Genome-wide association study of fiber yield-related traits uncovers the novel genomic regions and candidate genes in Indian upland cotton (Gossypium hirsutum L.).

Upland cotton (Gossypium hirsutum L.) is a major fiber crop that is cultivated worldwide and has significant economic importance. India harbors the largest area for cotton cultivation, but its fiber yield is still compromised and ranks 22nd in terms of productivity. Genetic improvement of cotton fiber yield traits is one of the major goals of cotton breeding, but the understanding of the genetic architecture underlying cotton fiber yield traits remains limited and unclear. To better decipher the genetic variation associated with fiber yield traits, we conducted a comprehensive genome-wide association mapping study using 117 Indian cotton germplasm for six yield-related traits. To accomplish this, we generated 2,41,086 high-quality single nucleotide polymorphism (SNP) markers using genotyping-by-sequencing (GBS) methods. Population structure, PCA, kinship, and phylogenetic analyses divided the germplasm into two sub-populations, showing weak relatedness among the germplasms. Through association analysis, 205 SNPs and 134 QTLs were identified to be significantly associated with the six fiber yield traits. In total, 39 novel QTLs were identified in the current study, whereas 95 QTLs overlapped with existing public domain data in a comparative analysis. Eight QTLs, qGhBN_SCY_D6-1, qGhBN_SCY_D6-2, qGhBN_SCY_D6-3, qGhSI_LI_A5, qGhLI_SI_A13, qGhLI_SI_D9, qGhBW_SCY_A10, and qGhLP_BN_A8 were identified. Gene annotation of these fiber yield QTLs revealed 2,509 unique genes. These genes were predominantly enriched for different biological processes, such as plant cell wall synthesis, nutrient metabolism, and vegetative growth development in the gene ontology (GO) enrichment study. Furthermore, gene expression analysis using RNAseq data from 12 diverse cotton tissues identified 40 candidate genes (23 stable and 17 novel genes) to be transcriptionally active in different stages of fiber, ovule, and seed development. These findings have revealed a rich tapestry of genetic elements, including SNPs, QTLs, and candidate genes, and may have a high potential for improving fiber yield in future breeding programs for Indian cotton.

Different GCMs yet similar outcome: predicting the habitat distribution of Shorea robusta C.F. Gaertn. in the Indian Himalayas using CMIP5 and CMIP6 climate models.

Climate change impact on the habitat distribution of umbrella species presents a critical threat to the entire regional ecosystem. This is further perilous if the species is economically important. Sal (Shorea robusta C.F. Gaertn.), a climax forest forming Central Himalayan tree species, is one of the most valuable timber species and provides several ecological services. Sal forests are under threat due to over-exploitation, habitat destruction, and climate change. Sal's poor natural regeneration and its unimodal density-diameter distribution in the region illustrate the peril to its habitat. We, modelled the current as well as future distribution of suitable sal habitats under different climate scenarios using 179 sal occurrence points and 8 bioclimatic environmental variables (non-collinear). The CMIP5-based RCP4.5 and CMIP6-based SSP245 climate models under 2041-2060 and 2061-2080 periods were used to predict the impact of climate change on sal's future potential distribution area. The niche model results predict the mean annual temperature and precipitation seasonality as the most influential sal habitat governing variables in the region. The current high suitability region for sal was 4.36% of the total geographic area, which shows a drastic decline to 1.31% and 0.07% under SSP245 for 2041-60 and 2061-80, respectively. The RCP-based models predicted more severe impact than SSP; however, both RCP and SSP models showed complete loss of high suitability regions and overall shift of species northwards in the Uttarakhand state. We could identify the current and future suitable habitats for conserving sal population through assisted regeneration and management of other regional issues.

Morpho-physiological and demographic responses of three threatened Ilex species to changing climate aligned with species distribution models in future climate scenarios.

