Genomic-regions associated with cold stress tolerance in Asia-adapted tropical maize germplasm.

Maize is gaining impetus in non-traditional and non-conventional seasons such as off-season, primarily due to higher demand and economic returns. Maize varieties directed for growing in the winter season of South Asia must have cold resilience as an important trait due to the low prevailing temperatures and frequent cold snaps observed during this season in most parts of the lowland tropics of Asia. The current study involved screening of a panel of advanced tropically adapted maize lines to cold stress during vegetative and flowering stage under field conditions. A suite of significant genomic loci (28) associated with grain yield along and agronomic traits such as flowering (15) and plant height (6) under cold stress environments. The haplotype regression revealed 6 significant haplotype blocks for grain yield under cold stress across the test environments. Haplotype blocks particularly on chromosomes 5 (bin5.07), 6 (bin6.02), and 9 (9.03) co-located to regions/bins that have been identified to contain candidate genes involved in membrane transport system that would provide essential tolerance to the plant. The regions on chromosome 1 (bin1.04), 2 (bin 2.07), 3 (bin 3.05-3.06), 5 (bin5.03), 8 (bin8.05-8.06) also harboured significant SNPs for the other agronomic traits. In addition, the study also looked at the plausibility of identifying tropically adapted maize lines from the working germplasm with cold resilience across growth stages and identified four lines that could be used as breeding starts in the tropical maize breeding pipelines.

Genetic gains in tropical maize hybrids across moisture regimes with multi-trait-based index selection.

Unpredictable weather vagaries in the Asian tropics often increase the risk of a series of abiotic stresses in maize-growing areas, hindering the efforts to reach the projected demands. Breeding climate-resilient maize hybrids with a cross-tolerance to drought and waterlogging is necessary yet challenging because of the presence of genotype-by-environment interaction (GEI) and the lack of an efficient multi-trait-based selection technique. The present study aimed at estimating the variance components, genetic parameters, inter-trait relations, and expected selection gains (SGs) across the soil moisture regimes through genotype selection obtained based on the novel multi-trait genotype-ideotype distance index (MGIDI) for a set of 75 tropical pre-released maize hybrids. Twelve traits including grain yield and other secondary characteristics for experimental maize hybrids were studied at two locations. Positive and negative SGs were estimated across moisture regimes, including drought, waterlogging, and optimal moisture conditions. Hybrid, moisture condition, and hybrid-by-moisture condition interaction effects were significant (p ≤ 0.001) for most of the traits studied. Eleven genotypes were selected in each moisture condition through MGIDI by assuming 15% selection intensity where two hybrids, viz., ZH161289 and ZH161303, were found to be common across all the moisture regimes, indicating their moisture stress resilience, a unique potential for broader adaptation in rainfed stress-vulnerable ecologies. The selected hybrids showed desired genetic gains such as positive gains for grain yield (almost 11% in optimal and drought; 22% in waterlogging) and negative gains in flowering traits. The view on strengths and weaknesses as depicted by the MGIDI assists the breeders to develop maize hybrids with desired traits, such as grain yield and other yield contributors under specific stress conditions. The MGIDI would be a robust and easy-to-handle multi-trait selection process under various test environments with minimal multicollinearity issues. It was found to be a powerful tool in developing better selection strategies and optimizing the breeding scheme, thus contributing to the development of climate-resilient maize hybrids.

Rust (Uromyces viciae-fabae Pers. de-Bary) of Pea (Pisum sativum L.): Present Status and Future Resistance Breeding Opportunities.

