International Crops Research Institute for the Semi-Arid Tropics
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Transcriptome profiling reveals the expression and regulation of genes associated with Fusarium wilt resistance in chickpea (Cicer arietinum L.)
Get PDFFusarium wilt (FW) is one of the most significant biotic stresses limiting chickpea production worldwide. To dissect the molecular mechanism of FW resistance in chickpea, comparative transcriptome analyses of contrasting resistance sources of chickpea genotypes under control and Fusarium oxysporum f. sp. ciceris (Foc) inoculated conditions were performed. The high-throughput transcriptome sequencing
generated about 1137 million sequencing reads from 24 samples representing two resistant genotypes, two susceptible genotypes, and two near-isogenic lines under
control and stress conditions at two-time points (7th- and 12th-day post-inoculation). The analysis identified 5182 differentially expressed genes (DEGs) between different
combinations of chickpea genotypes. Functional annotation of these genes indicated their involvement in various biological processes such as defense response, cell wall biogenesis, secondary metabolism, and disease resistance. A significant number (382) of transcription factor encoding genes exhibited differential expression patterns under stress. Further, a considerable number of the identified DEGs (287) co-localized with previously reported quantitative trait locus for FWresistance. Several resistance/susceptibility-related genes, such as SERINE/THREONINE PROTEIN KINASE, DIRIGENT, and MLO exhibiting contrasting expression patterns in resistant and susceptible genotypes upon Foc inoculation, were identified. The results presented in the study provide valuable insights into the transcriptional dynamics associated with FW stress response in chickpea and provide candidate genes for the
development of disease-resistant chickpea cultivars
Exploring the sorghum race level diversity utilizing 272 sorghum accessions genomic resources
Get PDFDue to evolutionary divergence, sorghum race populations exhibit significant
genetic and morphological variation. A k-mer-based sorghum race sequence
comparison identified the conserved k-mers of all 272 accessions from sorghum
and the race-specific genetic signatures identified the gene variability in 10,321
genes (PAVs). To understand sorghum race structure, diversity and
domestication, a deep learning-based variant calling approach was employed
in a set of genotypic data derived from a diverse panel of 272 sorghum
accessions. The data resulted in 1.7 million high-quality genome-wide SNPs
and identified selective signature (both positive and negative) regions through a
genome-wide scan with different (iHS and XP-EHH) statistical methods. We
discovered 2,370 genes associated with selection signatures including 179
selective sweep regions distributed over 10 chromosomes. Co-localization of
these regions undergoing selective pressure with previously reported QTLs and
genes revealed that the signatures of selection could be related to the
domestication of important agronomic traits such as biomass and plant height.
The developed k-mer signatures will be useful in the future to identify the
sorghum race and for trait and SNP markers for assisting in plant
breeding programs
Potential for increasing groundnut production in Tanzania by enhancing technical efficiency: A stochastic meta-frontier analysis
Get PDFGroundnut crop is one of the major sources of financial and food security for a large number of Tanzanian smallholder farmers. However, the production of groundnuts in Tanzania is underdeveloped, and yields are reportedly 2.5 to 3 times lower than in other African nations such as Nigeria. There are a number of factors that contribute to lower yields including the cultivation of outdated plant varieties, increased climate variability, the infestation of pests and diseases, and the use of outdated farming techniques. To analyze the scope for increasing groundnut production, this study investigates and compares the technical efficiencies (TEs) and technological gap ratios (TGRs) in Tanzania’s four main groundnut-producing regions, namely the Central zone, Lake Zone, Southern zone, Southern highland zone, by using a two-step meta frontier model. We used ICRISAT data collected under the Tropical Legume-III project during 2017–18. Our results show a very low level of technical efficiency of groundnut production in the regions and significant regional differences in TEs, TGRs, and Meta Technical Efficiencies (MTEs). The study identifies a tremendous scope to increase groundnut productivity and production in Tanzania by enhancing its production efficiency and the key drivers that may help harness this potential
Scaling up land restoration in Niger: insights from a national workshop
Get PDFThis report provides a summary of the key outcomes of the Niger FMNR Scaling National Workshop held between 12th
and 13th July 2023 in Niamey. The workshop was organized in collaboration of Catholic Relief Services (CRS) Niger,
ICRISAT (International Crops Research Institute for the semi-Arid tropics), and DGDT/F (Direction of Sustainable Forest and Land Management (DGDT/F) to support Niger’s attainment of its Farmer Managed Natural regeneration (FMNR)
ambition and to bring together diverse stakeholders. Over 52 people from 15 organizations participated and reflected
upon and celebrated the many achievements and emerging approaches for sustainability and scaling FMNR and