The success of a species in future climate change scenarios depends on its morphological, physiological, and demographic adaptive responses to changing climate. The existence of threatened species against climate adversaries is constrained due to their small population size, narrow genetic base, and narrow niche breadth. We examined if ecological niche model (ENM)-based distribution predictions of species align with their morpho-physiological and demographic responses to future climate change scenarios. We studied three threatened Ilex species, viz., Ilex khasiana Purkay., I. venulosa Hook. f., and I. embelioides Hook. F, with restricted distribution in Indo-Burma biodiversity hotspot. Demographic analysis of the natural populations of each species in Meghalaya, India revealed an upright pyramid suggesting a stable population under the present climate scenario. I. khasiana was confined to higher elevations only while I. venulosa and I. embelioides had wider altitudinal distribution ranges. The bio-climatic niche of I. khasiana was narrow, while the other two species had relatively broader niches. The ENM-predicted potential distribution areas under the current (2022) and future (2050) climatic scenarios (General Circulation Models (GCMs): IPSL-CM5A-LR and NIMR-HADGEM2-AO) revealed that the distribution of highly suitable areas for the most climate-sensitive I. khasiana got drastically reduced. In I. venulosa and I. embelioides, there was an increase in highly suitable areas under the future scenarios. The eco-physiological studies showed marked variation among the species, sites, and treatments (p < 0.05), indicating the differential responses of the three species to varied climate scenarios, but followed a similar trend in species performance aligning with the model predictions.

Bioclimatic modeling and FACE study forecast a bleak future for wheat production in India.

Since the impact of future climate change on wheat productivity is inconsistent, we studied geographic distribution and yield of wheat using two global General Circulation Models (GCMs) and Free Air CO2/O3 Enrichment (FACE) experiments. The GCMs (IPSL-CM5A-LR and NIMR-HADGEM2-AO) with four Representative Concentration Pathways (RCPs) and 19 bioclimatic variables were used for distribution/ecological niche modeling (ENM). Currently cultivated eight wheat cultivars were exposed to individual treatment of (i) ambient CO2, temperature, and ozone (ACO + AO + AT) representing the present climate scenario, and (ii) elevated CO2 (550 ppm) (ECO), (iii) elevated temperature (+ 2 °C) (ET), (iv) elevated O3 (ambient + 20 ppb) (EO), (v) elevated CO2 + elevated O3 (ECO + EO), and (vi) elevated CO2 + elevated temperature + elevated O3 (ECO + EO + ET) under FACE facility simulating the future climate change scenarios in 2050. The niche models predicted a reduction in climatically suitable areas for wheat, and identified "maximum temperature" as the most influencing factor for area reduction. The elevated CO2, O3, and temperature individually and in combinations had differential impacts on the yield of wheat cultivars. Only two cultivars, viz., DBW 184 and DBW 187 did not exhibit yield decline suggesting their suitability in the future climate change scenario. Since the performance of six out of eight cultivars significantly declined under simulated FACE experiment, and ENM predicted reduction in wheat cultivation area under RCP 8.5 in 2050, it was concluded that future of wheat cultivation in India is bleak. The study further indicates that coupling of bioclimatic modeling and FACE experiment can effectively predict the impact of climate change on different crops.

Evolution of novel strains of Ensifer nodulating the invasive legume Leucaena leucocephala (Lam.) de Wit in different climatic regions of India through lateral gene transfer.

More than 200 root-nodule bacterial strains were isolated from Leucaena leucocephala growing at 42 sampling sites across 12 states and three union territories of India. Genetic diversity was observed among 114 strains from various climatic zones; based on recA, these were identified as strains of Ensifer, Mesorhizobium, Rhizobium, and Bradyrhizobium. In multilocus sequence analysis (MLSA) strains clustered into several novel clades and lineages. Ensifer were predominant nodulating genotype isolated from majority of alkaline soils, while Mesorhizobium and Rhizobium strains were isolated from a limited sampling in North-Eastern states with acidic soils. Positive nodulation assays of selected Ensifer representing different genetic combinations of housekeeping and sym genes suggested their broad host range within the closely related mimosoid genera Vachellia, Senegalia, Mimosa, and Prosopis. Leucaena selected diverse strains of Ensifer and Mesorhizobium as symbionts depending on available soil pH, climatic, and other edaphic conditions in India. Lateral gene transfer seems to play a major role in genetic diversification of Ensifer exhibited in terms of Old World vs. Neotropical genetic make-up and mixed populations at several sites. Although Neotropical Ensifer strains were most symbiotically effective on Leucaena, the native Ensifer are promiscuous and particularly well-adapted to a wide range of sampling sites with varied climates and edaphic factors.

