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In India, agricultural production is a crucial factor for economic growth. However, plants can be attacked by diseases that range from mild to severe, leading to their destruction. Therefore, it is essential to detect plant diseases at an early stage to prevent such damage. To address this issue, we propose a Hybrid Xception transfer learning with crossover optimized kernel extreme learning machine (HXTL-COKELM) method for identifying healthy and diseased plant leaves. The proposed approach preprocesses and extracts image features using transfer learning with the Xception model to improve computation accuracy before classification. Additionally, we developed a crossover-based tasmanian devil-optimized kernel extreme learning machine model to optimize the KELM's parameters using the TDO algorithm. We collected a dataset with 43,466 images of plant leaves from healthy and diseased plants to train, test, and validate the CNN model. Finally, we evaluated the system's efficacy using performance metrics such as accuracy, recall, specificity, F1-score, and kappa static value. Our experimental findings show that the proposed HXTL-COKELM method achieves a 98.9% accuracy rate, outperforming existing methods. The HXTL-COKELM model also exhibits superior overall performance. Thus, the proposed HXTL-COKELM model can effectively detect plant leaf diseases. [ABSTRACT FROM AUTHOR]

This study describes the settling velocity phenomenon and deals with the methods for its estimation. The accuracy of three previously proposed settling velocity equations is also checked in this study. After graphical and statistical analysis, the authors proposed generalized reduced gradient (GRG) and hybrid generalized reduced gradient–genetic algorithm (hybrid GRG-GA) approaches for the estimation of settling velocity. Hybrid GRG-GA-based settling velocity approach showed more precise results than GRG approach. In addition, hybrid GRG-GA and GRG approaches were compared with previously proposed equations using 226 data points. The graphical and statistical analysis shows that the hybrid GRG-GA and GRG approaches give better agreement with observed data points as compared to previously proposed equations. Application of hybrid GRG-GA reduces the sum of square of error in fall velocity by over 70% and 30% on an average as compared to previous equations during training and testing, respectively. This study highlights that the hybrid GRG-GA approach could be efficiently used for calculating the settling velocity. [ABSTRACT FROM AUTHOR]

In this article, we have considered the problem of first sign change of Fourier coefficients of a primitive cusp form at a sparse sequence, where elements of the sparse sequence can be written as a sum of two squares. Following the methods of Kohnen–Sengupta, we give an effective upper bound on elements of such a sparse sequence to have first sign change. [ABSTRACT FROM AUTHOR]

In this article, we have considered the problem of first sign change of Fourier coefficients of a primitive cusp form at a sparse sequence, where elements of the sparse sequence can be written as a sum of two squares. Following the methods of Kohnen–Sengupta, we give an effective upper bound on elements of such a sparse sequence to have first sign change. [ABSTRACT FROM AUTHOR]

Plant bioregulators (PBRs) represent low-cost chemicals for boosting plant defense, especially under stress conditions. In the present study, redox based PBRs such as thiourea (TU; a non-physiological thiol-based ROS scavenger) and hydrogen peroxide (H2O2; a prevalent biological ROS) were assessed for their ability to mitigate NaCl stress in rice variety IR 64. Despite their contrasting redox chemistry, TU or H2O2 supplementation under NaCl [NaCl + TU (NT) or NaCl + H2O2 (NH)] generated a reducing redox environment in planta, which improved the plant growth compared with those of NaCl alone treatment. This was concomitant with better K+ retention and upregulated expression of NaCl defense related genes including HAK21, LEA1, TSPO and EN20 in both NT and NH treated seedlings. Under field conditions, foliar applications of TU and H2O2, at vegetative growth, pre-flowering and grain filling stages, increased growth and yield attributes under both control and NaCl stress conditions. Principal component analysis revealed glutathione reductase dependent reduced ROS accumulation in source (flag leaves) and sucrose synthase mediated sucrose catabolism in sink (developing inflorescence), as the key variables associated with NT and NH mediated effects, respectively. In addition, photosystem-II efficiency, K+ retention and source-sink relationship were also improved in TU and H2O2 treated plants. Taken together, our study highlights that reducing redox environment acts as a central regulator of plant's tolerance responses to salt stress. In addition, TU and H2O2 are proposed as potential redox-based PBRs for boosting rice productivity under the realistic field conditions. [ABSTRACT FROM AUTHOR]

Background: Anti-EGFR-based therapies have limited success in HNSCC patients. Predictive biomarkers are greatly needed to identify the patients likely to be benefited from these targeted therapies. Here, we present the prognostic and predictive association of biomarkers in HPV-negative locally advanced (LA) HNSCC patients.Methods: Treatment-naive tumour tissue samples of 404 patients, a subset of randomised Phase 3 trial comparing cisplatin radiation (CRT) versus nimotuzumab plus cisplatin radiation (NCRT) were analysed to evaluate the expression of HIF1α, EGFR and pEGFR by immunohistochemistry and EGFR gene copy change by FISH. Progression-free survival (PFS), locoregional control (LRC) and overall survival (OS) were estimated by Kaplan-Meier method. Hazard ratios were estimated by Cox proportional hazard models.Results: Baseline characteristics of the patients were balanced between two treatment groups (CRT vs NCRT) and were representative of the trial cohort. The median follow-up was of 39.13 months. Low HIF1α was associated with better PFS [HR (95% CI) = 0.62 (0.42-0.93)], LRC [HR (95% CI) = 0.56 (0.37-0.86)] and OS [HR (95% CI) = 0.63 (0.43-0.93)] in the CRT group. Multivariable analysis revealed HIF1α as an independent negative prognostic biomarker. For patients with high HIF1α, NCRT significantly improved the outcomes [PFS:HR (95% CI) = 0.55 (0.37-0.82), LRC:HR (95% CI) = 0.55 (0.36-0.85) and OS:HR (95% CI) = 0.54 (0.36-0.81)] compared to CRT. While in patients with low HIF1α, no difference in the clinical outcomes was observed between treatments. Interaction test suggested a predictive value of HIF1α for OS (P = 0.008).Conclusions: High HIF1α expression is a predictor of poor clinical response to CRT in HPV-negative LA-HNSCC patients. These patients with high HIF1α significantly benefited with the addition of nimotuzumab to CRT.Clinical Trial Registration: Registered with the Clinical Trial Registry of India (Trial registration identifier-CTRI/2014/09/004980). [ABSTRACT FROM AUTHOR]

