Alternate phenotype–genotype selection for developing superior high-yielding irrigated rice lines

Increase grain yield potential is one of the most important objectives of any cereal crop breeding program. To efficiently develop superior rice lines by the introgression of favorable alleles for yield and yield component traits, a strategy of alternate phenotype–genotype selection was used. The present study aimed to (i) investigate the allelic diversity of loci associated with major yield-component traits and (ii) phenotype and genotype advanced populations derived from crosses between NERICA-L-20 and Giza178 for yield component traits using agro-morphological descriptors and GRiSP polymorphic markers to select superior high-yielding rice lines. A total of 100 F2:3 progeny were selected from 1000 F2 plants and genotyped with 16 polymorphic markers linked to four major yield- component traits. Four promising F2:3 lines (ARS 563–14, ARS 563–62, ARS 563–286, and ARS 563–41) bearing combinations of desirable alleles were selected. A selected set of 20 F2:4 lines showed moderate to high heritability for all target traits. Fourteen F2:5 lines derived from ARS 563–14 and 17 F2:5 from ARS 563–286 families were evaluated in preliminary trials to estimate yield gain. The three top lines, ARS 563–286–16-1-1, ARS 563–286–5-1-1, and ARS 563–14–10-1-1, showed an increase of more than 10% grain yield over the best check, Sahel 108, which is widely cultivated in the Senegal River valley. The 16 markers linked to the target yield component traits can be used to fast-track breeding programs targeting rice productivity

Rice Fields Chemical and Physical Properties and the Implications on Breeding Strategie

Soil related constraints are major limiting factors in crop production in the Sahel. The objective of this study was to assess the properties of farmer's fields soil and irrigation water in Niger and the implications in rice improvement. Composite soil samples were collected from irrigated and non-irrigated fields. Sample of irrigation water was also collected. Physical and chemical analyses were performed in the laboratory. The results showed that most of rice fields were clayey and the non irrigated ones were mostly sandy. The soils were acidic and saline, the electrical conductivity ranged from 2.2 to 16.5 decisiemens per meter. The T-test showed that total dissolved salt, sodium adsorption ratio, cation exchange capacity, and organic matter percentage were significantly higher in irrigated fields than non-irrigated fields. The irrigated soils pH varied from 3.2 to 6.8, the electrical conductivity was greater than 4, and the sodium adsorption ratio was below 13 while the exchangeable sodium percentage was below 15. The irrigation water samples varied in term of ion content from site to site. The total sodium quantity estimated to be deposited varied from 87 kg/ha/year to 218 kg/ha/year. Rice fields' soils are saline and are getting worsened by irrigation water that contains salt. Therefore, the development of rice varieties that could withstand osmotic and ionic salt stress is necessary for sustainable production in the Sahel ecozone

Evaluation of sixteen reference evapotranspiration methods under sahelian conditions in the Senegal River Valley

Study region: Reference evapotranspiration (ETo) plays a key role in irrigation sys-tems design, water management under irrigated and rainfed production. Underthe sahelian conditions in the Senegal River Valley that receives less than 300 mmannual rainfall, rice crop water use should be estimated for the sustainability of theresource. Study focus: However the Penman–Monteith (PM) equation is revealed the mostaccurate one; it necessitates several climatic parameters that are not always avail-able mostly in the developing countries. The objective of this study was to evaluatethe performance of 16 ETo equations against the ASCE-PM equation under thesahelian conditions at Ndiaye and Fanaye (Senegal) for alternate equation forETo estimation with less climatic parameters. The results showed that the Har-greaves, modified Hargreaves, Ravazzani and Tralkovic equations systematicallyoverestimated ETo with the highest percentage error of estimate (PE). In contrast,Makkink–Hansen, Oudin and Turc equations systematically underestimated ETo.Temperature based equations of Romenenko and Schendel performed relativelybetter at Fanaye with 5.5% and 9.6% PE, fitting slopes of 0.92 and 1.05, and meanratio (MR) of 1.00 and 1.14, respectively. Mass transfer equations of Trabert andMahringer also had good performance compared to the Penman–Monteith equa-tion. New hydrological insights for the region: Overall, Valiantzas, Trabert, Romanenko,Schendel and Mahringer equations were the promising equations that could be usedfor reference evapotranspiration estimation in the Senegal River Valley

Effects of Alternate Wetting and Drying Irrigation Regime and Nitrogen Fertilizer on Yield and Nitrogen Use Efficiency of Irrigated Rice in the Sahel

