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Management of groundwater drought risk by reliability theory and copula model in Sina basin, India
No full textA probabilistic-based groundwater model is developed to address the spatio-temporal distribution of the severity and duration of groundwater droughts for an aquifer having high groundwater fluctuations over space and time. Many studies were performed in the past to analyse the groundwater drought using various hydrological and meteorological indices. However, the study of joint probability distribution of groundwater drought risk and return period remains as a research gap in past literatures. Hence, in the current study this gap was fulfilled by developing a DSS module that calculates Groundwater Drought Risk (GDR) and Environmental Hazard Index (EHI) based on the probability distribution method. Thereafter, the return period of drought event both in terms of severity and duration was calculated by the Copula method. The model is developed for Sina basin, which is in the state of Maharashtra (India). The groundwater levels from 133 wells distributed spatially over the basin are selected to estimate the groundwater drought status for the period 1990–2009. Standardised Water Index is used for quantifying the groundwater droughts over the basin and found a continuous decline in the groundwater level over the time. Hence, a tool has been formulated for the assessment of risk imposed by the over mining of groundwater resources in the Sina basin. The decisive tool works on the principle of reliability analysis, which accounts for the calculation of GDR and EHI for Mild, Moderate, Severe and Extreme drought bands for each well. The risk obtained is assessed for its severity and duration based on a joint probability Copula module. The results showed that mild and moderate drought conditions prevails in the entire basin for the period 1990–2009. From the data set, a 25.2% increase in groundwater resistance is observed from mild to moderate drought band and a 25% increase is observed from severe to extreme drought band in the selected time period. The GDR for severe and extreme bands is affecting localised regions with high intensity. Based on the EHI values, the Beed region in the northeastern region of the Sina basin is very vulnerable to external stresses and requires immediate attention. The return period of severity and duration of different drought events are analysed by the Copula model and the results show that majority of the drought events in the mild and moderate bands are occurring below 2 years. These results examine the present groundwater drought situation in Sina basin and by properly managing the groundwater resource, the obtained risk can be minimised and many wells can be conserved by carefully addressing its EHI. This paper identifies and highlights hotspots in various time horizons and shows that if continuous abstraction persists, it likely accelerates the groundwater in absence of proper management plans. This model analysed the present groundwater drought scenario of the Sina basin and the results will be helpful for the policymakers for preparing better management strategies for the sustainable development of groundwater
Advances in “Omics” Approaches for Improving Toxic Metals/Metalloids Tolerance in Plants
Get PDFFood safety has emerged as a high-urgency matter for sustainable agricultural production. Toxic metal contamination of soil and water significantly affects agricultural productivity, which is further aggravated by extreme anthropogenic activities and modern agricultural practices, leaving food safety and human health at risk. In addition to reducing crop production, increased metals/metalloids toxicity also disturbs plants’ demand and supply equilibrium. Counterbalancing toxic metals/metalloids toxicity demands a better understanding of the complex mechanisms at physiological, biochemical, molecular, cellular, and plant level that may result in increased crop productivity. Consequently, plants have established different internal defense mechanisms to cope with the adverse effects of toxic metals/metalloids. Nevertheless, these internal defense mechanisms are not adequate to overwhelm the metals/metalloids toxicity. Plants produce several secondary messengers to trigger cell signaling, activating the numerous transcriptional responses correlated with plant defense. Therefore, the recent advances in omics approaches such as genomics, transcriptomics, proteomics, metabolomics, ionomics, miRNAomics, and phenomics have enabled the characterization of molecular regulators associated with toxic metal tolerance, which can be deployed for developing toxic metal tolerant plants. This review highlights various response strategies adopted by plants to tolerate toxic metals/metalloids toxicity, including physiological, biochemical, and molecular responses. A seven-(omics)-based design is summarized with scientific clues to reveal the stress-responsive genes, proteins, metabolites, miRNAs, trace elements, stress-inducible phenotypes, and metabolic pathways that could potentially help plants to cope up with metals/metalloids toxicity in the face of fluctuating environmental conditions. Finally, some bottlenecks and future directions have also been highlighted, which could enable sustainable agricultural production