Key message: Comparative assessment identified naïve interaction model, and naïve and informed interaction GS models suitable for achieving higher prediction accuracy in groundnut keeping in mind the high genotype × environment interaction for complex traits. Genomic selection (GS) can be an efficient and cost-effective breeding approach which captures both small- and large-effect genetic factors and therefore promises to achieve higher genetic gains for complex traits such as yield and oil content in groundnut. A training population was constituted with 340 elite lines followed by genotyping with 58 K 'Axiom_Arachis' SNP array and phenotyping for key agronomic traits at three locations in India. Four GS models were tested using three different random cross-validation schemes (CV0, CV1 and CV2). These models are: (1) model 1 (M1 = E + L) which includes the main effects of environment (E) and line (L); (2) model 2 (M2 = E + L + G) which includes the main effects of markers (G) in addition to E and L; (3) model 3 (M3 = E + L + G + GE), a naïve interaction model; and (4) model 4 (E + L + G + LE + GE), a naïve and informed interaction model. Prediction accuracy estimated for four models indicated clear advantage of the inclusion of marker information which was reflected in better prediction accuracy achieved with models M2, M3 and M4 as compared to M1 model. High prediction accuracies (> 0.600) were observed for days to 50% flowering, days to maturity, hundred seed weight, oleic acid, rust@90 days, rust@105 days and late leaf spot@90 days, while medium prediction accuracies (0.400–0.600) were obtained for pods/plant, shelling %, and total yield/plant. Assessment of comparative prediction accuracy for different GS models to perform selection for untested genotypes, and unobserved and unevaluated environments provided greater insights on potential application of GS breeding in groundnut. [ABSTRACT FROM AUTHOR]

Key message: Groundnut has entered now in post-genome era enriched with optimum genomic and genetic resources to facilitate faster trait dissection, gene discovery and accelerated genetic improvement for developing climate-smart varieties. Cultivated groundnut or peanut (Arachis hypogaea), an allopolyploid oilseed crop with a large and complex genome, is one of the most nutritious food. This crop is grown in more than 100 countries, and the low productivity has remained the biggest challenge in the semiarid tropics. Recently, the groundnut research community has witnessed fast progress and achieved several key milestones in genomics research including genome sequence assemblies of wild diploid progenitors, wild tetraploid and both the subspecies of cultivated tetraploids, resequencing of diverse germplasm lines, genome-wide transcriptome atlas and cost-effective high and low-density genotyping assays. These genomic resources have enabled high-resolution trait mapping by using germplasm diversity panels and multi-parent genetic populations leading to precise gene discovery and diagnostic marker development. Furthermore, development and deployment of diagnostic markers have facilitated screening early generation populations as well as marker-assisted backcrossing breeding leading to development and commercialization of some molecular breeding products in groundnut. Several new genomics applications/technologies such as genomic selection, speed breeding, mid-density genotyping assay and genome editing are in pipeline. The integration of these new technologies hold great promise for developing climate-smart, high yielding and more nutritious groundnut varieties in the post-genome era. [ABSTRACT FROM AUTHOR]

Key message: Two novel and adjacent genomics and candidate genes for bacterial wilt resistance were identified on chromosome B02 in peanut variety Zhonghua 6 using both traditional QTL mapping and QTL-seq methods. Peanut (Arachis hypogaea) is an important oilseed crop worldwide. Utilization of genetic resistance is the most economic and effective approach to control bacterial wilt, one of the most devastating plant diseases, in peanut production. To accelerate the genetic improvement of bacterial wilt resistance (BWR) in peanut breeding programs, quantitative trait locus (QTL) mapping has been conducted for two resistant varieties. In this context, we deployed linkage mapping as well as sequencing-based mapping approach, QTL-seq, to identify genomic regions and candidate genes for BWR in another highly resistant variety Zhonghua 6. The recombination inbred line population (268 progenies) from the cross Xuhua 13 × Zhonghua 6 was used in BWR evaluation across five environments. QTL mapping using both SSR- and SNP-based genetic maps identified a stable QTL (qBWRB02-1) on chromosome B02 with 37.79–78.86% phenotypic variation explained (PVE) across five environments. The QTL-seq facilitated further dissection of qBWRB02-1 into two adjacent genomic regions, qBWRB02-1-1 (2.81–4.24 Mb) and qBWRB02-1-2 (6.54–8.75 Mb). Mapping of newly developed Kompetitive allele-specific PCR (KASP) markers on the genetic map confirmed their stable expressions across five environments. The effects of qBWRB02-1-1 (49.43–68.86% PVE) were much higher than qBWRB02-1-2 (3.96–6.48% PVE) and other previously reported QTLs. Nineteen putative candidate genes affected by 49 non-synonymous SNPs were identified for qBWRB02-1-1, and ten of them were predicted to code for disease resistance proteins. The major and stable QTL qBWRB02-1-1 and validated KASP markers could be deployed in genomics-assisted breeding (GAB) to develop improved peanut varieties with enhanced BWR. [ABSTRACT FROM AUTHOR]

In this article, we investigate the sign changes of the sequence of coefficients at sum of two squares where the coefficients are the Fourier coefficients of the normalized Hecke eigen cusp form for the full modular group. We provide the quantitative result for the number of sign changes of the sequence in a small interval. [ABSTRACT FROM AUTHOR]