The objectives of this study were to investigate water saving strategies in the paddy field and to evaluate the performance of some of the newly released rice varieties. Field experiments were conducted at Fanaye in the Senegal River Valley during two rice growing seasons in 2015. Three irrigation regimes ((i) continuous flooding, (ii) trigging irrigation at soil matric potential (SMP) of 30 kPa, (iii) trigging irrigation at SMP of 60 kPa) were tested in an irrigated lowland rice field. Irrigation regimes (ii) and (iii) are alternate wetting and drying (AWD) cycles. Four inbred rice varieties (NERICA S-21, NERICA S-44, Sahel 210 and Sahel 222) and one hybrid rice (Hybrid AR032H) were evaluated under five nitrogen fertilizer rates (0, 50, 100, 150 and 200 kg N ha−1). The results showed that rice yield varied from 0.9 to 12 t ha−1. The maximum yield of 12 t ha−1 was achieved by NERICA S-21 under AWD 30 kPa at 150 kg N ha−1. The AWD irrigation management at 30 kPa resulted in increasing rice yield, rice water use and nitrogen use efficiency and reducing the irrigation applications by 27.3% in comparison with continuous flooding. AWD30 kPa could be adopted as a water saving technology for water productivity under paddy production in the Senegal River Middle Valley. Additional research should be conducted in the upper Valley, where soils are sandier and water is less available, for the sustainability and the adoption of the irrigation water saving practices across the entire Senegal River Valley

Suitable management options to improve the productivity of rice cultivars under salinity stress

Growing rice in saline soils by minimizing damage on growth and yield remains a challenge. We conducted field experiments in the Africa Rice research field located in the Senegal River delta (16° 11ʹ N, 16° 15ʹ W) to study the effects of three management options of fertilization e.g. (i) nitrogen, phosphorus, and potassium fertilization: NPK; (ii) NPK combined with zinc: NPK-Zn, and (iii) NPK combined with gypsum: NPK-gypsum on the soil salinity level, the nutrient uptake and the productivity of different rice cultivars. The whole objective of this study is to determine how zinc or gypsum associated to NPK fertilizer can improve the growth and productivity of rice crop in saline soil. Results showed that the initial soil salinity level was reduced rapidly in plots treated with gypsum. The leaf-K/Na ratio, agronomic nitrogen use efficiency (ANUE), and grain yield of rice cultivars under the salinity stress were improved by the NPK-gypsum and NPK-Zn options relatively to the NPK option, suggesting that NPK-gypsum and NPK-Zn are suitable management options in reducing adverse effect of low K/Na, low ANUE as well as to improve rice yield under salinity stress

Climate smart rice innovations to reduce the impact of climate change on the livelihood of value chain actors

Introduction Rice is a major source of nutrients, largely contributing to the food and nutrition security for millions of people in Africa although most countries still rely on huge imports to meet local demand. Extreme temperatures, drought, flooding, and high salinity are climate change related stresses that negatively affect rice yield and grain quality. Thus, tackling these constraints is a critical action to increasing rice self sufficiency in Cameroon and Africa in general. Methods The Africa Rice Center in partnership with the National Agricultural Research and Extension Services of its 28 member States operating within the framework of the Africa-wide Taskforces has developed, tested, validated, and are deploying breeding, agronomic and post-harvest approaches to mitigate the negative impacts of climate change on rice yield and quality in Africa. Results Breeding approaches have led to the development of drought, cold, submergence, stagnation flood, salinity, and anaerobic germination tolerant varieties that are also resistant or tolerant to biotic stresses. These have demonstrated better yields and grain quality under stressed conditions compared to counterparts lacking those specific traits. The system of rice intensification and alternate wetting and drying, mid-season drainage, smart-valleys approach for inland development, solar-powered irrigation system, no-till and rice straw mulching are agronomic approaches developed and these approaches have demonstrated significant increase in yield and grain quality compared to alternative approached under climate change stress conditions. Post-harvest approaches have focused on reducing grain breakages, chalkiness, mycotoxin contamination, insecticide and fungicide use, deforestation and value addition to broken rice and rice milling byproducts using environmentally friendly methods. Post-harvest innovations here include using improved rice parboiling fueled by rice husk, solar-powered hermetic storage systems, processing of fine broken rice into flour for porridges and bakery products and use of rice husk fan-assisted stoves for household cooking and the cottage processing industry. Conclusions and recommendations Although climate change is a serious threat to rice production affecting both yield and quality, African governments will have to implement policy measures that enhance the scaling and adoption of climate smart rice innovation developed by AfricaRice to mitigate the impact of climate change if they aspire to reduce rice imports

Assessment of Genetic Variation and Population Structure of Diverse Rice Genotypes Adapted to Lowland and Upland Ecologies in Africa Using SNPs

