International Crops Research Institute for the Semi-Arid Tropics
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Using an incomplete block design to allocate lines to environments improves sparse genome-based prediction in plant breeding
Get PDFGenomic selection (GS) is a predictive methodology that trains statistical machine-learning models with a reference population that is used to perform genome-enabled predictions of new lines. In plant breeding, it has the potential to increase the speed and reduce the cost of selection. However, to optimize resources, sparse testing methods have been proposed. A common approach is to guarantee a proportion of nonoverlapping and overlapping lines allocated randomly in locations, that is, lines appearing in some locations but not in all. In this study we propose using incomplete block designs (IBD), principally, for the allocation of lines to locations in such a way that not all lines are observed in all locations. We compare this allocation with a random allocation of lines to locations guaranteeing that the lines are allocated to the same number of locations as under the IBD design. We implemented this benchmarking on several crop data sets under the Bayesian genomic best linear unbiased predictor (GBLUP) model, finding that allocation under the principle of IBD outperformed random allocation by between 1.4% and 26.5% across locations, traits, and data sets in terms of mean square error. Although a wide range of performance improvements were observed, our results provide evidence that using IBD for the allocation of lines to locations can help improve predictive performance compared with random allocation. This has the potential to be applied to large-scale plant breeding programs
Raffinose Family Oligosaccharides: Friend or Foe for Human and Plant Health?
Get PDFRaffinose family oligosaccharides (RFOs) are widespread across the plant kingdom, and their concentrations are related to the environment, genotype, and harvest time. RFOs are known to carry out many functions in plants and humans. In this paper, we provide a comprehensive review of RFOs, including their beneficial and anti-nutritional properties. RFOs are considered anti-nutritional factors since they cause flatulence in humans and animals. Flatulence is the single most important factor that deters consumption and utilization of legumes in human and animal diets. In plants, RFOs have been reported to impart tolerance to heat, drought, cold, salinity, and disease resistance besides regulating seed germination, vigor, and longevity. In humans, RFOs have beneficial effects in the large intestine and have shown prebiotic potential by promoting the growth of beneficial bacteria reducing pathogens and putrefactive bacteria present in the colon. In addition to their prebiotic potential, RFOs have many other biological functions in humans and animals, such as anti-allergic, anti-obesity, anti-diabetic, prevention of non-alcoholic fatty liver disease, and cryoprotection. The wide-ranging applications of RFOs make them useful in food, feed, cosmetics, health, pharmaceuticals, and plant stress tolerance; therefore, we review the composition and diversity of RFOs, describe the metabolism and genetics of RFOs, evaluate their role in plant and human health, with a primary focus in grain legumes
Drivers of Pigeon Pea Consumption Among School-Aged Children in Central Tanzania
Get PDFBackground: Protein energy malnutrition (PEM) and iron deficiencies (ID) are of major public health concern in Tanzania including among school-aged children. PEM and ID in early childhood have serious, long-term consequences because they impede motor, sensory, social and emotional development, growth retardation, poor cognitive development, learning disability of children, lowered resistance to infectious diseases, and reduced physical work capacity. The objective of this study was to elucidate the drivers of pigeon pea consumption among school-aged children in Dodoma district, Central Tanzania. Understanding these drivers would be useful in promoting pigeon pea consumption among school-aged children as one of the strategies to increase dietary protein and iron intake.
Methods: This study was a cross-sectional study in which data were collected using a questionnaire based on a combination of the Theory of Planned Behavior and Health Belief Model. The data were collected from caregivers (n = 138) in four villages in Kongwa district, Dodoma region, Central Tanzania. We used correlations and multiple regressions to assess associations between constructs and identify predictive constructs. Mann–Whitney U tests were used for score comparisons with a significant p-value set at <0.10.
Results: Health value was significantly correlated with health behavior identity (rs = 0.63, p < 0.001) and also significantly predicted health behavior identity (rs = 0.49, p = 0.001). The constructs cues to action and control belief were significantly associated with intention (β = −0.41, p = 0.059 and β = 0.06, p = 0.019 respectively). Finally, we observed that intention was a significant predictor of behavior (β = 1.38, p = 0.001). We also observed a significant negative interaction between perceived barriers and intention to consume pigeon pea (β = −0.04, p = 0.006), indicating that perceived barriers limit intention to consume pigeon pea.
Conclusion and Implication: Our findings indicate that when the caregiver places increased importance on preventing her school-aged child from being iron or protein deficient or indeed anemic (health value), it results in a positive evaluation of the effectiveness of giving pigeon pea to address these nutrient deficiencies. Programs and efforts aimed at promoting pigeon pea consumption should focus on educating caregivers on iron and protein deficiency and the role that pigeon pea could play in addressing these. However, perceived barriers such as pest infestation during storage need to be addressed to increase pigeon pea consumption. The involvement of post-harvest management specialists is therefore crucial. Along with this, increasing productivity and crop management is also crucial to ensure year-round affordable supply of pigeon pea
Stability of advanced medium duration genotypes across seasons for yield in pigeonpea [Cajanus cajan (L.) millsp.]