Natural algal bloom consists of promising algal species which could be a feasible option for the source of bulk biomass and biodiesel production. It has been found in five natural fresh water algal blooms (Uttar Pradesh, India), containing high nitrogen (N) (4.6 ± 0.32 mg/L) and phosphorus (P) (4.12 ± 0.29 mg/L) concentration during spring (23.9–25.9 °C) and summer season (32.0–35.0 °C). Among the isolated algae from naturally occurring bloom, Chlorella sorokiniana MKP01 exhibited highest biomass (1.02 ± 0.02 g/L) and lipid content (174.1 ± 9.6 mg/L) in untreated tap water and urea/single super phosphate (SSP) in the ratio (2:1). The biodiesel quality was assessed and found to be with the Indian and international standards. Algal bloom was artificially developed in the open pond containing 10,000 l tap water supplemented with Urea/SSP (2:1) for a consistent supply of bulk biomass, yielded 8 kg of total biomass and lipid 1.3 kg. [ABSTRACT FROM AUTHOR]

Ploidy difference between wild Arachis species and cultivated genotypes hinder transfer of useful alleles for agronomically important traits. To overcome this genetic barrier, two synthetic tetraploids, viz., ISATGR 1212 (A. duranensis ICG 8123 × A. ipaensis ICG 8206) and ISATGR 265-5A (A. kempff-mercadoi ICG 8164 × A. hoehnei ICG 8190), were used to generate two advanced backcross (AB) populations. The AB-populations, namely, AB-pop1 (ICGV 91114 × ISATGR 1212) and AB-pop2, (ICGV 87846 × ISATGR 265-5A) were genotyped with DArT and SSR markers. Genetic maps were constructed for AB-pop1 and AB-pop2 populations with 258 loci (1415.7 cM map length and map density of 5.5 cM/loci) and 1043 loci (1500.8 cM map length with map density of 1.4 cM/loci), respectively. Genetic analysis identified large number of wild segments in the population and provided a good source of diversity in these populations. Phenotyping of these two populations identified several introgression lines with good agronomic, oil quality, and disease resistance traits. Quantitative trait locus (QTL) analysis showed that the wild genomic segments contributed favourable alleles for foliar disease resistance while cultivated genomic segments mostly contributed favourable alleles for oil quality and yield component traits. These populations, after achieving higher stability, will be useful resource for genetic mapping and QTL discovery for wild species segments in addition to using population progenies in breeding program for diversifying the gene pool of cultivated groundnut. [ABSTRACT FROM AUTHOR]

Efficiency of breeding programs of legume crops such as chickpea, pigeonpea and groundnut has been considerably improved over the past decade through deployment of modern genomic tools and technologies. For instance, next-generation sequencing technologies have facilitated availability of genome sequence assemblies, re-sequencing of several hundred lines, development of HapMaps, high-density genetic maps, a range of marker genotyping platforms and identification of markers associated with a number of agronomic traits in these legume crops. Although marker-assisted backcrossing and marker-assisted selection approaches have been used to develop superior lines in several cases, it is the need of the hour for continuous population improvement after every breeding cycle to accelerate genetic gain in the breeding programs. In this context, we propose a sequence-based breeding approach which includes use of independent or combination of parental selection, enhancing genetic diversity of breeding programs, forward breeding for early generation selection, and genomic selection using sequencing/genotyping technologies. Also, adoption of speed breeding technology by generating 4–6 generations per year will be contributing to accelerate genetic gain. While we see a huge potential of the sequence-based breeding to revolutionize crop improvement programs in these legumes, we anticipate several challenges especially associated with high-quality and precise phenotyping at affordable costs, data analysis and management related to improving breeding operation efficiency. Finally, integration of improved seed systems and better agronomic packages with the development of improved varieties by using sequence-based breeding will ensure higher genetic gains in farmers' fields. [ABSTRACT FROM AUTHOR]

An effort was made in the present study to identify the main effect and epistatic quantitative trait locus (QTL) for the morphological and yield-related traits in peanut. A recombinant inbred line (RIL) population derived from TAG 24 × GPBD 4 was phenotyped in seven environments at two locations. QTL analysis with available genetic map identified 62 main-effect QTLs (M-QTLs) for ten morphological and yield-related traits with the phenotypic variance explained (PVE) of 3.84-15.06%. Six major QTLs (PVE > 10%) were detected for PLHT, PPP, YPP, and SLNG. Stable M-QTLs appearing in at least two environments were detected for PLHT, LLN, YPP, YKGH, and HSW. Five M-QTLs governed two traits each, and 16 genomic regions showed co-localization of two to four M-QTLs. Intriguingly, a major QTL reported to be linked to rust resistance showed pleiotropic effect for yield-attributing traits like YPP (15.06%, PVE) and SLNG (13.40%, PVE). Of the 24 epistatic interactions identified across the traits, five interactions involved six M-QTLs. Three interactions were additive × additive and remaining two involved QTL × environment (QE) interactions. Only one major M-QTL governing PLHT showed epistatic interaction. Overall, this study identified the major M-QTLs for the important productivity traits and also described the lack of epistatic interactions for majority of them so that they can be conveniently employed in peanut breeding. [ABSTRACT FROM AUTHOR]

Let (S,ω) be a weighted abelian semigroup, let Mω(S) be the semigroup of ω-bounded multipliers of S, and let A be a strictly convex commutative Banach algebra with identity. It is shown that T is an onto isometric multiplier of ℓ¹(S, ω, A) if and only if there exists an invertible σ ∈ Mω(S), a unitary point a ∈ A, and a k > 0 such that T(f) = ka ∑x∈S f(x)δσ(x) for each f = ∑x∈S f(x)δx ∈ ℓ¹(S, ω, A). It is also shown that an isomorphism from ℓ¹(S1, ω1, A) onto ℓ¹(S2, ω2, B) induces an isomorphism from M(ℓ¹(S1, ω1, A)), the set of all multipliers of ℓ¹(S1, ω1, A), onto M(ℓ¹(S2, ω2, B)). [ABSTRACT FROM AUTHOR]