Chloroplast Genome of Lithocarpus dealbatus (Hook.f. & Thomson ex Miq.) Rehder Establishes Monophyletic Origin of the Species and Reveals Mutational Hotspots with Taxon Delimitation Potential

There is phylogenetic ambiguity in the genus Lithocarpus and subfamily Quercoideae (Family: Fagaceae). Lithocarpus dealbatus, an ecologically important tree, is the dominant species among the Quercoideae in India. Although several studies have been conducted on the species' regeneration and ecological and economic significance, limited information is available on its phylo-genomics. To resolve the phylogeny in Quercoideae, we sequenced and assembled the 161,476 bp chloroplast genome of L. dealbatus, which has a large single-copy section of 90,732 bp and a small single-copy region of 18,987 bp, separated by a pair of inverted repeat regions of 25,879 bp. The chloroplast genome contained 133 genes, of which 86 were protein-coding genes, 39 were transfer RNAs, and eight were ribosomal RNAs. Analysis of repeat elements and RNA editing sites revealed interspecific similarities within the Lithocarpus genus. DNA diversity analysis identified five highly diverged coding and noncoding hotspot regions in the four genera, which can be used as polymorphic markers for species/taxon delimitation across the four genera of Quercoideae viz., Lithocarpus, Quercus, Castanea, and Castanopsis. The chloroplast-based phylogenetic analysis among the Quercoideae established a monophyletic origin of Lithocarpus, and a closer evolutionary lineage with a few Quercus species. Besides providing insights into the chloroplast genome architecture of L. dealbatus, the study identified five mutational hotspots having high taxon-delimitation potential across four genera of Quercoideae.

Impact of heavy metals on water quality and indigenous Bacillus spp. prevalent in rat-hole coal mines.

The present study reports pollution evaluation indices employed to assess the intensity of metal pollution in water systems affected by acid mine drainage from rat-hole coal mines prevalent in North-east India. The concentration of seven eco-toxic metals was evaluated from coal mine waters which showed concentration order of Iron (Fe) > Manganese (Mn) > Zinc (Zn) > Chromium (Cr) > Lead (Pb) > Copper (Cu) > Cadmium (Cd). The water samples were acidic with mean pH 2.67 and burdened with dissolved solids (924.8 mg/L). The heavy metal pollution index (HPI) and heavy metal evaluation index (HEI) displayed high and medium range of pollution level in majority of the water samples. Statistical correlation suggested strong positive correlation between metals such as Cr with Mn (r = 0.780), Mn with Fe (r = 0.576), Cr with Fe (r = 0.680), Pb with Mn (r = 0.579) and Cr with Pb (r = 0.606), indicating Mn, Pb, Fe and Cr to be major metal contaminants; an unequivocal affirmation of degradation in water quality. The sampled waters had lower heavy metal concentration during monsoon and post-monsoon seasons. The commonly occurring bacterial species Bacillus pseudomycoides and Bacillus siamensis were chosen to understand their behavioral responses toward metal contamination. Findings demonstrated that Bacillus spp. from control environment had low tolerance to metals stress as evident from their MTC, MIC and growth curve studies. The survival of the native isolates across varying pH, salinity and temperature in the coal mine areas suggest these isolates as promising candidates for reclamation of rat-hole coal mining sites.

