International Crops Research Institute for the Semi-Arid Tropics
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Marker-Assisted Breeding in Major Insect Pest of Sorghum Crop
No full textThe fundamental concept behind marker-assisted breeding revolves around the identification and utilization of genetic markers linked to biotic stress resistance traits. These markers act as guideposts within the plant’s DNA, allowing breeders to precisely identify the presence of desirable traits without the need for extensive field testing. While the use of resistant germplasms in breeding programs targeting improved sorghum resistance to various biotic stresses has been relatively limited, it presents a significant opportunity for expansion and enhancement in sorghum pest management strategies. To seize this opportunity, continued research endeavors are imperative. By delving deeper into the identification and integration of resistant traits, there exists the potential for substantial progress in sorghum breeding programs. The incorporation of marker-assisted breeding techniques into these programs aims to elevate crop productivity and ensure food security while simultaneously reducing the dependence on chemical pesticides. This approach offers a more sustainable and environmentally friendly method for managing pests in sorghum cultivation
Adapting smallholder irrigation systems to extreme events: a case of the Transforming Irrigation in Southern Africa (TISA) project in Zimbabwe
Get PDFSmallholder irrigation schemes are vulnerable to increased climate variability and change, particularly increased water stress. This paper explores whether the introduction of Agricultural Innovation Platforms and soil monitoring tools in smallholder irrigation schemes can improve the adaptive capacity of farmers and schemes in the Insiza District. Drawing on household survey and qualitative data, collected through the Transforming Irrigation in Southern Africa project, we analyse a comprehensive set of measures across four domains: field, household, community and markets. We find that social capacity and increased climate adaptation can be built with modest cost through combined social and technological interventions
Using cross-country datasets for association mapping in Arachis hypogaea L.
Get PDFGroundnut (Arachis hypogaea L.) is one of the most important climate-resilient oil crops in sub-Saharan Africa. There is a significant yield gap for groundnut in Africa because of poor soil fertility, low agricultural inputs, biotic and abiotic stresses. Cross-country evaluations of promising breeding lines can facilitate the varietal development process. The objective of our study was to characterize popular test environments in Uganda (Serere and Nakabango) and Malawi (Chitala and Chitedze) and identify genotypes with stable superior yields for potential future release. Phenotypic data were generated for 192 breeding lines for yield-related traits, while genotypic data were generated using skim-sequencing. We observed significant variation (p < 0.001; p < 0.01; p < 0.05) across genotypes for all yield-related traits: days to flowering (DTF), pod yield (PY), shelling percentage, 100-seed weight, and grain yield within and across locations. Nakabango, Chitedze, and Serere were clustered as one mega-environment with the top five most stable genotypes being ICGV-SM 01709, ICGV-SM 15575, ICGV-SM 90704, ICGV-SM 15576, and ICGV-SM 03710, all Virginia types. Population structure analysis clustered the genotypes in three distinct groups based on market classes. Eight and four marker-trait associations (MTAs) were recorded for DTF and PY, respectively. One of the MTAs for DTF was co-localized within an uncharacterized protein on chromosome 13, while another one (TRv2Chr.11_3476885) was consistent across the two countries. Future studies will need to further characterize the candidate genes as well as confirm the stability of superior genotypes across seasons before recommending them for release.