Yield under drought stress is a highly complex trait with large influence to even a minor fluctuation in the environmental conditions. Genomics-assisted breeding holds great promise for improving such complex traits more efficiently in less time, but requires markers associated with the trait of interest. In this context, a recombinant inbred line mapping population (TAG 24 × ICGV 86031) was used to identify markers associated with quantitative trait loci (QTLs) for yield and yield related traits at two important locations of West Africa under well watered and water stress conditions. Among the traits analyzed under WS condition, the harvest index (HI) and the haulm yield (HYLD) were positively correlated with the pod yield (PYLD) and showed intermediate broad sense heritability. QTL analysis using phenotyping and genotyping data resulted in identification of 52 QTLs. These QTLs had low phenotypic variance (<12 %) for all the nine traits namely plant height, primary branching, SPAD chlorophyll meter reading, percentage of sound mature kernels, 100 kernel weight, shelling percentage, HI, HYLD and PYLD. Interestingly, few QTLs identified in this study were also overlapped with previously reported QTLs detected for drought tolerance related traits identified earlier in Indian environmental conditions using the same mapping population. Accumulating these many small-effect QTLs into a single genetic background is nearly impossible through marker-assisted backcrossing and even marker-assisted recurrent selection. Under such circumstances, the deployment of genomic selection is the most appropriate approach for improving such complex traits with more precision and in less time. [ABSTRACT FROM AUTHOR]

Key message: Successful introgression of a major QTL for rust resistance, through marker-assisted backcrossing, in three popular Indian peanut cultivars generated several promising introgression lines with enhanced rust resistance and higher yield. Abstract: Leaf rust, caused by Puccinia arachidis Speg, is one of the major devastating diseases in peanut ( Arachis hypogaea L.). One QTL region on linkage group AhXV explaining upto 82.62 % phenotypic variation for rust resistance was validated and introgressed from cultivar 'GPBD 4' into three rust susceptible varieties ('ICGV 91114', 'JL 24' and 'TAG 24') through marker-assisted backcrossing (MABC). The MABC approach employed a total of four markers including one dominant (IPAHM103) and three co-dominant (GM2079, GM1536, GM2301) markers present in the QTL region. After 2-3 backcrosses and selfing, 200 introgression lines (ILs) were developed from all the three crosses. Field evaluation identified 81 ILs with improved rust resistance. Those ILs had significantly increased pod yields (56-96 %) in infested environments compared to the susceptible parents. Screening of selected 43 promising ILs with 13 markers present on linkage group AhXV showed introgression of the target QTL region from the resistant parent in 11 ILs. Multi-location field evaluation of these ILs should lead to the release of improved varieties. The linked markers may be used in improving rust resistance in peanut breeding programmes. [ABSTRACT FROM AUTHOR]

This paper aims to present the mechanism of scour and empirical equations for evaluating local scour with and without a countermeasure around the bridge pier. A critical review of scour countermeasures, mainly hydraulic, structural, and biotechnical, extending to the present time is done. Hydraulic countermeasures consist of river training structures and bed armoring. Structures placed parallel, perpendicular, or at an angle to the flow aiming to modify it is the purpose of river training works. Armoring is done through the use of riprap, partially grouted riprap, cable-tied blocks, grout-filled containers, and gabions. Structural countermeasures include foundation strengthening and pier geometry modifications. Extending footings, underpinning, and pile- underpinning are related to foundation strengthening, while pier geometry modifications include different pier features such as shapes, textures, slots, and collars. Biotechnical countermeasures include using vegetation riprap, geosynthetic polymer, live staking, and bio-stabilization using extracellular polymeric substances. Different combinations of countermeasures are also discussed. In hydraulic and structural countermeasures, riprap and collars are most commonly used due to their efficiency in scour reduction and economic feasibility. Bio-stabilization using extracellular polymeric substances is a novel measure for scour prevention. From the literature, it is concluded that pier modifications are the most effective and active area of research in which lenticular pier shape, lenticular hooked, and airfoil-shaped collar are best suited for reducing the local scour around the pier. Finally, the limitations of the countermeasures mentioned above are presented. [ABSTRACT FROM AUTHOR]

Key message: Twenty-eight QTLs for LLS disease resistance were identified using an amphidiploid constructed mapping population, a favorable 530-kb chromosome segment derived from wild species contributes to the LLS resistance. Late leaf spot (LLS) is one of the major foliar diseases of peanut, causing serious yield loss and affecting the quality of kernel and forage. Some wild Arachis species possess higher resistance to LLS as compared with cultivated peanut; however, ploidy level differences restrict utilization of wild species. In this study, a synthetic amphidiploid (Ipadur) of wild peanuts with high LLS resistance was used to cross with Tifrunner to construct TI population. In total, 200 recombinant inbred lines were collected for whole-genome resequencing. A high-density bin-based genetic linkage map was constructed, which includes 4,809 bin markers with an average inter-bin distance of 0.43 cM. The recombination across cultivated and wild species was unevenly distributed, providing a novel recombination landscape for cultivated-wild Arachis species. Using phenotyping data collected across three environments, 28 QTLs for LLS disease resistance were identified, explaining 4.35–20.42% of phenotypic variation. The major QTL located on chromosome 14, qLLS14.1, could be consistently detected in 2021 Jiyang and 2022 Henan with 20.42% and 12.12% PVE, respectively. A favorable 530-kb chromosome segment derived from Ipadur was identified in the region of qLLS14.1, in which 23 disease resistance proteins were located and six of them showed significant sequence variations between Tifrunner and Ipadur. Allelic variation analysis indicating the 530-kb segment of wild species might contribute to the disease resistance of LLS. These associate genomic regions and candidate resistance genes are of great significance for peanut breeding programs for bringing durable resistance through pyramiding such multiple LLS resistance loci into peanut cultivars. [ABSTRACT FROM AUTHOR]

