International Crops Research Institute for the Semi-Arid Tropics
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Evaluation of machine learning models for prediction of daily reference evapotranspiration in semi-arid India
No full textReference evapotranspiration (ET0) is controlled by climatic factors; hence, its estimation provides an idea about the atmospheric demand of water. Machine learning techniques like elastic net (ELNET), K-nearest neighbours (KNN), multivariate adaptive regression splines (MARS), partial least squares regression (PSLR), random forest (RF), support vector regression (SVR), XGBoost and cubist were employed to predict daily reference evapotranspiration based on daily weather parameters of twenty years. Penman-Monteith method was used as the reference method for ET0 estimation. All models performed well during calibration showing higher coefficient of determination (R2) which ranged from 0.97 (for PLSR) to 1 (for cubist models). Mean absolute error during calibration ranges from 0.027 mm-1 d-1 for cubist to 0.607 mm-1 d-1 for ELNET. Cubist model (R2= 1, MAE = 0.017 mm d-1, RMSE = 0.027 mm d-1) outper formed other models during the calibration. During validation, the coefficient of determination (R2) for the machine learning models varied from 0.819 to 1, RMSE varied from 0.06 to 0.60 mm d-1 and MAE varied from 0.031 to 0.38 mm d-1. Based on statistical parameters, best performance was observed for cubist model (R2 = 1, RMSE = 0.06 mm d-1, MAE = 0.031 mm d-1) among the studied machine learning models for the prediction of reference evapotranspiration. Hence, the cubist model may be used to estimate daily reference evapotranspiration for the studied region
Development of trait-specific genetic stocks derived from wild Cicer species as novel sources of resistance to important diseases for chickpea improvement
Get PDFLow level of resistance to major diseases such as ascochyta blight (AB), botrytis grey mould (BGM) and dry root rot (DRR) in the cultivated chickpea genepool necessitates harnessing wild Cicer species. Sixty-eight accessions belonging to eight annual wild Cicer species and seven chickpea cultivars were screened for AB, BGM and DRR under controlled environmental conditions over the years. Intra-accession variability was observed among wild Cicer accessions for each disease. Hence, progenies of single resistant plants were selected for further evaluations and the trait-specific genetic stocks (TGS) were developed for each disease after re-screening following the single seed descent method. For AB, a high level of resistance was identified in four accessions belonging to tertiary genepool species, ICC 17334 (Cicer judaicum), ICC 17302, ICC 17308 and ICC 20177 (C. bijugum). Nine accessions, ICC 17160, ICC 17264, ICC 17270, ICC 20170, ICC 20186, ICC 20225, ICC 20247, ICC 20251 and IG 72941 of primary (C. reticulatum) and one accession, ICC 20190 of secondary (C. echinospermum)
genepool species were resistant to BGM whereas, four accessions, ICC 20187 (C. reticulatum) and ICC 20218, ICC 20244 and ICC 20257 (C. echinospermum) were resistant to DRR. Development and utilization of these TGS in chickpea pre-breeding will assist in developing disease-resistant chickpea cultivars with broad genetic base
Editorial: Disease and pest resistance in rice
Get PDFRice (Oryza sativa L.), as one of the most important crops worldwide, has been widely adopted as a model for studying cereal crops and monocot plants. Rice production is severely threatened by pathogens and pests during the entire growth season, causing an estimated 10%–30% yield loss annually (Douglas, 2018; Savary et al., 2019). Therefore, disease and pest resistance has been one of the major goals in rice breeding. However, rice improvement has encountered a bottleneck largely due to the lack of useful disease
resistance (R) genes and molecular approaches in breeding programs. Most R genes have limited application because of race-specificity. Therefore, the identification and application of novel R genes with broad-spectrum resistance have been a big challenge. Among many rice diseases, those causing the most relevant yield losses include the rice
fungal blast caused by Magnaporthe oryzae (M. oryzae), bacterial blight caused by Xanthomonas oryzae pv. oryzae (Xoo), sheath blight caused by the necrotrophic fungus
Rhizoctonia solani (R. solani), false smut caused by the obligate biotrophic fungus Ustilaginoidea virens (Cke.) Tak (U. virens), and viral diseases including rice tungro virus and rice stripe virus. In addition, insect pests and plant parasitic nematodes have also caused huge yield loss of rice. Over the past 30 years, impressive advancements have been achieved in R gene discovery and molecular mechanisms of disease resistance and growth defense trade-offs (Deng et al., 2020; Li et al., 2020). These achievements have greatly
facilitated the breeding of new disease and pest resistance cultivars. Within this specific topic on ‘Disease and Pest Resistance in Rice’, we aim to provide new knowledge on R gene discovery, mechanisms of rice immunity and resistance against pathogens and insects, and technology for rice improvement. Launched in Oct, 2021, this topic received 16 manuscripts in total and ultimately published 5 papers after peer-view, including four research articles and one review. We also regret that other submissions were not accepted for publication after reviewing