Get PDFBackground
Yield is polygenically inherited and highly influenced by G x E interaction higher magnitude of G x E interaction among genotypes invalidates the fitness of genotypes across the environments. Hence, quantification G x E interaction and identification of stable genotypes across environments will enhance production and productivity of pigeonpea.
Methods
The stable performance of the thirty three advanced medium duration lines of pigeonpea along with six check varieties across the seasons were examined during kharif-2017, 2018 and 2019 at Zonal Agricultural Research Station, (ZARS) Kalaburagi, Karnataka, India. The advanced medium duration genotypes was contributed by six research stations belongs six states in India.
Result
Considering all stability parameters the genotype ICPL 20108 found stable, high yielding and had desirable agronomic traits. The genotype GRG 177 though ranked first for mean yield, it exhibited nonlinear regression indicating highly sensitiveness to different environments. The genotype GRG 152 had second highest mean yield with bi<1 (bi= regression) and non significant deviation from regression co-efficient indicating its specific suitability to unfavorable/poor/low input environments. The genotypes BDN-2014-1, ICPL 20098 and AGL-1603-4 had average yield above population mean and exhibited stable performance across environments
Evaluation and application of the CROPGRO-soybean model for determining optimum sowing windows of soybean in the Nigeria savannas
Get PDFSoybean production is limited by poor soil fertility and unstable rainfall due to climate variability in the Nigeria savannas. There is a decline in the amount and duration of rainfall as one moves from the south to north of the savanna zones. The use of adapted soybean varieties and optimum sowing windows are avenues to increase productivity in the face of climate variability. Crop simulation models can be used as tools for the evaluation of alternative management options for a particular location, including fertilizer application rates, plant density, sowing dates and land use. In this study, we evaluated the performance of the Cropping System Model (CSM)-CROPGRO-Soybean to determine optimum sowing windows for three contrasting soybean varieties (TGX1835-10E, TGX1904-6F and TGX1951-3F) cultivated in the Nigeria savannas. The model was calibrated using data from ten field experiments conducted under optimal conditions at two sites (BUK and Dambatta) in Kano in the Sudan savanna (SS) agro-ecology over four growing seasons. Data for model evaluation were obtained from independent experiment for phosphorus (P) response trials conducted under rainfed conditions in two locations (Zaria and Doguwa) in the northern Guinea savanna (NGS) zone. The model calibration and evaluation results indicated good agreement between the simulated and observed values for the measured parameters. This suggests that the CROPGRO-Soybean model was able to accurately predict the performance of soybean in the Nigeria savannas. Results from long-term seasonal analysis showed significant differences among the agro-ecologies, sowing windows and the soybean varieties for grain yield. Higher yields are simulated among the soybean varieties in Zaria in the NGS than in Kano the SS and Jagiri in the southern Guinea savanna (SGS) agro-ecological zones. Sowing from June 1 to July 5 produced optimal yield of TGX1951-3F and TGX1835-10E beyond which yield declined in Kano. In Zaria and Jagiri the simulated results show that, sowing from June 1 to July 12 are appropriate for all the varieties. The variety TGX1951-3F performed better than TGX1904-6F and TGX1835-10E in all the agro-ecologies. The TGX1951-3F is, therefore, recommended for optimum grain yield in the savannas of northern Nigeria. However, the late maturing variety TGX1904-6F is not recommended for the SS due to the short growing season in this zone
Differential Physio-Biochemical and Metabolic Responses of Peanut (Arachis hypogaea L.) under Multiple Abiotic Stress Conditions
Get PDFThe frequency and severity of extreme climatic conditions such as drought, salinity, cold, and heat are increasing due to climate change. Moreover, in the field, plants are affected by multiple abiotic stresses simultaneously or sequentially. Thus, it is imperative to compare the effects of stress combinations on crop plants relative to individual stresses. This study investigated the differential regulation of physio-biochemical and metabolomics parameters in peanut (Arachis hypogaea L.) under individual (salt, drought, cold, and heat) and combined stress treatments using multivariate correlation analysis. The results showed that combined heat, salt, and drought stress compounds the stress effect of individual stresses. Combined stresses that included heat had the highest electrolyte leakage and lowest relative water content. Lipid peroxidation and chlorophyll contents did not significantly change under combined stresses. Biochemical parameters, such as free amino acids, polyphenol, starch, and sugars, significantly changed under combined stresses compared to individual stresses. Free amino acids increased under combined stresses that included heat; starch, sugars, and polyphenols increased under combined stresses that included drought; proline concentration increased under combined stresses that included salt. Metabolomics data that were obtained under different individual and combined stresses can be used to identify molecular phenotypes that are involved in the acclimation response of plants under changing abiotic stress conditions. Peanut metabolomics identified 160 metabolites, including amino acids, sugars, sugar alcohols, organic acids, fatty acids, sugar acids, and other organic compounds. Pathway enrichment analysis revealed that abiotic stresses significantly affected amino acid, amino sugar, and sugar metabolism. The stress treatments affected the metabolites that were associated with the tricarboxylic acid (TCA) and urea cycles and associated amino acid biosynthesis pathway intermediates. Principal component analysis (PCA), partial least squares-discriminant analysis (PLS-DA), and heatmap analysis identified potential marker metabolites (pinitol, malic acid, and xylopyranose) that were associated with abiotic stress combinations, which could be used in breeding efforts to develop peanut cultivars that are resilient to climate change. The study will also facilitate researchers to explore different stress indicators to identify resistant cultivars for future crop improvement programs