Key message: Integrating GAB methods with high-throughput phenotyping, genome editing, and speed breeding hold great potential in designing future smart peanut cultivars to meet market and food supply demands. Cultivated peanut (Arachis hypogaea L.), a legume crop greatly valued for its nourishing food, cooking oil, and fodder, is extensively grown worldwide. Despite decades of classical breeding efforts, the actual on-farm yield of peanut remains below its potential productivity due to the complicated interplay of genotype, environment, and management factors, as well as their intricate interactions. Integrating modern genomics tools into crop breeding is necessary to fast-track breeding efficiency and rapid progress. When combined with speed breeding methods, this integration can substantially accelerate the breeding process, leading to faster access of improved varieties to farmers. Availability of high-quality reference genomes for wild diploid progenitors and cultivated peanuts has accelerated the process of gene/quantitative locus discovery, developing markers and genotyping assays as well as a few molecular breeding products with improved resistance and oil quality. The use of new breeding tools, e.g., genomic selection, haplotype-based breeding, speed breeding, high-throughput phenotyping, and genome editing, is probable to boost genetic gains in peanut. Moreover, renewed attention to efficient selection and exploitation of targeted genetic resources is also needed to design high-quality and high-yielding peanut cultivars with main adaptation attributes. In this context, the combination of genomics-assisted breeding (GAB), genome editing, and speed breeding hold great potential in designing future improved peanut cultivars to meet market and food supply demands. [ABSTRACT FROM AUTHOR]

The published online version of this article unfortunately missed to capture Rajeev K. Varshney as co-corresponding author. There should have been two corresponding authors for this paper (Rajeev K. Varshney and Ramesh S. Bhat). The correct declaration is shown below. [ABSTRACT FROM AUTHOR]

Single nucleotide polymorphisms (SNPs) are the most abundant DNA sequence variation in the genomes which can be used to associate genotypic variation to the phenotype. Therefore, availability of a high-density SNP array with uniform genome coverage can advance genetic studies and breeding applications. Here we report the development of a high-density SNP array 'Axiom_Arachis' with 58 K SNPs and its utility in groundnut genetic diversity study. In this context, from a total of 163,782 SNPs derived from DNA resequencing and RNA-sequencing of 41 groundnut accessions and wild diploid ancestors, a total of 58,233 unique and informative SNPs were selected for developing the array. In addition to cultivated groundnuts (Arachis hypogaea), fair representation was kept for other diploids (A. duranensis, A. stenosperma, A. cardenasii, A. magna and A. batizocoi). Genotyping of the groundnut 'Reference Set' containing 300 genotypes identified 44,424 polymorphic SNPs and genetic diversity analysis provided in-depth insights into the genetic architecture of this material. The availability of the high-density SNP array 'Axiom_Arachis' with 58 K SNPs will accelerate the process of high resolution trait genetics and molecular breeding in cultivated groundnut. [ABSTRACT FROM AUTHOR]

Key Message: The candidate gene AhLBA1 controlling lateral branch angel of peanut was fine-mapped to a 136.65-kb physical region on chromosome 15 using the BSA-seq and QTL mapping. Lateral branch angel (LBA) is an important plant architecture trait of peanut, which plays key role in lodging, peg soil penetration and pod yield. However, there are few reports of fine mapping and quantitative trait loci (QTLs)/cloned genes for LBA in peanut. In this project, a mapping population was constructed using a spreading variety Tifrunner and the erect variety Fuhuasheng. Through bulked segregant analysis sequencing (BSA-seq), a major gene related to LBA, named as AhLBA1, was preliminarily mapped at the region of Chr.15: 150-160 Mb. Then, using traditional QTL approach, AhLBA1 was narrowed to a 1.12 cM region, corresponding to a 136.65-kb physical interval of the reference genome. Of the nine genes housed in this region, three of them were involved in hormone metabolism and regulation, including one "F-box protein" and two "2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase (2OG oxygenase)" encoding genes. In addition, we found that the level of some classes of cytokinin (CK), auxin and ethylene showed significant differences between spreading and erect peanuts at the junction of main stem and lateral branch. These findings will aid further elucidation of the genetic mechanism of LBA in peanut and facilitating marker-assisted selection (MAS) in the future breeding program. [ABSTRACT FROM AUTHOR]

Genomic regions governing water deficit stress tolerance were identified in peanut using a recombinant inbred line (RIL) population derived from an elite variety TMV 2 and its narrow leaf mutant TMV 2-NLM, which was evaluated over six-seasons at Dharwad (non-stress) and Tirupati (water-stress) in India. Stress condition could differentiate the RILs much better than the non-stress condition for the physiological traits. A linkage map with 700 markers was used to identify the quantitative trait loci (QTLs). Three sets of best linear unbiased predictions (BLUPs) were estimated for the drought tolerance traits for the rainy and post-rainy seasons at Dharwad and post-rainy seasons at Tirupati, and employed for single marker analysis, composite interval mapping and multiple QTL mapping. Of the 305 significant marker-trait associations for the 11 traits, only 21 were of major effect for pod yield per plant (PYPP), specific dry weight at 70 days after sowing (SDW_70) and specific leaf area at 70 DAS (SLA_70). Three major main effect QTLs were identified for PYPP with the highest phenotypic variance explained (PVE) of 10.5%. Nine QTLs with the highest PVE of 18.4% were identified for SDW_70, of which four QTLs were also governing SLA_70 with the highest PVE of 15.7%. A few of them were also involved in epistatic interactions, and formed multiple QTL mapping models. Five major QTLs for SDW_70 were stable over both the locations. Candidate genes with SNPs and AhMITE1 insertion were identified for the major QTL regions. A rare nonsynonymous SNP at Ah02_1558700 within the gene ArahyW1P0U6 governing PYPP was detected. Functional analysis of these candidate genes may be useful for future genetic modifications in addition to validating and using the linked markers for improving drought tolerance in peanut. [ABSTRACT FROM AUTHOR]