Modelling the dynamics and phenotypic consequences of tiller outgrowth and cessation in sorghum
Get PDFTillering affects canopy leaf area, and hence crop growth via capture of light, water and nutrients. Depending on the season, variation in tillering can result in increased or decreased yield. Reduced tillering has been associated with water-saving and enhanced yield in water-limited conditions. The objective of this study was to develop a generic model of the dynamics of tillering in sorghum incorporating key genetic and environmental controls. The dynamic of tillering was defined in four key phases—pre-tillering, tiller emergence, cessation of tiller emergence and cessation of tiller growth. Tillering commenced at full expansion of leaf four and thereafter was synchronized with leaf appearance. The potential total number of tillers (TTN) was dependent on a genetic propensity to tiller and an index of assimilate availability dependent on the shoot source–sink balance. Cessation of tiller emergence could occur before TTN depending on extent of competition from neighbours. Subsequent cessation of growth of emerged tillers was related to the extent of internal competition for assimilate among plant organs, resulting in prediction of final fertile tiller number (FTN). The model predicted tillering dynamics well in an experiment with a range in plant density. Plausibility simulations of FTN conducted for diverse field conditions in the Australian sorghum belt reflected expectations. The model is able to predict FTN as an emergent property. Its utility to explore GxMxE crop adaptation landscapes, guide molecular discovery, provide a generic template for other cereals and link to advanced methods for enhancing genetic gain in crops were discussed
Genomic and phenotypic characterization of finger millet indicates a complex diversification history
Get PDFAdvances in sequencing technologies mean that insights into crop diversification can now be explored in crops beyond major staples. We use a genome assembly of finger millet, an allotetraploid orphan crop, to analyze DArTseq single nucleotide polymorphisms (SNPs) at the whole and sub-genome level. A set of 8778 SNPs and 13 agronomic traits was used to characterize a diverse panel of 423 landraces from Africa and Asia. Through principal component analysis (PCA) and discriminant analysis of principal components, four distinct groups of accessions were identified that coincided with the primary geographic regions of finger millet cultivation. Notably, East Africa, presumed to be the crop's origin, exhibited the lowest genetic diversity. The PCA of phenotypic data also revealed geographic differentiation, albeit with differing relationships among geographic areas than indicated with genomic data. Further exploration of the sub-genomes A and B using neighbor-joining trees revealed distinct features that provide supporting evidence for the complex evolutionary history of finger millet. Although genome-wide association study found only a limited number of significant marker-trait associations, a clustering approach based on the distribution of marker effects obtained from a ridge regression genomic model was employed to investigate trait complexity. This analysis uncovered two distinct clusters. Overall, the findings suggest that finger millet has undergone complex and context-specific diversification, indicative of a lengthy domestication history. These analyses provide insights for the future development of finger millet
Editorial: Dissecting complex gene families to understand their roles in climate-resilience
Get PDFClimate resilience is an important trait that the global plant research community focuses on, for ensuring food and nutritional security. Understanding the genetic determinants underlying this complex trait is key for tweaking the candidate genes, alleles, or QTLs, to enhance climate resilience. Genomics plays a major role in decoding the plant genomes to identify the coding and non-coding elements present within the DNA. Single-copy genes are present scarcely among the coding elements, whereas the remaining genes are encoded as gene families. More than one member of a particular gene family allows the genes to perform a multitude of functions, and their expression is tightly regulated at different levels. Whole genome sequencing reveals the information of genes and their corresponding gene families in the given genome. Characterization of these gene families provides insights into their structural and functional diversity. Thus, recent studies focus on dissecting the structural and functional aspects of gene families, which further identify the candidate genes for downstream characterization. Given the importance of genome-wide analyses in delineating the functional roles of different gene families in imparting climate resilience, the Research Topic invited articles on this aspect of gene family analyses
Author Correction: Genetic approaches for assessment of phosphorus use efficiency in groundnut (Arachis hypogaea L.)
