International Crops Research Institute for the Semi-Arid Tropics
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ICRISAT Annual Report 2023
Get PDFICRISAT thanks its donors, partners and supporters for enabling us to keep delivering the innovations that overcome hunger, malnutrition, poverty and environmental degradation for the 2.1 billion people who reside in the drylands of Asia, sub-Saharan Africa and beyond
Genome-wide association study and expression of candidate genes for Fe and Zn concentration in sorghum grains
Get PDFSorghum germplasm showed grain Fe and Zn genetic variability, but a few varieties were biofortified with these minerals. This work contributes to narrowing this gap. Fe and Zn concentrations along with 55,068 high-quality GBS SNP data from 140 sorghum accessions were used in this study. Both micronutrients exhibited good variability with respective ranges of 22.09–52.55 ppm and 17.92–43.16 ppm. Significant marker-trait associations were identified on chromosomes 1, 3, and 5. Two major effect SNPs (S01_72265728 and S05_58213541) explained 35% and 32% of Fe and Zn phenotypic variance, respectively. The SNP S01_72265728 was identified in the cytochrome P450 gene and showed a positive effect on Fe accumulation in the kernel, while S05_58213541 was intergenic near Sobic.005G134800 (zinc-binding ribosomal protein) and showed negative effect on Zn. Tissue-specific in silico expression analysis resulted in higher levels of Sobic.003G350800 gene product in several tissues such as leaf, root, flower, panicle, and stem. Sobic.005G188300 and Sobic.001G463800 were expressed moderately at grain maturity and anthesis in leaf, root, panicle, and seed tissues. The candidate genes expressed in leaves, stems, and grains will be targeted to improve grain and stover quality. The haplotypes identified will be useful in forward genetics breeding
Allele Mining for Crop Genomic Designing in Peanut
No full textThe dissection of naturally existing allelic variations in the candidate genes responsible for crucial agronomic traits is made possible by allele mining. Allele mining may now be used to analyze the precise allelic variations of functional genes found in a variety of peanut cultivars as a result of the finding, isolation, and characterization of several genes in peanut. The complex alleles serve as a reservoir of diversity to produce an array of functional genes. One of the primary mechanisms governing the evolution and development of R genes is regular sequence exchange. The generation of allele-specific markers for use in marker-assisted selection, together with the identification of new alleles and haplotypes, can be accomplished by allele mining. In modern plant breeding that is driven by genomics, allele mining can be seen as a crucial link between the efficient usage of genetic and genomic resources. The information presented here is crucial for giving the peanut breeder a valuable introduction to allele mining and its methods for the ground-breaking finding of novel alleles concealed in hereditary variation, which is essential for crop development. This chapter explores the theoretical underpinnings and use of allele mining techniques for the identification of alleles and their possible implications for peanut improvement
Meta-transcriptomic identification of groundnut RNA viruses in western Kenya and the novel detection of groundnut as a host for Cauliflower mosaic virus
Get PDFBackground
Groundnut (Arachis hypogaea L.) is the 13th most important global crop grown throughout the tropical and subtropical regions of the world. One of the major constraints to groundnut production is viruses, which are also the most economically important and most abundant pathogens among cultivated legumes. Only a few studies have reported the characterization of RNA viruses in cultivated groundnuts in western Kenya, most of which deployed classical methods of detecting known viruses.
Methods
We sampled twenty-one symptomatic and three asymptomatic groundnut leaf samples from farmers' fields in western Kenya. Total RNA was extracted from the samples followed by First-strand cDNA synthesis and sequencing on the Illumina HiSeq 2500 platform. After removing host and rRNA sequences, high-quality viral RNA sequences were de novo assembled and viral genomes annotated using the publicly available NCBI virus database. Multiple sequence alignment and phylogenetic analysis were done using MEGA X.
Results
Bioinformatics analyses using as low as ∼3.5 million reads yielded complete and partial genomes for Cauliflower mosaic virus (CaMV), Cowpea polerovirus 2 (CPPV2), Groundnut rosette assistor virus (GRAV), Groundnut rosette virus (GRV), Groundnut rosette virus satellite RNA (satRNA) and Peanut mottle virus (PeMoV) falling within the species demarcation criteria. This is the first report of CaMV and the second report of CPPV2 on groundnut hosts in the world. Confirmation of the detected viruses was further verified through phylogenetic analyses alongside reported publicly available highly similar viruses. PeMoV was the only seed-borne virus reported.