Plain Language Summary
Most countries in eastern and southern Africa derive their groundnut breeding lines from International Crops Research Institute for the Semi-Arid Tropics breeding program based in Malawi. In some cases, the same genotype is released in several countries under different names. However, the evaluation of the genotypes is often taken independently in each of the countries, leading to duplication of work. A more cost-effective method is to identify similar environments across different countries and evaluate the same genotypes across such environments. In this study, we evaluated 192 groundnut genotypes across four environments, two each from Uganda and Malawi. Additive main effects and multiplicative interaction analysis clustered the Ugandan sites and Chitedze in one mega-environment, implying that future evaluations could take advantage of such environments towards varietal releases. We also used the same data to detect marker-trait associations across the different locations for agronomic traits. Our results revealed more consistent results within Uganda than Malawi
Customization, Parameterization, and Scaling of the iSAT: An ICT based Agro Advisory platform for location-specific Informed Decision-Making
Get PDFFollowing the successful demonstration of the iSAT system's ability to generate data-driven, science-based weather advisories, efforts were undertaken to scale the system and improve its capabilities. The focus was on four key areas; expanded crop coverage to cover a wider range of crops, flexible information access to accommodate local information and user preferences, targeted and timely advisories tailored to specific crop growth stages and delivered at the right time and multilingual and multi-format advisories (SMS, mobile app, WhatsApp, website) to reach a diverse audience. To achieve these goals, the ISAT system was modified in several ways. Location-specific information was incorporated through lookup tables, mobile apps, and direct input, the decision-making process was refined to generate advisories that align with farmers' specific needs, advisories were produced in two formats: SMS-friendly and detailed versions for mobile apps, WhatsApp, and websites and options were added to translate advisories into local languages. The challenges and limitations in realising the full potential of context-specific advisories include availability of reliable and consistent data, tailoring advisories to specific conditions that requires further refinement and adaptation, effective delivery through various mobile devices and platforms, government policies on bulk SMS and data privacy, language barriers requiring translation and localization for reaching a wider audience and user awareness and capacity to utilize them information effectively. By addressing these challenges, the ISAT system can continue to evolve and provide even more valuable and impactful services to farmers and agricultural stakeholders
Development of reverse transcription recombinase polymerase amplification assay for rapid diagnostics of Peanut mottle virus
Get PDFPeanut mottle virus (PeMoV) is a single-stranded RNA virus transmitted through seeds and aphids that affects peanut crops worldwide. Currently, Enzyme Linked Immune-Sorbent assays and Reverse-Transcription Polymerase Chain Reaction techniques are widely employed to detect PeMoV in infected plants. ELISA is labor-intensive and time-consuming, as it involves the preparation of buffers and the production of polyclonal antibodies. Even though RT-PCR bypasses the need for buffer preparation and antibody production, it demands trained professional’s manpower, requires expensive equipment like thermal cyclers, and involves complex procedures such as RNA isolation and cDNA conversion. To avoid these constraints, there is a need for a fast, reliable, efficient, and economical method for detecting PeMoV to ensure the production of healthy seeds. This study optimized the Reverse Transcriptase Recombinase Polymerase Amplification (RT-RPA) method by eliminating the steps of RNA extraction, cDNA conversion, and the use of a thermal cycler. The optimized RT-RPA assay successfully detected PeMoV at concentrations as low as 10–6 and 10–7 dilutions (1 and 0.1 µg/µl) of both RNA an-6d crude sap templates, demonstrating high sensitivity comparable to the routine RT-PCR assay. The new RT-RPA technique was tested against other viruses that infect peanuts like the Peanut stunt Virus, Tomato spotted wilt virus and Peanut bud necrosis virus, this technique demonstrated great specificity and no cross-reactivity. The developed RT-RPA using a crude leaf sap template is time-saving, less laborious, not very complicated, high specificity, sensitivity, economical and efficient. Therefore, laboratories with limited resources can use the RT-RPA assay for preliminary screening of PeMoV in nurseries, farm and glasshouse conditions, and quarantine stations. The current study reports the development, optimization and validation of Reverse Transcriptase Recombinase Polymerase Amplification (RT-RPA) using crude sap as template for the onsite detection of PeMoV infection in peanut crops under field conditions for the first time