Get PDFProduction of phosphorus efficient genotypes can reduce environmental pollution. Identification of P-efficient groundnut genotypes is a need of the hour to sustain in P-deficient soils. The pot experiment showed significant differences between genotypes (G) and treatments (T) for all the traits and G × T interaction for majority of traits. The G × T × Y interaction effects were also significant for all the traits except leaf P% (LP%), leaf acid phosphatase (LAP) and root dry weight (RDW). In lysimeter experiment, the effect of G, T and G × T were significant for leaf dry weight (LDW), stem dry weight (SDW), total transpiration (TT) and transpiration efficiency (TE). For traits, LDW, SDW, TT, TE, ICGV 00351 and ICGS 76; for SDW, TT, ICGV 02266 are best performers under both P-sufficient and deficient conditions. Based on P-efficiency indices and surrogate traits of P-uptake, ICGV’s 02266, 05155, 00308, 06040 and 06146 were considered as efficient P-responding genotypes. From GGE biplot, ICGV 06146 under P-deficient and TAG 24 under both P-sufficient and deficient conditions are portrayed as best performer. ICGV 06146 was identified as stable pod yielder and a promising genotype for P-deficient soils. The genotypes identified in this study can be used as a parent in developing mapping population to decipher the genetics and to devleop groundnut breeding lines suitable to P-deficient soils
Inefficient Water Pricing and Incentives for Conservation
Get PDFFarmers often buy water using fixed fees—rather than with marginal prices. We use two randomized controlled trials in Bangladesh to study the relationship between marginal prices, adoption of a water-saving technology, and water usage. Our first experiment shows that the technology only saves water when farmers face marginal prices. Our second experiment finds that an encouragement to voluntarily convert to hourly pumping charges does not save water. Taken together, efforts to conserve water work best when farmers face marginal prices, but simply giving an option for marginal pricing is insufficient to trigger water-saving investments and reduce irrigation demands
Understanding the dynamics and identify entry points to build resilience in groundnut value chain in Senegal: A group model building approach
Get PDFThis working paper focuses on analyzing the dynamics of the peanut value chain in Senegal and identifying entry points to enhance its resilience. Using an innovative Group Model Building approach, the study explores the complexities of the chain, which is central to Senegalese agriculture, covering 40% of the total cultivated area. The groundnut value chain, largely in the hands of smallholders, is a crucial income source for the rural population. However, it faces challenges such as climate pressures, aging infrastructure, and unregulated trader entry, exacerbating vulnerability despite stakeholder efforts. Supply complexities include factors like production systems, climatic conditions, and access to essential inputs. Seeds and fertilizers are critical, but farmers struggle with insufficient quantities, ineffective governance, and limited access to mechanization. This results in low productivity, unstable yields, and high production costs. Climate risks, compounded by low access to climate information services (CIS) and climate- smart agricultural practices (CSAP) training, further impact yields and increase vulnerability. Land degradation adds another dimension to climate risk, affecting both yield and land use for peanut production. The study recommends an innovative Group Model Building approach to gain insights into the groundnut value chain dynamics through causal loop diagrams. The objective is to formulate policy recommendations to strengthen the sustainability and resilience of the peanut value chain, addressing challenges related to inputs, climate risks, and training
Evaluation of millets for physio-chemical and root morphological traits suitable for resilient farming and nutritional security in Eastern Himalayas
Get PDFIntroduction:Millets are nutritionally superior and climate-resilient short-duration crops and hold a prominent place in cropping sequences around the world. They have immense potential to grow in a marginal environment due to diverse
adaptive mechanisms. Methods: An experiment was conducted in an organic production system in the North Eastern Himalayan foothills of India for 3 consecutive years by evaluating
high-yielding varieties (HYVs) of different millets, viz., finger millet, foxtail millet, little millet, barnyard millet, proso millet, and browntop millet, along with local
landraces of finger millets (Sikkim-1 and Sikkim-2; Nagaland-1 and Nagaland-2) to identify stable, high-yielding, and nutritionally superior genotypes suited for
the region. Results: Among the various millets, finger millet, followed by little millet and foxtail millet, proved their superiority in terms of productivity (ranging between 1.16 and 1.43Mg ha−1) compared to other millets. Among different varieties of finger millets, cv. VL Mandua 352 recorded the highest average grain yield (1.43Mg ha−1) followed by local landraces, Nagaland-2 (1.31Mg ha−1) and Sikkim-1 (1.25Mg ha−1). Root traits such as total root length, root volume, average diameter of roots, and root surface area were significantly higher in finger millet landraces Nagaland-1, Nagaland-2, and Sikkim-1 compared to the rest of the millet genotypes. The different millets were found to be rich sources of protein as recorded in foxtail millet cv. SiA 3088 (12.3%), proso millet cv. TNAU 145 (11.5%), and finger millet landraces, Sikkim-1 and Nagaland-2 (8.7% each). Finger millet landrace Sikkim-2 recorded the highest omega-6 content (1.16%), followed by barnyard millet cv. VL 207 (1.09%). Barnyard millet cv. VL 207 recorded the highest polyunsaturated fatty acid (PUFA) content (1.23%), followed by foxtail millet cv. SiA 3088 (1.09%). The local finger millet landraces Sikkim-1 and Sikkim-2 recorded the highest levels of histidine (0.41%) and tryptophan (0.12%), respectively. Sikkim-1 and Nagaland-2 recorded the highest level of thiamine (0.32%) compared to the HYVs. Conclusion: These findings indicate that finger millet has great potential in the organic production system of the North Eastern Himalayan Region (NEHR) of India, and apart from HYVs like VL Mandua 352, local landraces, viz., Nagaland-2 and Sikkim-1, should also be promoted for ensuring food and nutritional security in this fragile ecosystem