Analysis of rainfall distribution and its changing pattern plays a vital role in managing water resources in a region. This work examined the spatio-temporal variability and trend of rainfall on yearly and season-wise scales during 1971–2013 in the Wainganga river basin situated in middle India. The Mann–Kendall (MK) test was implemented for identifying the temporal variation in rainfall trends. The magnitude of this changing trend was estimated by applying Sen's slope (SS) method. A paired sample t-test was also employed to appraise the statistical significance of changes in rainfall data. The results of MK and SS tests show both upward and downward trends. The results show positive and negative trends in the south-eastern and northwestern parts of the study area for annual rainfall. The monsoon rainfall also shows very close proximity with annual rainfall data trends. The t-test states that the observed changes in precipitation are statistically significant. After trend and pattern analysis, state-space models (SSMs) were used to predict rainfall for future scenarios. Four SSMs (single, double, and triple exponential, autoregressive integrated moving average (ARIMA)) were employed for rainfall prediction. The analysis shows that the ARIMA is best for rainfall prediction with architecture of (0,0,0) (2,1,0) and can be used in Wainganga River basin. [ABSTRACT FROM AUTHOR]

Iron deficiency chlorosis (IDC) under calcareous and alkaline soils is a significant abiotic stress affecting the growth and yield of peanut. In this study, the genomic regions governing IDC tolerance were mapped using a recombinant inbred line (RIL) population derived from TMV 2 (susceptible to IDC) and TMV 2-NLM (tolerant to IDC), which was phenotyped during the rainy seasons of 2019 and 2020 in the iron-deficient calcareous plots. The best linear unbiased prediction (BLUP) values for IDC tolerance traits like visual chlorotic rating (VCR), and SPAD chlorophyll meter reading (SCMR) were used for QTL analysis along with a genetic map carrying 700 GBS-derived SNP, AhTE and SSR markers. In total, 11 and 12 main-effect QTLs were identified for VCR and SCMR, respectively. Among them three QTLs were major with the phenotypic variance explained (PVE) of 10.3–34.4% for VCR, and two QTL were major for SCMR with PVE of 11.5–11.7%. A region (159.3–178.3 cM) on chromosome Ah13 carrying two QTLs (one each for VCR and SCMR) was consistent with the previous report. A SNP marker, Ah14_138037990 identified from single marker analysis for VCR was located in the intronic region of the gene Arahy.QA0C1, which is important for protein-binding. Overall, this study identified new QTLs and also validated QTL for IDC tolerance. These genomic resources could be useful for genomics-assisted breeding of peanut for IDC tolerance. [ABSTRACT FROM AUTHOR]

River morphological dynamics are complex phenomena in natural and environmental flows. In particular, the sediment transport around braid mid-channel bars has not gained enough understanding from previous research. The effect of submergence ratio on the turbulence behavior in the proximity of the bar has been investigated in this study. The spatial distribution of turbulent flow in the proximity of bar has been studied by plotting the depth-averaged two-dimensional contours of turbulent kinetic energy. The high value of TKE has been observed in regions just downstream from the bar. It is due to the vortex shedding occurring in that region. The interaction of sweep and ejection events have been analyzed using the parameter Dominance Function obtained from the ratio of occurrence probability of ejection events to the occurrence probability of sweep events. This outcome indicates that the depth averaged parameter Dominance Function has successfully predicted the high scouring region which makes it an ideal parameter for analyzing the scour phenomena in real-world water management projects. The high scouring zone lies in the close proximity of the bar. This shows that the scouring effect from the bar is limited to its close region. The magnitude of scouring occurring at the upstream region of the bar also increases with the increment of submergence ratio. The relationship of quadrant event inclination angles with the sediment transport occurring in the proximity of bar has been also studied, where an Angle Ratio parameter has been utilized for linking the bed elevation change with the inclination angle. The results indicate that the AR parameter has been successfully tested in this study to show its competence to represent the turbulent burst-induced bed sedimentation and scouring. [ABSTRACT FROM AUTHOR]

Rice grain shape and nutritional quality traits have high economic value for commercial production of rice and largely determine the market price, besides influencing the global food demand for high-quality rice. Detection, mapping and exploitation of quantitative trait loci (QTL) associated with kernel elongation and grain quality in Basmati rice is considered as an efficient strategy for improving the kernel elongation and grain quality trait in rice varieties. Genetic information in rice for most of these traits is scanty and needed interventions through the use of molecular markers. A recombinant inbred lines (RIL) population consisting of 130 lines generated from the cross involving Basmati 370, a superior quality Basmati variety and Pusa Basmati 1121, a Basmati derived variety were used to map the QTLs for 9 important grain quality and yield related traits. Correlation studies showed that various components of yield show a significant positive relationship with grain yield. A genetic map was constructed using 70 polymorphic simple sequence repeat (SSR) markers spanning a genetic distance of 689.3 cM distributed over 12 rice chromosomes. Significant variation was observed and showed transgressive segregation for grain quality traits in RIL population. A total of 20 QTLs were identified associated with nine yield and quality traits. Epistatic interactions were also identified for grain quality related traits indicating complex genetic nature inheritance. Therefore, the identified QTLs and flanking marker information could be utilized in the marker-assisted selection to improve kernel elongation and nutritional grain quality traits in rice varieties. [ABSTRACT FROM AUTHOR]

The new COVID-19 coronavirus disease has emerged as a global threat and not just to human health but also the global economy. Due to the pandemic, most countries affected have therefore imposed periods of full or partial lockdowns to restrict community transmission. This has had the welcome but unexpected side effect that existing levels of atmospheric pollutants, particularly in cities, have temporarily declined. As found by several authors, air quality can inherently exacerbate the risks linked to respiratory diseases, including COVID-19. In this study, we explore patterns of air pollution for ten of the most affected countries in the world, in the context of the 2020 development of the COVID-19 pandemic. We find that the concentrations of some of the principal atmospheric pollutants were temporarily reduced during the extensive lockdowns in the spring. Secondly, we show that the seasonality of the atmospheric pollutants is not significantly affected by these temporary changes, indicating that observed variations in COVID-19 conditions are likely to be linked to air quality. On this background, we confirm that air pollution may be a good predictor for the local and national severity of COVID-19 infections. [ABSTRACT FROM AUTHOR]