Evaluation of 17 sweet potato (Ipomoea batatas L.) genotypes across five environments for high yield and stability
Get PDFThe study was carried out in five regions of Bangladesh—Gazipur, Bogura, Jamalpur, Jashore, and Chattogram—utilizing a randomized complete block design and involving 17 genotypes of sweet potatoes. The objective was to evaluate the performance, environmental adaptability and stability on root yield. The analysis was carried out using fixed and random effects models. Results revealed that BARI Mistialu-12 had the highest storage root yield (45.35 t/ha). Among the locations, Bogura, (sandy loam soil), achieved the highest yield at 37.05 t/ha, followed by Jamalpur (36.15 t/ha), . The ANOVA showed significant variation in root yield across genotype (G), environment (E), and their interaction (GEI). Both the additive and multiplicative interaction effect models (AMMI) and a linear mixed model (LMM) confirmed substantial GEI variance. Considering LMM, 53.58% of the total variation was due to genotypes, with a selection accuracy of 94%, leading to the use of a best linear unbiased prediction (BLUP) index for genotype selection. BARI Mistialu-12, BARI Mistialu-16, BARI Mistialu-11, BARI Mistialu-8, BARI Mistialu-2, and BARI Mistialu-13 were identified as high-performing genotypes in the BLUP index. Based on AMMI stability value (ASV), the first two principal components explained 74.60% of the total GEI variance (20.16%), with BARI Mistialu-14 being the most stable genotype. Additionally, the interaction principal components axis (IPCA) analysis identified Bogura, Jashore, and Chattogram as key testing sites for root yield. The weighted average of absolute scores (WAAS) biplot highlighted BARI Mistialu-16 as the most stable variety. In the mega-environment analysis, BARI Mistialu-11 and BARI Mistialu-2 excelled in Jamalpur, while BARI Mistialu-12 and BARI Mistialu-16 led in Gazipur, Bogura, and Jashore. Bogura was found to be the best location for production. These findings are crucial for future breeding efforts to expand the sweet potato industry, demonstrating consistent high-yield potential across various agro-ecological conditions
Assessment of the genetic diversity and population structure in Moringa oleifera accessions using DNA markers and phenotypic descriptors
No full textMoringa (Moringa oleifera Lam.) is one of the multipurpose trees with significant promise as a high-value crop of industrial importance, having nutritional, therapeutic, and prophylactic properties. Genetic diversity is a cornerstone of any crop improvement program and plays a key role in the selection of promising parental lines for hybrid breeding. Morphological and molecular markers have been proven to be potential tools for the evaluation of genetic diversity, crop genetic improvement, and conservation of plant genetic resources. In the current study, morphological descriptors, RAPD, and SCoT markers were used to determine genetic diversity among 28 M. oleifera accessions. Significant morphological variations were noted for several economic traits across the accessions studied. Four primary clusters were visible on the dendrogram based on phenotypic markers, indicating clustering of accession from a shared geographical habitat. No correlation was estimated between morphological traits, indicating an environmental influence. Three RAPD and seven SCoT primer sets produced 37 and 46 markers, with 53.2 and 71.3% polymorphisms, respectively. Based on genotypic data and the UPGMA approach, all 28 accessions were separated into two major clusters in the phylogenetic tree, irrespective of any geographical areas. The clustering pattern indicates widespread plant species and rapid gene flow through cross-pollination in Moringa populations. Three subpopulations of the involved accessions were identified by population structure analysis; however, there was only a weak link with the location of plant cultivation. The expected heterozygosity for the three subpopulations varied from 0.23 to 0.32, as per R-based structural analysis. AMOVA's attribution of 86% and 19% of all variations to within- and between-populations, respectively, indicates that there has been gene flow across geographic regions. The PCA showed a wide distribution of genotypes in the scatterplot, also suggesting huge genetic variation among the M. oleifera population. The study revealed a significant level of genetic diversity among M. oleifera accessions, which can be harnessed to conserve plant genetic resources and develop high-yielding, nutrient-dense Moringa cultivars
Genome-wide association mapping identifies novel SNPs for root nodulation and agronomic traits in chickpea
Get PDFIntroduction: The chickpea (Cicer arietinum L.) is well-known for having climate resilience and atmospheric nitrogen fixation ability. Global demand for nitrogenous fertilizer is predicted to increase by 1.4% annually, and the loss of billions of dollars in farm profit has drawn attention to the need for alternative sources of nitrogen. The ability of chickpea to obtain sufficient nitrogen via its symbiotic relationship with Mesorhizobium ciceri is of critical importance in determining the growth and production of chickpea.