Multigene phylogeny and haplotype analysis reveals predominance of oomycetous fungus, Phytophthora meadii (McRae) associated with fruit rot disease of arecanut in India
Get PDFAn oomycetous fungus Phytophthora causing fruit rot is the most devastating disease of arecanut in different agro-climatic zones of Karnataka with varied climatic profiles. The main aim of this investigation was to characterize the geo-distant Phytophthora populations infecting arecanut using robust morphological, multi-gene phylogeny and haplotype analysis. A total of 48 geo-distant fruit rot infected samples were collected during the South-West monsoon of 2017–19. Pure culture of the suspected pathogen was isolated from the infected nuts and pathogenic ability was confirmed and characterized. Colony morphology revealed typical whitish mycelium with stellate or petalloid pattern and appearance with torulose hyphae. Sporangia were caducous, semipapillate or papillate, globose, ellipsoid or ovoid-obpyriform in shape and sporangiophores were irregularly branched or simple sympodial in nature. Subsequent multi-gene phylogeny (ITS, β-tub, TEF-1α and Cox-II) and sequence analysis confirmed the identity of oomycete as Phytophthora meadii which is predominant across the regions studied. We identified 49 haplotypes representing the higher haplotype diversity with varying relative haplotype frequency. Comprehensive study confirmed the existence of substantial variability among geo-distant populations (n = 48) of P. meadii. The knowledge on population dynamics of the pathogen causing fruit rot of arecanut generated from this investigation would aid in developing appropriate disease management strategies to curtail its further occurrence and spread in arecanut ecosystem
Does improved oleic acid content due to marker-assisted introgression of ahFAD2 mutant alleles in peanuts alter its mineral and vitamin composition?
Get PDFPeanuts (Arachis hypogaea L.) with high oleic acid content have extended shelf life and several health benefits. Oleic, linoleic, and palmitic acid contents in peanuts are regulated by ahFAD2A and ahFAD2B mutant alleles. In the present study, ahFAD2A and ahFAD2B mutant alleles from SunOleic 95R were introgressed into two popular peanut cultivars, GG-7 and TKG19A, followed by markers-assisted selection (MAS) and backcrossing (MABC). A total of 22 MAS and three MABC derived lines were developed with increased oleic acid (78–80%) compared to those of GG 7 (40%) and TKG 19A (50%). Peanut kernel mineral and vitamin composition remained unchanged, while potassium content was altered in high oleic ingression lines. Two introgression lines, HOMS Nos. 37 and 113 had over 10% higher pooled pod yield than respective best check varieties. More than 70% recurrent parent genome recovery was observed in HOMS-37 and HOMS-113 through recombination breeding. However, the absence of recombination in the vicinity of the target locus resulted in its precise introgression along with ample background genome recovery. Selected introgression lines could be released for commercial cultivation based on potential pod yield and oleic acid content
Development and Validation of Diagnostic KASP Markers for Brown Planthopper Resistance in Rice
Get PDFRice (Oryza sativa L.) is an important source of nutrition for the world’s burgeoning population that often faces yield loss due to infestation by the brown planthopper (BPH, Nilaparvata lugens (Stål)). The development of rice cultivars with BPH resistance is one of the crucial precedences in rice breeding programs. Recent progress in high-throughput SNP-based genotyping technology has made it possible to develop markers linked to the BPH more quickly than ever before. With this view, a genome-wide association study was undertaken for deriving marker-trait associations with BPH damage scores and SNPs from genotyping-by-sequencing data of 391 multi-parent advanced generation inter-cross (MAGIC) lines. A total of 23 significant SNPs involved in stress resistance pathways were selected from a general linear model along with 31 SNPs reported from a FarmCPU model in previous studies. Of these 54 SNPs, 20 were selected in such a way to cover 13 stress-related genes. Kompetitive allele-specific PCR (KASP) assays were designed for the 20 selected SNPs and were subsequently used in validating the genotypes that were identified, six SNPs, viz, snpOS00912, snpOS00915, snpOS00922, snpOS00923, snpOS00927, and snpOS00929 as efficient in distinguishing the genotypes into BPH-resistant and susceptible clusters. Bph17 and Bph32 genes that are highly effective against the biotype 4 of the BPH have been validated by gene specific SNPs with favorable alleles in M201, M272, M344, RathuHeenati, and RathuHeenati accession. These identified genotypes could be useful as donors for transferring BPH resistance into popular varieties with marker-assisted selection using these diagnostic SNPs. The resistant lines and the significant SNPs unearthed from our study can be useful in developing BPH-resistant varieties after validating them in biparental populations with the potential usefulness of SNPs as causal markers