Conclusion
Our findings demonstrate the power of Next Generation Sequencing in the discovery and identification of novel viruses in groundnuts. The detection of the new viruses indicates the complexity of virus diseases in groundnuts and would require more focus in future studies to establish the effect of the viruses as sole or mixed infections on the crop. The detection of PeMoV with potential origin from Malawi indicates the importance of seed certification and cross-boundary seed health testing
APSIM-based modeling approach to understand sorghum production environments in Mali
Get PDFSorghum production system in the semi-arid region of Africa is characterized by low yields which are generally attributed to high rainfall variability, poor soil fertility, and biotic factors. Production constraints must be well understood and quantified to design effective sorghum-system improvements. This study uses the state-of-the-art in silico methods and focuses on characterizing the sorghum production regions in Mali for drought occurrence and its effects on sorghum productivity. For this purpose, we adapted the APSIM-sorghum module to reproduce two cultivated photoperiod-sensitive sorghum types across a latitude of major sorghum production regions in Western Africa. We used the simulation outputs to characterize drought stress scenarios. We identified three main drought scenarios: (i) no-stress; (ii) early pre-flowering drought stress; and (iii) drought stress onset around flowering. The frequency of drought stress scenarios experienced by the two sorghum types across rainfall zones and soil types differed. As expected, the early pre-flowering and flowering drought stress occurred more frequently in isohyets 600 mm, but was affected by the drought stress in the lower rainfall zones 600 mm. The findings from this study provide the entry point for further quantitative testing of the Genotype × Environment × Management options required to optimize sorghum production in Mali
Genetic stability analysis of early maturing pigeonpea genotypes using AMMI and WAASB models
Get PDFIn the present study, 27 early maturing pigeonpea genotypes were evaluated over multi-locations for yielding potential and analyzed using analysis of variance (ANOVA), additive main effect and multiplicative interaction (AMMI) model and Weighted Average of Absolute Scores (WAASB) models. ANOVA displayed significant variation among genotypes, environments and genotype-environment interaction. AMMI models further explained the main and interaction effects with PC1 and PC2 covering 81.8% and 18.2% variance, respectively. AMMI biplots and WAASB matrix denoted ICP 14444, ICP 8817 and ICP 11890 to be potential early maturing, high yielding stable lines across the tested locations. Warangal and Kanpur noted to be the best environments with least and highest discriminating ability respectively. ICP 11543, ICP 16309, ICP 6992 were identified as best-fit cultivars for Patancheru, Warangal and Kanpur, respectively
Pearl Millet Genetic Improvement for Food and Nutrition Security
No full textGlobal food production practices are challenged by climate change factors, such as increased temperature, increased CO 2 emissions, and drought. Pearl millet [ Pennisetum glaucum (L.) R. Br.] is an excellent dryland crop that withstands varied edaphic and climatic conditions (42 °C temperature and 350 mm rainfall). Pearl millet is rich in protein (15%) and essential minerals (296 mg/100 g P; 307 mg/100 g K; 42 mg/100 g Ca; 137 mg/100 g Mg; 75 mg/kg Fe, and 40 mg/kg Zn). Therefore, pearl millet not only serves as a major staple food in the semi-arid tropics of India and Africa but also serves as the cheapest source of household nutrition. The availability of genetic variation for nutrition in pearl millet leads to additional expansion to fulfill maximum daily requirements. Biofortification improves grain mineral and vitamin content. HarvestPlus, in collaboration with International Crops Research Institute for the Semi-Arid Tropics and other public and private partners, has disseminated several biofortified hybrids and open-pollinated varieties that will aid in the reduction of malnutrition in India and sub-Saharan Africa. The application of modern genomic technology and speed breeding would substantially accelerate biofortification traits mainstreaming. The advanced pearl millet breeding program, therefore, should include essential nutrition traits in the products and their commercialization consortia. Nutri-dense varieties and hybrids must ensure value propositions in the smart-food products and its supply chain for human well-being
Characterization of Blackgram Germplasm [Vigna mungo (L.) Hepper] for Yield and Resistance to Yellow Mosaic Disease