identified how these can be amplified. Through this interaction, synergies between initiatives were enhanced and areas for coordinated implementation and monitoring discussed. Mechanisms that will better harness the collective strengths of government with non-government organizations were also discussed
Delineating Marker-Trait Associations for Fusarium Wilt in Chickpea Using the Axiom® CicerSNP Array
No full textFusarium wilt (FW) caused by Fusarium oxysporum f. sp. ciceri is a devastating disease of chickpea (Cicer arietinum). To identify promising resistant genotypes and genomic loci for FW resistance, a core set of 179 genotypes of chickpea was tested for FW reactions at the seedling and reproductive stages under field conditions and controlled conditions in the greenhouse. Our results revealed that at the seedling stage, most of the genotypes were resistant, whereas at the reproductive stage, most of the genotypes were susceptible. Genotyping using a 50K Axiom® CicerSNP Array and trait data of FW together led to the identification of 26 significant (P ≤ E-05) marker-trait associations (MTAs) for FW resistance. Among the 26 MTAs, 12 were identified using trait data recorded in the field (three at the seedling and nine at the reproductive stage), and 14 were identified using trait data recorded under controlled conditions in the greenhouse (six at the seedling and eight at the reproductive stage). The phenotypic variation explained by these MTAs varied from 11.75 to 15.86%, with an average of 13.77%. Five MTAs were classified as major, explaining more than 15% of the phenotypic variation for FW, and two were declared stable, being identified in two environments. One of the promising stable and major MTAs (Affx_123280060) detected in field conditions at the reproductive stage was also detected in greenhouse conditions at the seedling and reproductive stages. The stable and major (>15% PVE) MTAs can be used in chickpea breeding programs
Diagnosis of Fusarium oxysporum f. sp. ciceris causing Fusarium wilt of chickpea using loop‑mediated isothermal amplification (LAMP) and conventional end‑point PCR
Get PDFFusarium oxysporum (Fo) is ubiquitous in soil and forms a species complex of pathogenic and putatively non-pathogenic strains. Pathogenic strains cause disease in over 150 plant species. Fusarium oxysporum f. sp. ciceris (Foc) is a major fungal pathogen causing Fusarium wilt in chickpeas (Cicer arietinum). In some countries such as Australia, Foc is a high-priority pest of biosecurity concern. Specific, sensitive, robust and rapid diagnostic assays are essential for effective disease management on the farm and serve as an effective biosecurity control measure. We developed and validated a novel and highly specific PCR and a LAMP assay for detecting the Indian Foc race 1 based on a putative effector gene uniquely present in its genome. These assays were assessed against 39 Fo formae speciales and found to be specific, only amplifying the target species, in a portable real-time fluorometer (Genie III) and qPCR machine in under 13 min with an anneal derivative temperature ranging from 87.7 to 88.3 °C. The LAMP assay is sensitive to low levels of target DNA (> 0.009 ng/µl). The expected PCR product size is 143 bp. The LAMP assay developed in this study was simple, fast, sensitive and specific and could be explored for other Foc races due to the uniqueness of this marker to the Foc genome
Data-driven approaches to improve water-use efficiency and drought resistance in crop plants
No full textWith the increasing population, there lies a pressing demand for food, feed and fibre, while the changing climatic conditions pose severe challenges for agricultural production worldwide. Water is the lifeline for crop production; thus, enhancing crop water-use efficiency (WUE) and improving drought resistance in crop varieties are crucial for overcoming these challenges. Genetically-driven improvements in yield, WUE and drought tolerance traits can buffer the worst effects of climate change on crop production in dry areas. While traditional crop breeding approaches have delivered impressive results in increasing yield, the methods remain time-consuming and are often limited by the existing allelic variation present in the germplasm. Significant advances in breeding and high-throughput omics technologies in parallel with smart agriculture practices have created avenues to dramatically speed up the process of trait improvement by leveraging the vast volumes of genomic and phenotypic data. For example, individual genome and pan-genome assemblies, along with transcriptomic, metabolomic and proteomic data from germplasm collections, characterised at phenotypic levels, could be utilised to identify marker-trait associations and superior haplotypes for crop genetic improvement. In addition, these omics approaches enable the identification of genes involved in pathways leading to the expression of a trait, thereby providing an understanding of the genetic, physiological and biochemical basis of trait variation. These data-driven gene discoveries and validation approaches are essential for crop improvement pipelines, including genomic breeding, speed breeding and gene editing. Herein, we provide an overview of prospects presented using big data-driven approaches (including artificial intelligence and machine learning) to harness new genetic gains for breeding programs and develop drought-tolerant crop varieties with favourable WUE and high-yield potential traits
Effect of different Sowing Windows on Major Insect Pests and Host Plant Resistance to Pod Borer, Helicoverpa armigera in Pigeonpea (Cajanus cajan (L.) Millsp.)