Comprehensive transcriptomic analysis of two RIL parents with contrasting salt responsiveness identifies polyadenylated and non-polyadenylated flower lncRNAs in chickpea
No full textSalinity severely affects the yield of chickpea. Understanding the role of lncRNAs can shed light on chickpea salt tolerance mechanisms. However, because lncRNAs are encoded by multiple sites within the genome, their classification to reveal functional versatility at the transcriptional and the post-transcriptional levels is challenging. To address this, we deep sequenced 24 salt-challenged flower transcriptomes from two parental genotypes of a RIL population that significantly differ in salt tolerance ability. The transcriptomes for the first time included 12polyadenylated and 12 non-polyadenylated RNA libraries to a sequencing depth of~50 million reads. The ab initio transcriptome assembly comprised ~34082 transcripts from three biological replicates of salt-tolerant (JG11) and salt-sensitive (ICCV2) flowers. A total of 9419 lncRNAs responding to salt stress were identified, 2345 of which were novel lncRNAs specific to chickpea.The expression of poly(A+) lncRNAs and naturally antisense transcribed RNAs suggest their role in post-transcriptional modification and gene silencing. Notably, 178 differentially expressed lncRNAs were induced in the tolerant genotype but repressed in the sensitive genotype. Co-expression network analysis revealed that the induced lncRNAs interacted with the FLOWERING LOCUS(FLC), chromatin remodelling and DNA methylation genes, thus inducing flowering during salt stress. Furthermore, 26 lncRNAs showed homology with reported lncRNAs such as COOLAIR, IPS1 and AT4, thus confirming the role of chickpea lncRNAs in controlling flowering time as a crucial salt tolerance mechanism in tolerant chickpea genotype. These robust set of differentially expressed lncRNAs provide a deeper insight into the regulatory mechanisms controlled by lncRNAs under salt stress
Potential Targets for CRISPR/Cas Knockdowns to Enhance Genetic Resistance Against Some Diseases in Wheat (Triticum aestivum L.)
No full textWheat is one of the most important food crops worldwide. Even though wheat yields have increased considerably in recent years, future wheat production is predicted to face enormous challenges due to global climate change and new versions of diseases. CRISPR/Cas technology is a clean gene technology and can be efficiently used to target genes prone to biotic stress in wheat genome. Herein, the published research papers reporting the genetic factors corresponding to stripe rust, leaf rust, stem rust, powdery mildew, fusarium head blight and some insect pests were critically reviewed to identify negative genetic factors (Susceptible genes) in bread wheat. Out of all reported genetic factors related to these disease, 33 genetic factors (S genes) were found as negative regulators implying that their down-regulation, deletion or silencing improved disease tolerance/resistance. The results of the published studies provided the concept of proof that these 33 genetic factors are potential targets for CRISPR/Cas knockdowns to improve genetic tolerance/resistance against these diseases in wheat. The sequences of the 33 genes were retrieved and re-mapped on the latest wheat reference genome IWGSC RefSeq v2.1. Phylogenetic analysis revealed that pathogens causing the same type of disease had some common conserved motifs and were closely related. Considering the significance of these disease on wheat yield, the S genes identified in this study are suggested to be disrupted using CRISPR/Cas system in wheat. The knockdown mutants of these S genes will add to genetic resources for improving biotic stress resistance in wheat crop
Genebanks and market participation: evidence from groundnut farmers in Malawi
Get PDFBackground: Genebanks contribute to poverty reduction as well as food and nutritional security by being one of the
main sources of diversity for the development of improved crop varieties. While the welfare implications of adopting
improved varieties have been documented in many rural settings, little attention has been placed on genebanks that
often supply key traits and genetic diversity to plant breeders by providing seed samples. In this study, we examined the contribution of the genebank housed by the International Crops Research Institute (ICRISAT) to the development of improved groundnut varieties used by farmers in Malawi. We then related this apportioned genebank contribution to market outcomes, such as market participation and the quantity of groundnut sold in markets.
Methods: Pedigree data obtained through consultations with genebank scientists and breeders were used in combination with a three-wave balanced household-level panel dataset of 447 smallholder farmers in Malawi. Different econometric techniques were used, including a double hurdle model to understand market participation and quantity of groundnuts sold.