Chemodiversity and molecular variability in the natural populations (India) of Gloriosa superba (L.) and correlation with eco- geographical factors for the identification of elite chemotype(s).

Gloriosa superba L. has economic significance due to colchicine, a bioactive compound used for gout. In present study metabolic and molecular variability in natural population of species was analyzed and correlated with edaphic and climatic factors. Thirty populations (wild) of G. superba were mapped from 10 different eco-regions of India at an elevation range of 10-1526 m, having no morphotypic variations. The two known biologically active alkaloids colchicine (ranged from 0.015-0.516%) and gloriosine (0.19-0.44%) were significantly varied (p < 0.05) among populations, leading to the identification of four elite chemotypes. Molecular variability from ISSR data divides the population in different sub clusters at intra-specific level, presenting the high similarity percentage with bootstrap value of 66-100%. Principal component analysis (PCA) revealed that elite chemotypes are related to temperature, precipitation and aridity gradient. The rhizospheric soil selenium was significantly correlated with colchicine content in G. superba.

The dark cloud with a silver lining: Assessing the impact of the SARS COVID-19 pandemic on the global environment.

The Severe Acute Respiratory Syndrome-Coronavirus Disease 2019 (COVID-19) pandemic caused by a novel coronavirus known as SARS-CoV-2 has caused tremendous suffering and huge economic losses. We hypothesized that extreme measures of partial-to-total shutdown might have influenced the quality of the global environment because of decreased emissions of atmospheric pollutants. We tested this hypothesis using satellite imagery, climatic datasets (temperature, and absolute humidity), and COVID-19 cases available in the public domain. While the majority of the cases were recorded from Western countries, where mortality rates were strongly positively correlated with age, the number of cases in tropical regions was relatively lower than European and North American regions, possibly attributed to faster human-to-human transmission. There was a substantial reduction in the level of nitrogen dioxide (NO2: 0.00002 mol m-2), a low reduction in CO (<0.03 mol m-2), and a low-to-moderate reduction in Aerosol Optical Depth (AOD: ~0.1-0.2) in the major hotspots of COVID-19 outbreak during February-March 2020, which may be attributed to the mass lockdowns. Our study projects an increasing coverage of high COVID-19 hazard at absolute humidity levels ranging from 4 to 9 g m-3 across a large part of the globe during April-July 2020 due to a high prospective meteorological suitability for COVID-19 spread. Our findings suggest that there is ample scope for restoring the global environment from the ill-effects of anthropogenic activities through temporary shutdown measures.

Ecological niche modeling as a cumulative environmental impact assessment tool for biodiversity assessment and conservation planning: A case study of critically endangered plant Lagerstroemia minuticarpa in the Indian Eastern Himalaya.

Cumulative environmental impact assessment (CEIA) at river basin level for hydroelectric projects is an evolving concept and has proved to be a useful tool to assess the cumulative impact of developmental projects on the natural ecosystems. However, the generality of CEIA studies is often contested because of methodological limitations, especially in the domain of biodiversity conservation and conservation planning. Ecological niche modeling (ENM) can be a useful tool in CEIA studies for conservation planning of threatened plants in hydroelectric project (HEP) areas. We elucidate this hypothesis taking the example of Lagerstroemia minuticarpa Debberm. ex P.C. Kanjilal, a critically endangered tree species in the Indian Eastern Himalaya. Standard ecological methods were employed to document occurrence records, estimate population size, and characterize habitats. ENM was used to estimate the species potential environmental niche and distribution areas. The possible impacts of HEPs on the potential habitats were predicted by overlaying the HEPs on the potential area map as well as using the conceptual network diagram. The study revealed that the species occupies an environmental niche characterized by humid to per-humid conditions, and is distributed mostly in the Lohit and Teesta basins. Potential areas of the species with high environmental suitability coincide with 19 HEPs, which point to a potential threat to the survival of the species. Network diagram indicated that project activities might deteriorate the habitats thereby affecting the population and regeneration of the species. Our study provides a framework for developing appropriate measures for species conservation and reintroduction at basin level using ENM.