Using interspecific crosses involving Oryza glaberrima Steud. as donor and O. sativa L. as recurrent parents, rice breeders at the Africa Rice Center developed several 'New Rice for Africa (NERICA)' improved varieties. A smaller number of interspecific and intraspecific varieties have also been released as ‘Advanced Rice for Africa (ARICA)’. The objective of the present study was to investigate the genetic variation, relatedness, and population structure of 330 widely used rice genotypes in Africa using DArTseq-based single nucleotide polymorphisms (SNPs). A sample of 11 ARICAs, 85 NERICAs, 62 O. sativa spp. japonica, and 172 O. sativa spp. indica genotypes were genotyped with 27,560 SNPs using diversity array technology (DArT)-based sequencing (DArTseq) platform. Nearly 66% of the SNPs were polymorphic, of which 15,020 SNPs were mapped to the 12 rice chromosomes. Genetic distance between pairs of genotypes that belong to indica, japonica, ARICA, and NERICA varied from 0.016 to 0.623, from 0.020 to 0.692, from 0.075 to 0.763, and from 0.014 to 0.644, respectively. The proportion of pairs of genotypes with genetic distance > 0.400 was the largest within NERICAs (35.1% of the pairs) followed by ARICAs (18.2%), japonica (17.4%), and indica (5.6%). We found one pair of japonica, 11 pairs of indica, and 35 pairs of NERICA genotypes differing by <2% of the total scored alleles, which was due to 26 pairs of genotypes with identical pedigrees. Cluster analysis, principal component analysis, and the model-based population structure analysis all revealed two distinct groups corresponding to the lowland (primarily indica and lowland NERICAs) and upland (japonica and upland NERICAs) growing ecologies. Most of the interspecific lowland NERICAs formed a sub-group, likely caused by differences in the O. glaberrima genome as compared with the indica genotypes. Analysis of molecular variance revealed very great genetic differentiation (FST = 0.688) between the lowland and upland ecologies, and 31.2% of variation attributable to differences within cluster groups. About 8% (1,197 of 15,020) of the 15,020 SNPs were significantly (P < 0.05) different between the lowland and upland ecologies and formed contrasting haplotypes that could clearly discriminate lowland from upland genotypes. This is the first study using high density markers that characterized NERICA and ARICA varieties in comparison with indica and japonica varieties widely used in Africa, which could aid rice breeders on parent selection for developing new improved rice germplasm

Genomic Characterization of Skin and Soft Tissue Streptococcus pyogenes Isolates from a Low-Income and a High-Income Setting.

Streptococcus pyogenes is a leading cause of human morbidity and mortality, especially in resource-limited settings. The development of a vaccine against S. pyogenes is a global health priority to reduce the burden of postinfection rheumatic heart disease. To support this, molecular characterization of circulating S. pyogenes isolates is needed. We performed whole-genome analyses of S. pyogenes isolates from skin and soft tissue infections in Sukuta, The Gambia, a low-income country (LIC) in West Africa where there is a high burden of such infections. To act as a comparator to these LIC isolates, skin infection isolates from Sheffield, United Kingdom (a high-income country [HIC]), were also sequenced. The LIC isolates from The Gambia were genetically more diverse (46 emm types in 107 isolates) than the HIC isolates from Sheffield (23 emm types in 142 isolates), with only 7 overlapping emm types. Other molecular markers were shared, including a high prevalence of the skin infection-associated emm pattern D and the variable fibronectin-collagen-T antigen (FCT) types FCT-3 and FCT-4. Fewer of the Gambian LIC isolates carried prophage-associated superantigens (64%) and DNases (26%) than did the Sheffield HIC isolates (99% and 95%, respectively). We also identified streptococcin genes unique to 36% of the Gambian LIC isolates and a higher prevalence (48%) of glucuronic acid utilization pathway genes in the Gambian LIC isolates than in the Sheffield HIC isolates (26%). Comparison to a wider collection of HIC and LIC isolate genomes supported our findings of differing emm diversity and prevalence of bacterial factors. Our study provides insight into the genetics of LIC isolates and how they compare to HIC isolates. IMPORTANCE The global burden of rheumatic heart disease (RHD) has triggered a World Health Organization response to drive forward development of a vaccine against the causative human pathogen Streptococcus pyogenes. This burden stems primarily from low- and middle-income settings where there are high levels of S. pyogenes skin and soft tissue infections, which can lead to RHD. Our study provides much needed whole-genome-based molecular characterization of isolates causing skin infections in Sukuta, The Gambia, a low-income country (LIC) in West Africa where infection and RHD rates are high. Although we identified a greater level of diversity in these LIC isolates than in isolates from Sheffield, United Kingdom (a high-income country), there were some shared features. There were also some features that differed by geographical region, warranting further investigation into their contribution to infection. Our study has also contributed data essential for the development of a vaccine that would target geographically relevant strains