Results: We found households to be using six improved groundnut varieties, four of which were traced to the
ICRISAT genebank. We analyzed pedigrees of the varieties and apportioned the ancestral contribution of the genebank
accessions. Linking the improved varieties grown by farmers with genebank ancestry to market outcomes, we observed a positive association between the ICRISAT genebank and market participation. We could not establish a robust effect on the quantity of groundnuts sold conditional on participation. We found the results to be driven by the area under improved groundnuts.
Conclusion: The ICRISAT genebank has provided accessions that confer useful traits to improved varieties of
groundnut adopted by farmers in Malawi. Our analysis indicates that access to genetic resources from genebanks
has resulted in the development of improved varieties with traits that are preferred by farmers such as higher yields
and resistance to diseases. The adoption of these improved varieties led to increased production surplus and reduced
transaction costs, allowing farmers to better participate in local groundnut markets. The study points to the crucial
role of genebanks as important sources of crop diversity for improved food security and incomes of smallholder farmers
Immunity elicitors for induced resistance against the downy mildew pathogen in pearl millet
Get PDFPearl millet (Pennisetum glaucum (L.) R. Br.) is a globally important cereal whose production is severely constrained by downy mildew caused by Sclerospora graminicola (Sacc.). In this study, immunity eliciting properties of 3,5‑dichloroanthranilic acid (DCA), Cell Wall Glucan (CWG), Lipopolysaccharide (LPS), and Glycinebetaine (GB) was deciphered through enzymatic and protein studies based on
elicitor treatment activated defense mechanisms. Glycinebetaine, LPS, CWS and DCA elicited enzyme activities and gene expression of the defense enzymes, such as β‑1,3‑glucanase, phenylalanine ammonia lyase (PAL), peroxidase (POX), polyphenol oxidase (PPO), lipoxygenase (LOX) and defense protein hydroxyproline‑rich glycoproteins (HRGPs). However, the speed and the extent of elicitation
differed. High levels of enzyme activities and gene expression in elicitor‑treated P. glaucum positively
correlated with the increased downy mildew resistance. A very rapid and large changes in elicitor-treated seedlings, in contrast to the delayed, smaller changes in the untreated susceptible control seedlings suggests that the rate and magnitude of defense gene expression are important for effective manifestation of defense against pathogen. As compared to other elicitors and control, GB promoted
increase in enzyme activities and gene expression, implicating that GB is a promising elicitor of downy
mildew resistance in P. glaucum
Distribution and pathogenic diversity in Fusarium udum Butler isolates: the causal agent of pigeonpea Fusarium wilt
Get PDFBackground: Fusarium wilt (Fusarium udum Butler), an important soil-borne disease of pigeonpea [Cajanus cajan
(L.)], causes significant yield losses across the major pigeonpea production regions. Widespread and high diversity in F. udum hampers the breeding for pigeonpea wilt resistance. The study aimed to elucidate the pathogenic diversity and distribution of F. udum variants in major pigeonpea growing regions of India. Results: The roving survey was conducted in major pigeonpea-growing states of India to collect the F. udum isolates. Pathogenic variability of 60 F. udum isolates which are selected from diverse geographical locations and pathogenicity test were performed against 11 pigeonpea host differentials cultivars [ICP 8858, ICP 8859, ICP 8862, ICP 8863, ICP 9174, C 11, BDN 1, BDN 2, LRG 30, ICP 2376 and Bahar (ICP 7197)]. The current study indicated distribution of F. udum isolates
into nine variants (0, 1, 2, 3, 4, 5, 6, 7 and 8). Variant-2 and 3 were found to be widespread and predominant in most
pigeonpea producing regions. Variant-7 (Karnataka) and Variant-8 (Madhya Pradesh and Maharashtra) were found
highly virulent, as most of the host differentials were susceptible to these variants. Three host differential cultivars namely ICP 9174, BDN-2 and Bahar (ICP 7197) were found resistant to most of the F. udum isolates.
Conclusion: The present study generated significant information in terms of variants of F. udum which could be used further for the deployment of location-specific wilt resistant cultivars for optimized disease-management strategies. Study is also useful for development of broad-based wilt resistant cultivars to curtail the possible epidemics