Selection of Bradyrhizobium or Ensifer symbionts by the native Indian caesalpinioid legume Chamaecrista pumila depends on soil pH and other edaphic and climatic factors.

Nodules of Chamaecrista pumila growing in several locations in India were sampled for anatomical studies and for characterization of their rhizobial microsymbionts. Regardless of their region of origin, the nodules were indeterminate with their bacteroids contained within symbiosomes which were surrounded by pectin. More than 150 strains were isolated from alkaline soils from the Thar Desert (Rajasthan), wet-acidic soils of Shillong (Meghalaya), and from trap experiments using soils from four other states with different agro-ecological regions. Molecular phylogenetic analysis based on five housekeeping (rrs, recA, glnII, dnaK andatpD) and two symbiotic (nodA and nifH) genes was performed for selected strains. Chamaecrista pumila was shown to be nodulated by niche-specific diverse strains of either Ensifer or Bradyrhizobium in alkaline (Thar Desert) to neutral (Tamil Nadu) soils and only Bradyrhizobium strains in acidic (Shillong) soils. Concatenated core gene phylogenies showed four novel Ensifer-MLSA types and nine Bradyrhizobium-MLSA types. Genetically diverse Ensifer strains harbored similar sym genes which were novel. In contrast, significant symbiotic diversity was observed in the Bradyrhizobium strains. The C. pumila strains cross-nodulated Vigna radiata and some wild papilionoid and mimosoid legumes. It is suggested that soil pH and moisture level played important roles in structuring the C. pumila microsymbiont community.

Microenvironmental heterogeneity caused by anthropogenic LULC foster lower plant assemblages in the riparian habitats of lentic systems in tropical floodplains.

Anthropogenic land use and land cover (LULC) create a heterogeneous environment in the floodplains. This heterogeneity may be governing plant species assemblages, diversity, and dominance patterns in the riparian habitats of the lentic systems in tropical floodplains. We tested this hypothesis in the floodplains of Barak river basin in northeast India following standard methods of plant and soil sampling/analysis and multivariate statistical tools. Plant community studies in the riparian habitats of the selected lentic systems were done at monthly intervals for a period of one year, while soil sampling and analysis were done at bimonthly intervals. Standard data visualization plots and canonical correspondence analysis (CCA) were used to assess spatiotemporal variations in species richness and diversity, environmental heterogeneity, and species-environment association. The study revealed that anthropogenic land use and land cover significantly affects species assemblage, diversity, and dominance in the riparian habitats. The variations in vegetation structure and composition with respect to the adjoining land use type plausibly have implications on the structure and functioning of the lentic systems. Thus, the study recommends that a holistic approach involving the riparian areas is required for effective management of tropical floodplains.

Modelling Hotspots for Invasive Alien Plants in India.

Identification of invasion hotspots that support multiple invasive alien species (IAS) is a pre-requisite for control and management of invasion. However, till recently it remained a methodological challenge to precisely determine such invasive hotspots. We identified the hotspots of alien species invasion in India through Ecological Niche Modelling (ENM) using species occurrence data from the Global Biodiversity Information Facility (GBIF). The predicted area of invasion for selected species were classified into 4 categories based on number of model agreements for a region i.e. high, medium, low and very low. About 49% of the total geographical area of India was predicted to be prone to invasion at moderate to high levels of climatic suitability. The intersection of anthropogenic biomes and ecoregions with the regions of 'high' climatic suitability was classified as hotspot of alien plant invasion. Nineteen of 47 ecoregions of India, harboured such hotspots. Most ecologically sensitive regions of India, including the 'biodiversity hotspots' and coastal regions coincide with invasion hotspots, indicating their vulnerability to alien plant invasion. Besides demonstrating the usefulness of ENM and open source data for IAS management, the present study provides a knowledge base for guiding the formulation of an effective policy and management strategy for controlling the invasive alien species.