Epigenetics is defined as changes in gene expression that are not associated with changes in DNA sequence but due to the result of methylation of DNA and post-translational modifications to the histones. These epigenetic modifications are known to regulate gene expression by bringing changes in the chromatin state, which underlies plant development and shapes phenotypic plasticity in responses to the environment and internal cues. This review articulates the role of histone modifications and DNA methylation in modulating biotic and abiotic stresses, as well as crop improvement. It also highlights the possibility of engineering epigenomes and epigenome-based predictive models for improving agronomic traits. [ABSTRACT FROM AUTHOR]

Drought is one of the main constraints in peanut production in West Texas and eastern New Mexico regions due to the depletion of groundwater. A multi-seasonal phenotypic analysis of 10 peanut genotypes revealed C76-16 (C-76) and Valencia-C (Val-C) as the best and poor performers under deficit irrigation (DI) in West Texas, respectively. In order to decipher transcriptome changes under DI, RNA-seq was performed in C-76 and Val-C. Approximately 369 million raw reads were generated from 12 different libraries of two genotypes subjected to fully irrigated (FI) and DI conditions, of which ~329 million (90.2%) filtered reads were mapped to the diploid ancestors of peanut. The transcriptome analysis detected 4,508 differentially expressed genes (DEGs), 1554 genes encoding transcription factors (TFs) and a total of 514 single nucleotide polymorphisms (SNPs) among the identified DEGs. The comparative analysis between the two genotypes revealed higher and integral tolerance in C-76 through activation of key genes involved in ABA and sucrose metabolic pathways. Interestingly, one SNP from the gene coding F-box protein (Araip.3WN1Q) and another SNP from gene coding for the lipid transfer protein (Aradu.03ENG) showed polymorphism in selected contrasting genotypes. These SNPs after further validation may be useful for performing early generation selection for selecting drought-responsive genotypes. [ABSTRACT FROM AUTHOR]

Since the building roof acts as hub for atmospheric sediment deposition, the attached microbes can enter rainwater storage tank with ease to cause health issue for rainwater users. This study aims to explore the trend of roof-top deposited microbes in the different areas of Ikorodu local Government Area at Lagos, Nigeria. This paper also tests the hypothesis that the roof sediment deposition being a significant source to home bacteria. The total deposition rate on the roof for 34 weeks, which include 17 rainy and 17 dry weeks, were investigated. The enumerated bacteria was obtained from the roof deposit samples, where four representative different sites have been analysed to study the solid depositions and microbes within the area thoroughly. The sites were selected judging by their levels of sanitation and vegetation rate. The experimental investigations showed that enumerated microbes and total suspended solid (TSS) depositions in the different areas were higher in the dry season compared to rainy season, and the highest deposition was experienced in the Harmattan period. In addition, the results showed that areas with poor drainage infrastructure and poor sanitation have the roof-top deposition with higher bacterial count than good sanitation areas; while the unpaved and unvegetated areas produced higher deposits than the paved and vegetated areas. In terms of contamination sources, this study has illustrated that the particulate deposition on the roof-top prior to collection has further contaminated the roof-harvested rainwater. [ABSTRACT FROM AUTHOR]

Key message: Genetic mapping identified large number of epistatic interactions indicating the complex genetic architecture for stem rot disease resistance. Groundnut (Arachis hypogaea) is an important global crop commodity and serves as a major source of cooking oil, diverse confectionery preparations and livestock feed. Stem rot disease caused by Sclerotium rolfsii is the most devastating disease of groundnut and can cause up to 100% yield loss. Genomic-assisted breeding (GAB) has potential for accelerated development of stem rot resistance varieties in short period with more precision. In this context, linkage analysis and quantitative trait locus (QTL) mapping for resistance to stem rot disease was performed in a bi-parental recombinant inbred line population developed from TG37A (susceptible) × NRCG-CS85 (resistant) comprising of 270 individuals. Genotyping-by-sequencing approach was deployed to generate single nucleotide polymorphism (SNP) genotyping data leading to development of a genetic map with 585 SNP loci spanning map distance of 2430 cM. QTL analysis using multi-season phenotyping and genotyping data could not detect any major main-effect QTL but identified 44 major epistatic QTLs with phenotypic variation explained ranging from 14.32 to 67.95%. Large number interactions indicate the complexity of genetic architecture of resistance to stem rot disease. A QTL of physical map length 5.2 Mb identified on B04 comprising 170 different genes especially leucine reach repeats, zinc finger motifs and ethyleneresponsive factors, etc., was identified. The identified genomic regions and candidate genes will further validate and facilitate marker development to deploy GAB for developing stem rot disease resistance groundnut varieties. [ABSTRACT FROM AUTHOR]

Peanut (Arachis hypogaea), a major source of vegetable oil in many Asian countries, has become an integral part of human diet globally due to its high nutritional properties and option to consume in different forms. In order to meet the demand of vegetable oil, many peanut breeding programs of China have intensified their efforts in increasing oil content in newly bred varieties for reducing the import of edible oils in China. In this context, transcriptome sequencing data generated on 49 peanut cultivars were analyzed to identify candidate genes and develop molecular markers for seed oil content across multiple environments. Transcriptome analysis identified 5458 differentially expressed genes (DEGs) including 2243 positive DEGs and 3215 negative DEGs involved in oil synthesis process. Genome-wide association study identified 48 significant insertion/deletion (InDel) markers associated with seed oil content across five environments. A comparative genomics and transcriptomics analysis detected a total of 147 common gene clusters located in 17 chromosomes. Interestingly, an InDel cluster associated with seed oil content on A03 chromosome was detected in three different environments. Candidate genes identified on A03 form a haplotype, in which variable alleles were found to be different in oil content in an independent population. This locus is important for understanding the genetic control of peanut oil content and may be useful for marker-assisted selection in peanut breeding programs. [ABSTRACT FROM AUTHOR]