Conventional and molecular breeding for disease resistance in chickpea: status and strategies
No full textChickpea (Cicer arietinum L.) is an important grain legume at the global level. Among different biotic stresses, diseases are the most important factor limiting its production, causing yield losses up to 100% in severe condition. The major diseases that adversely affect yield of chickpea include Fusarium wilt, Ascochyta blight and Botrytis gray mold. However, dry root rot, collar rot, Sclerotinia stem rot, rust, stunt disease and phyllody have been noted as emerging biotic threats to chickpea production in many production regions. Identification and incorporation of different morphological and biochemical traits are required through breeding to enhance genetic gain for disease resistance. In recent years, remarkable progress has been made in the development of trait-specific breeding lines, genetic and genomic resources in chickpea. Advances in genomics technologies have opened up new avenues to introgress genes from secondary and tertiary gene pools for improving disease resistance in chickpea. In this review, we have discussed important diseases, constraints and improvement strategies for enhancing disease resistance in chickpea
Microbial remediation of metals by marine bacteria
No full textToxic metals, often present in various xenobiotics, pose a serious threat to the environment and health. Industrial effluents loaded with hazardous levels of heavy metals may lead to various pathophysiological conditions like dermatitis, nephritis, cancer, and neuronal diseases. Several physical and chemical techniques like settling, sedimentation, evaporative recovery, coagulation, precipitation, floatation, ion exchange, flocculation, chemical oxidation, reduction, reverse osmosis, ultrafiltration, and electrodialysis are generally employed to remove heavy metals from the effluents. However, these methods are not fully efficient and generate a large amount of sludge which is difficult to dispose off. Hereby, microbial processes have gained importance for water treatment and metal removal. In this chapter, an elaborate account on the promises of marine bacteria for the efficient bioremoval of toxic metals is presented. Several marine bacteria like Marinomonas communis, Marinobacter santoriniensis, Pseudomonas pseudoalcaligenes, Exiguobacterium indicum, Rhodobium marinum, Rhodobacter sphaeroides, Alteromonas haloplanktis, Marinobacter hydrocarbonoclasticus, etc., have been reported to remove toxic metals like arsenic, cadmium, chromium, cobalt, copper, iron, lead, manganese, mercury, nickel, selenium vanadium, and zinc. The underlying mechanisms of metal removal using marine bacteria include biosorption, bioaccumulation, and bioconversion, which have also been discussed in detail. Further, the role of genetic elements like mer operon encoding mercury reductase enzyme, bmtA gene for metallothionein, and zntA gene for ATPase efflux systems is explained. Hence, marine bacteria can be applied for developing effective strategies for wastewater treatment of toxic heavy metals
Potential of engineering the myo-inositol oxidation pathway to increase stress resilience in plants
Get PDFMyo-inositol is one of the most abundant form of inositol. The myo-inositol (MI) serves as substrate to diverse biosynthesis pathways and hence it is conserved across life forms. The biosynthesis of MI is well studied in animals. Beyond biosynthesis pathway, implications of MI pathway and enzymes hold potential implications in plant physiology and crop improvement. Myo-inositol oxygenase (MIOX) enzyme catabolize MI into D-glucuronic acid (D-GlcUA). The MIOX enzyme family is well studied across few plants. More recently, the MI associated pathway’s crosstalk with other important biosynthesis and stress responsive pathways in plants has drawn attention. The overall outcome from different plant species studied so far are very suggestive that MI derivatives and associated pathways could open new directions to explore stress responsive novel metabolic networks. There are evidences for upregulation of MI metabolic pathway genes, specially MIOX under different stress condition. We also found MIOX genes getting differentially expressed according to developmental and stress signals in Arabidopsis and wheat. In this review we try to highlight the missing links and put forward a tailored view over myo-inositol oxidation pathway and MIOX proteins
Editorial: Functional Genomics in Plant Breeding 2.0
Get PDFScientists agree that the increased human impact on the environment since the 19th century has positioned our planet in a period of rapid and intense change, particularly to
our natural ecosystems. Most plants suffer from physiological and biochemical damages upon exposure to increased biotic and abiotic stresses. Regarding crops, stress-induced injuries, which are reflected in most metabolic processes, can cause substantial losses in
yield. Crop species are equipped with vast diversity in stress adaptation mechanisms. Although many of these mechanisms are universal, their relative importance may vary
from genotype to genotype. Consequently, some genotypes can cope with stress better than others. Genotypes that differ in stress adaptation/acclimation mechanisms serve as an
essential resource for studying these mechanisms. Based on available genotypic variability and given the considerable impact of genomic structural variation on gene function, we
need to increase our understanding of the genome and its relationship with the plant phenotype related to the trait of interest