Methods: To support findings on nodule formation in chickpea and to map the genomic regions for nodulation, an association panel consisting of 271 genotypes, selected from the global chickpea germplasm including four checks at four locations, was evaluated, and data were recorded for nodulation and 12 yield-related traits. A genome-wide association study (GWAS) was conducted using phenotypic data and genotypic data was extracted from whole-genome resequencing data of chickpea by creating a hap map file consisting of 602,344 single-nucleotide polymorphisms (SNPs) in the working set with best-fit models of association mapping.
Results and Discussion: The GWAS panel was found to be structured with sufficient diversity among the genotypes. Linkage disequilibrium (LD) analysis showed an LD decay value of 37.3 MB, indicating that SNPs within this distance behave as inheritance blocks. A total of 450 and 632 stringent marker–trait associations (MTAs) were identified from the BLINK and FarmCPU models, respectively, for all the traits under study. The 75 novel MTAs identified for nodulation traits were found to be stable. SNP annotations of associated markers were found to be related to various genes including a few auxins encoding as well as nod factor transporter genes. The identified significant MTAs, candidate genes, and associated markers have the potential for use in marker-assisted selection for developing high-nodulation cultivars after validation in the breeding populations
Genome-wide screening and characterization of phospholipase A (PLA)-like genes in sorghum (Sorghum bicolor L.)
Get PDFSorghum bicolor (L.) Moench is the fifth most cultivated crop worldwide, and it is used in many ways, but it has always gained less popularity due to the yield, pest, and environmental constraints. Improving genetic background and developing better varieties is crucial for better sorghum production in semi-arid tropical regions. This study focuses on the phospholipase A (PLA) family within sorghum, comprehensively characterising PLA genes and their expression across different tissues. The investigation identified 32 PLA genes in the sorghum genome, offering insights into their chromosomal localization, molecular weight, isoelectric point, and subcellular distribution through bioinformatics tools. PLA-like family genes are classified into three groups, namely patatin-related phospholipase A (pPLA), phospholipase A1 (PLA1), and phospholipase A2 (PLA2). In-silico chromosome localization studies revealed that these genes are unevenly distributed in the sorghum genome. Cis-motif analysis revealed the presence of several developmental, tissue and hormone-specific elements in the promoter regions of the PLA genes. Expression studies in different tissues such as leaf, root, seedling, mature seed, immature seed, anther, and pollen showed differential expression patterns. Taken together, genome-wide analysis studies of PLA genes provide a better understanding and critical role of this gene family considering the metabolic processes involved in plant growth, defence and stress response
Genome-Wide Mapping of Quantitative Trait Loci for Yield-Attributing Traits of Peanut
Get PDFPeanuts (Arachis hypogaea L.) are important high-protein and oil-containing legume crops adapted to arid to semi-arid regions. The yield and quality of peanuts are complex quantitative traits that show high environmental influence. In this study, a recombinant inbred line population (RIL) (Valencia-C × JUG-03) was developed and phenotyped for nine traits under two environments. A genetic map was constructed using 1323 SNP markers spanning a map distance of 2003.13 cM. Quantitative trait loci (QTL) analysis using this genetic map and phenotyping data identified seventeen QTLs for nine traits. Intriguingly, a total of four QTLs, two each for 100-seed weight (HSW) and shelling percentage (SP), showed major and consistent effects, explaining 10.98% to 14.65% phenotypic variation. The major QTLs for HSW and SP harbored genes associated with seed and pod development such as the seed maturation protein-encoding gene, serine-threonine phosphatase gene, TIR-NBS-LRR gene, protein kinase superfamily gene, bHLH transcription factor-encoding gene, isopentyl transferase gene, ethylene-responsive transcription factor-encoding gene and cytochrome P450 superfamily gene. Additionally, the identification of 76 major epistatic QTLs, with PVE ranging from 11.63% to 72.61%, highlighted their significant role in determining the yield- and quality-related traits. The significant G × E interaction revealed the existence of the major role of the environment in determining the phenotype of yield-attributing traits. Notably, the seed maturation protein-coding gene in the vicinity of major QTLs for HSW can be further investigated to develop a diagnostic marker for HSW in peanut breeding. This study provides understanding of the genetic factor governing peanut traits and valuable insights for future breeding efforts aimed at improving yield and quality