Contamination of crops with aflatoxin is a serious global threat to food safety. Aflatoxin production by Aspergillus flavus is exacerbated by drought stress in the field and by oxidative stress in vitro. We examined transcriptomes of three toxigenic and three atoxigenic isolates of A. flavus in aflatoxin conducive and non-conducive media with varying levels of H2O2 to investigate the relationship of secondary metabolite production, carbon source, and oxidative stress. We found that toxigenic and atoxigenic isolates employ distinct mechanisms to remediate oxidative damage, and that carbon source affected the isolates' expression profiles. Iron metabolism, monooxygenases, and secondary metabolism appeared to participate in isolate oxidative responses. The results suggest that aflatoxin and aflatrem biosynthesis may remediate oxidative stress by consuming excess oxygen and that kojic acid production may limit iron-mediated, non-enzymatic generation of reactive oxygen species. Together, secondary metabolite production may enhance A. flavus stress tolerance, and may be reduced by enhancing host plant tissue antioxidant capacity though genetic improvement by breeding selection. [ABSTRACT FROM AUTHOR]

B Correction to: Theoretical and Applied Climatology b https://doi.org/10.1007/s00704-022-04168-4 The affiliation of one of the authors (Pranaya Diwate) has been wrongly mentioned in the paper. Publisher's note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. [Extracted from the article]

Whitebacked planthopper (WBPH) along with brown planthopper (BPH) has emerged as a major pest of rice in several Asian countries. Development and cultivation of varieties resistant to both planthoppers is an ecologically acceptable strategy to manage these pests. Sinna Sivappu, a Sri Lankan landrace, was reported to be resistant to both planthoppers. While inheritance of BPH resistance has been reported, the genetics of WBPH resistance in this variety is not known. Using a mapping population of 255 F families from Taichung Native (TN)1/Sinna Sivappu cross and 128 polymorphic simple sequence repeat (SSR) markers, genes or quantitative trait loci (QTLs) for WBPH resistance quantified in ten phenotypic tests were identified, adopting classical Mendelian segregation, correlation and QTL analyses. The inheritance pattern suggested that a single recessive gene controlled regulation of seedling damage score. Antixenosis or nymphal preference was influenced by two complementary recessive genes, whereas tolerance in terms of days to wilt was under the influence of a single dominant gene. Several of these phenotypic tests recorded high degree of positive or negative correlation between them, suggesting dependence or redundancy of the tests. QTL analysis revealed 13 loci associated with nine traits. Five major-effect QTLs were detected for damage score (chromosome 6), nymphal survival (chromosome 12), and days to wilt (three QTLs on chromosome 4). We suggest involvement of four WBPH resistance genes in Sinna Sivappu, designated as wbph9(t), wbph10(t), wbph11(t), and Wbph12(t). One of the recessive genes could be allelic to any of the recessive genes reported in cluster C on chromosome 6 which might confer resistance to both BPH and WBPH. [ABSTRACT FROM AUTHOR]

An amendment to this paper has been published and can be accessed via a link at the top of the paper. [ABSTRACT FROM AUTHOR]

Tomato spotted wilt virus (TSWV) is a devastating disease to peanut growers in the South-eastern region of the United States. Newly released peanut cultivars in recent years are crucial as they have some levels of resistance to TSWV. One mapping population of recombinant inbred line (RIL) used in this study was derived from peanut lines of SunOleic 97R and NC94022. A whole genome re-sequencing approach was used to sequence these two parents and 140 RILs. A recombination bin-based genetic map was constructed, with 5,816 bins and 20 linkage groups covering a total length of 2004 cM. Using this map, we identified three QTLs which were colocalized on chromosome A01. One QTL had the largest effect of 36.51% to the phenotypic variation and encompassed 89.5 Kb genomic region. This genome region had a cluster of genes, which code for chitinases, strictosidine synthase-like, and NBS-LRR proteins. SNPs linked to this QTL were used to develop Kompetitive allele specific PCR (KASP) markers, and the validated KASP markers showed expected segregation of alleles coming from resistant and susceptible parents within the population. Therefore, this bin-map and QTL associated with TSWV resistance made it possible for functional gene mapping, map-based cloning, and marker-assisted breeding. This study identified the highest number of SNP makers and demonstrated recombination bin-based map for QTL identification in peanut. The chitinase gene clusters and NBS-LRR disease resistance genes in this region suggest the possible involvement in peanut resistance to TSWV. [ABSTRACT FROM AUTHOR]

Plant height is one of the most important architecture traits in crop plants. In peanut, the genetic basis of plant height remains ambiguous. In this context, we genotyped a recombinant inbred line (RIL) population with 140 individuals developed from a cross between two peanut varieties varying in plant height, Zhonghua 10 and ICG 12625. Genotyping data was generated for 1,175 SSR and 42 transposon polymorphic markers and a high-density genetic linkage map was constructed with 1,219 mapped loci covering total map length of 2,038.75 cM i.e., accounted for nearly 80% of the peanut genome. Quantitative trait locus (QTL) analysis using genotyping and phenotyping data for three environments identified 8 negative-effect QTLs and 10 positive-effect QTLs for plant height. Among these QTLs, 8 QTLs had a large contribution to plant height that explained ≥10% phenotypic variation. Two major-effect consensus QTLs namely cqPHA4a and cqPHA4b were identified with stable performance across three environments. Further, the allelic recombination of detected QTLs proved the existence of the phenomenon of transgressive segregation for plant height in the RIL population. Therefore, this study not only successfully reported a high-density genetic linkage map of peanut and identified genomic region controlling plant height but also opens opportunities for further gene discovery and molecular breeding for plant height in peanut. [ABSTRACT FROM AUTHOR]