL analysis for detecting TKW or KNS alleles useful for improving grain yield potential should consider the pleiotropic effects of the QTL or the association to other QTLs

Independent and combined effects of improved water, sanitation, and hygiene, and improved complementary feeding, on child stunting and anaemia in rural Zimbabwe: a cluster-randomised trial.

BACKGROUND: Child stunting reduces survival and impairs neurodevelopment. We tested the independent and combined effects of improved water, sanitation, and hygiene (WASH), and improved infant and young child feeding (IYCF) on stunting and anaemia in in Zimbabwe. METHODS: We did a cluster-randomised, community-based, 2 × 2 factorial trial in two rural districts in Zimbabwe. Clusters were defined as the catchment area of between one and four village health workers employed by the Zimbabwe Ministry of Health and Child Care. Women were eligible for inclusion if they permanently lived in clusters and were confirmed pregnant. Clusters were randomly assigned (1:1:1:1) to standard of care (52 clusters), IYCF (20 g of a small-quantity lipid-based nutrient supplement per day from age 6 to 18 months plus complementary feeding counselling; 53 clusters), WASH (construction of a ventilated improved pit latrine, provision of two handwashing stations, liquid soap, chlorine, and play space plus hygiene counselling; 53 clusters), or IYCF plus WASH (53 clusters). A constrained randomisation technique was used to achieve balance across the groups for 14 variables related to geography, demography, water access, and community-level sanitation coverage. Masking of participants and fieldworkers was not possible. The primary outcomes were infant length-for-age Z score and haemoglobin concentrations at 18 months of age among children born to mothers who were HIV negative during pregnancy. These outcomes were analysed in the intention-to-treat population. We estimated the effects of the interventions by comparing the two IYCF groups with the two non-IYCF groups and the two WASH groups with the two non-WASH groups, except for outcomes that had an important statistical interaction between the interventions. This trial is registered with ClinicalTrials.gov, number NCT01824940. FINDINGS: Between Nov 22, 2012, and March 27, 2015, 5280 pregnant women were enrolled from 211 clusters. 3686 children born to HIV-negative mothers were assessed at age 18 months (884 in the standard of care group from 52 clusters, 893 in the IYCF group from 53 clusters, 918 in the WASH group from 53 clusters, and 991 in the IYCF plus WASH group from 51 clusters). In the IYCF intervention groups, the mean length-for-age Z score was 0·16 (95% CI 0·08-0·23) higher and the mean haemoglobin concentration was 2·03 g/L (1·28-2·79) higher than those in the non-IYCF intervention groups. The IYCF intervention reduced the number of stunted children from 620 (35%) of 1792 to 514 (27%) of 1879, and the number of children with anaemia from 245 (13·9%) of 1759 to 193 (10·5%) of 1845. The WASH intervention had no effect on either primary outcome. Neither intervention reduced the prevalence of diarrhoea at 12 or 18 months. No trial-related serious adverse events, and only three trial-related adverse events, were reported. INTERPRETATION: Household-level elementary WASH interventions implemented in rural areas in low-income countries are unlikely to reduce stunting or anaemia and might not reduce diarrhoea. Implementation of these WASH interventions in combination with IYCF interventions is unlikely to reduce stunting or anaemia more than implementation of IYCF alone. FUNDING: Bill & Melinda Gates Foundation, UK Department for International Development, Wellcome Trust, Swiss Development Cooperation, UNICEF, and US National Institutes of Health.The SHINE trial is funded by the Bill & Melinda Gates Foundation (OPP1021542 and OPP113707); UK Department for International Development; Wellcome Trust, UK (093768/Z/10/Z, 108065/Z/15/Z and 203905/Z/16/Z); Swiss Agency for Development and Cooperation; US National Institutes of Health (2R01HD060338-06); and UNICEF (PCA-2017-0002)