Get PDFBlack gram is a highly nutritious legume crop primarily cultivated for its grains in Asian countries. Despite its significant importance due to its health benefits and organoleptic properties, its productivity remains low. The exploration and cataloging of genetic diversity are crucial initial steps towards maximizing production potential. The objective of this study was to evaluate 482 germplasm accessions of black gram for 14 quantitative traits (including grain yield and related characteristics) and 13 qualitative traits (such as plant growth, leaf structure, branching pattern, and pod morphology). Analysis of the phenotypic data revealed extensive variation in both quantitative and qualitative traits among the germplasm under study. Several germplasm accessions, including IC0619217, IC0279521, IC0472035, IC0393537, IC0321149, IC0331231, IC0530627, and IC0330889, exhibited numerous desirable traits that surpassed those of commercial checks. Heritability and genetic advance as a percentage of population means (GAM) were highest for PDM (60.795), GyPp (58.82), and PpP (56.89). Principal component analysis and correlation analysis indicated strong associations of traits such as PdL, PSD, PdpP, PpP with GyPp, while, days to maturity showed a negative association with grain yield. Furthermore, germplasm with traits such as insect tolerance (pod and leaf pubescence), drought tolerance (lanceolate leaves), and heat tolerance (central branching) were present in germplasm. This selected germplasm holds promise for use in urdbean genetic improvement programs
Farmer-centric Scaling of Agroecology Innovations Boosts Crop Productivity and Increases Adoption in Central Tanzania
Get PDFThe ResComm project, "Enabling a Resilient and Prosperous Community through Participatory Agroecological Practices in Central Tanzania," has significantly enhanced agricultural productivity and resilience among smallholder farmers. Using a lead farmer-centric approach across eight community learning sites, the project promoted integrated agroecological practices, including improved crop varieties, intercropping, tie ridges, and Fanya juu/ chini* soil conservation techniques. Between 2021 and 2023, over 650 farmers directly adopted these innovations, benefiting over 7,300 indirectly, with an additional 400 adopting them in 2024. Yields of pigeonpea and sorghum increased by up to 2–3 times, and adoption rates in participating villages reached 60–90%. The project also empowered women, who made up 45% of beneficiaries, and delivered environmental and economic benefits, including increased income and reduced land degradation. ResComm demonstrates the potential for scaling sustainable practices across similar regions, fostering agricultural transformation, improved livelihoods, and climate resilience
Sequential submergence and drought induce yield loss in rice by affecting redox homeostasis and source-to-sink sugar transport
No full textRice cultivation in the rainfed ecosystems of the eastern Indo-Gangetic plain (EIGP) frequently comes across abrupt alternation of submergence and drought during the vegetative and reproductive stages, respectively, within one growing season, and this may be exaggerated with climate change. Therefore, development of combined submergence and drought tolerant rice genotypes might be a timely effort to meet the growing food demand. However, till date no study has been executed on the combination of submergence and drought stress in the field conditions of the EIGP. The present study elucidated the performance of near isogenic lines (NILs) of rice developed for the EIGP through marker assisted pyramiding of quantitative trait loci (QTL) associated with submergence (Sub1) and drought (qDTY1.1 + qDTY2.1 + qDTY3.1) in the background of the popular, high yielding Indo-Gangetic rice variety Swarna. This study included the screening of sixteen rice NILs along with the check varieties Swarna and Swarna Sub1 under cumulative submergence and drought for four consecutive rice growing years (2019–2022). Individual submergence or drought or cumulative stress caused 76, 47, and 85% respective loss in average productivity compared to that of the control conditions. However, rice NILs IR96321–558–563-B-2–1–1, IR96321–315–323-B-3–1–3, IR96321–315–294-B-1–1–1–1, and IR96321–558–209-B-6–1–1 showed outstanding cumulative stress tolerance with sustainable photosynthetic performance and membrane stability. Furthermore, these rice NILs exhibited effective reactive oxygen species scavenging mediated by enhanced antioxidant enzyme activities in source (flag-leaf) and sink (anther) tissues that contributed to conserving the source-to-sink mobilization, leading to improved pollen viability and spikelet fertility under sequential stress conditions. The study identified combined submergence-drought tolerant rice NILs along with an optimum yield level to support global food security and also represented a model crop system to establish mechanisms of multi-stress tolerance in plants