Get PDFEffect of sowing dates, climatic variables on major insect pests population, and host plant resistance with special reference to pod borer Helicoverpa armigera (Hubner) in pigeon pea (Cajanus cajan (L.) ecosystem was studied on two cultivars namely, ICPL 87 and ICPL 88039. The insect pest population on two cultivars differed significantly across sowing dates. ICPL 87 was most vulnerable to insect pests as
it suffered more damage by the pod borer H. armigera, pod sucking bugs (Clavigralla tomentosicollis Stal.) than ICPL 88039. The maximum leaf/pod feeding insect population was recorded on first sowing and then gradually decline for the rest of the plantings. Maximum H. armigera egg population exhibited 21.10 on ICPL 87 in first sowing and at least 1.23 on ICPL 88039 in sixth sowing. Web forming insect pests Maruca virata (3.95) and leaf webber (4.66) weremaximum recorded on ICPL 88039 in second and first planting respectively. The leaf feeding beetle was recorded highest 6.29(ICPL 87) in the third planting. Amid two cultivars maximum insect-pests population was recorded on ICPL 87 when compared to ICPL 88039 except web forming insect Maruca and leaf webber due to its indeterminate genotypic character of ICPL 88039. Between the two genotypes, the sucking pests more preferred to ICPL 87 when compared ICPL 88039. Maximum jassids were recorded 12.76 and 8.38 (ICPL 87) in fourth sowing and third sowing respectively. It was observed that highest spider population recorded 2.23(ICPL 88039) in
first and second sowing. Ladybird beetle Coccinella transvasalis population recorded a maximum 8.52 (ICPL 87). The leaf webber (r= 0.449**) and pod bug (r= 0.421**) showed a highly significant positive correlation with maximum temperature and H. armigera larvae population exhibited highly significant positive correlation with minimum temperature (r= 0.491**) and morning relative humidity (r= 0.528**). Solar radiation also exhibited and showed a significant positive correlation with leaf webber (r= 533**)
Milletdb: a multi-omics database to accelerate the research of functional genomics and molecular breeding of millets
Get PDFMillets are a class of nutrient-rich coarse cereals with high resistance to abiotic stress; thus, they guarantee food security for people living in areas with extreme climatic conditions and provide stress-related genetic resources for other crops. However, no platform is available to provide a
comprehensive and systematic multi-omics analysis for millets, which seriously hinders the mining of stress-related genes and the molecular breeding of millets. Here, a free, webaccessible, user-friendly millets multi-omics database platform (Milletdb, http://milletdb.novogene.com) has been developed. The Milletdb contains six millets and their one related species genomes, graph-based pan-genomics of pearl millet, and stress-related multi-omics data, which enable Milletdb to be the most complete millets multi-omics database available. We stored GWAS (genome-wide association study) results of 20 yield-related trait data obtained under
three environmental conditions [field (no stress), early drought and late drought] for 2 years in the database, allowing users to identify stress-related genes that support yield improvement. Milletdb can simplify the functional genomics analysis of millets by providing users with 20
different tools (e.g., ‘Gene mapping’, ‘Co-expression’, ‘KEGG/GO Enrichment’ analysis, etc.). On the Milletdb platform, a gene PMA1G03779.1 was identified through ‘GWAS’, which has the potential to modulate yield and respond to different environmental stresses. Using the tools provided by Milletdb, we found that the stress-related PLATZs TFs (transcription factors) family expands in 87.5% of millet accessions and contributes to vegetative growth and abiotic stress responses. Milletdb can effectively serve researchers in the mining of key genes, genome editing and molecular breeding of millets
Trans situ conservation strategies to conserve the extinction risk species, Sesamum prostratum Retz., a crop wild relative of sesame being endemic to coastal strand habitat: a case study
No full textCoastal strands ecosystem is a narrow strip of land adjacent to seashore and is often prone to natural or man-made disturbances. Conserving the endangered and endemic plant species having coastal strands as their niche habitat is challenging and requires special conservation drives. One such endemic species along the coastal strands of Indian sub-continent (Eastern coasts of Southern India and Sri Lanka) is the potentially saline tolerant crop wild relative (CWR) of sesame, Sesamum prostratum Retz. In our recent collecting expedition for this species, we have reported the dwindling nature of this species’ occurrence and a risk assessment for this species as per the IUCN guidelines underscored to be of critically endangered (CR) category. The IUCN had already declared this endemic species as CR in Sri Lanka during 2012. Using this as a case study for the way forward, we discuss here on the appropriate management measures that can be taken up to efficiently conserve the endemic species of disturbed habitats to prevent them from the risk of extinction through suitable conservation measures. Importance of CWRs in crop improvement through trait introgression and crop diversification through de novo domestication events are demonstrated in rice and tomato using gene editing tools. Potentialities of the trans situ conservation measures, the most appropriate, to avoid further decline in the occurrences of S. prostratum Retz., and its applicability for other threatened (endemic) species of fragmented habitat is also discussed