Uromyces viciae-fabae Pers. de-Bary is an important fungal pathogen causing rust in peas (Pisum sativum L.). It is reported in mild to severe forms from different parts of the world where the pea is grown. Host specificity has been indicated in this pathogen in the field but has not yet been established under controlled conditions. The uredinial states of U. viciae-fabae are infective under temperate and tropical conditions. Aeciospores are infective in the Indian subcontinent. The genetics of rust resistance was reported qualitatively. However, non-hypersensitive resistance responses and more recent studies emphasized the quantitative nature of pea rust resistance. Partial resistance/slow rusting had been described as a durable resistance in peas. Such resistance is of the pre-haustorial type and expressed as longer incubation and latent period, poor infection efficiency, a smaller number of aecial cups/pustules, and lower units of AUDPC (Area Under Disease Progress Curve). Screening techniques dealing with slow rusting should consider growth stages and environment, as both have a significant influence on the disease scores. Our knowledge about the genetics of rust resistance is increasing, and now molecular markers linked with gene/QTLs (Quantitative Trait Loci) of rust resistance have been identified in peas. The mapping efforts conducted in peas came out with some potent markers associated with rust resistance, but they must be validated under multi-location trails before use in the marker-assisted selection of rust resistance in pea breeding programs.

Plasmid DNA Undergoes Two Compaction Regimes under Macromolecular Crowding.

The laser light scattering experiments were performed to explore the role of dextran (size (d): 2.6, 6.9, and 17.0 nm) in compacting the plasmids (pBS: 2.9 kbps; pCMV-Tag2B: 4.3 kbps; and pET28a: 5.3 kbps) in vitro in the volume fraction (ϕ) range 0.01 to 0.15 of the macromolecular crowder. Two compaction regimes were observed in terms of the radius of gyration (Rg) for plasmid-dextran combinations, wherein the plasmid diffusivity is governed by normal diffusion and subdiffusion, respectively. Generalized scaling, Rg ∼ ϕ-1/(1+x), where x represents the conformational geometry of plasmids, is reported. The plasmid conformation depends on the crowder's size, with larger conformational changes observed in the presence of smaller crowders. The second virial coefficient (A2) and translational diffusion coefficient (Dt) indicate that entropically driven depletion of crowders, excluded volume, and interplasmid repulsive interactions govern plasmids' conformational changes, validated herein from the scaling of Dt with molecular weight.

The catalytic core of Leishmania donovani RECQ helicase unwinds a wide spectrum of DNA substrates and is stimulated by replication protein A.

RecQ helicases are superfamily 2 (SF2) DNA helicases that unwind a wide spectrum of complex DNA structures in a 3' to 5' direction and are involved in maintaining genome stability. RecQ helicases from protozoan parasites have gained significant interest in recent times because of their involvement in cellular DNA repair pathways, making them important targets for drug development. In this study, we report biophysical and biochemical characterization of the catalytic core of a RecQ helicase from hemoflagellate protozoan parasite Leishmania donovani. Among the two putative RecQ helicases identified in L. donovani, we cloned, overexpressed and purified the catalytic core of LdRECQb. The catalytic core was found to be very efficient in unwinding a wide variety of DNA substrates like forked duplex, 3' tailed duplex and Holliday junction DNA. Interestingly, the helicase core also unwound blunt duplex with slightly less efficiency. The enzyme exhibited high level of DNA-stimulated ATPase activity with preferential stimulation by forked duplex, Holliday junction and 3' tailed duplex. Walker A motif lysine mutation severely affected the ATPase activity and significantly affected unwinding activity. Like many other RecQ helicases, L. donovani RECQb also possesses strand annealing activity. Unwinding of longer DNA substrates by LdRECQb catalytic core was found to be stimulated in the presence of replication protein A (LdRPA-1) from L. donovani. Detailed biochemical characterization and comparison of kinetic parameters indicate that L. donovani RECQb shares considerable functional similarity with human Bloom syndrome helicase.

Residues at the interface between zinc binding and winged helix domains of human RECQ1 play a significant role in DNA strand annealing activity.

RECQ1 is the shortest among the five human RecQ helicases comprising of two RecA like domains, a zinc-binding domain and a RecQ C-terminal domain containing the winged-helix (WH). Mutations or deletions on the tip of a ß-hairpin located in the WH domain are known to abolish the unwinding activity. Interestingly, the same mutations on the ß-hairpin of annealing incompetent RECQ1 mutant (RECQ1T1) have been reported to restore its annealing activity. In an attempt to unravel the strand annealing mechanism, we have crystallized a fragment of RECQ1 encompassing D2-Zn-WH domains harbouring mutations on the ß-hairpin. From our crystal structure data and interface analysis, we have demonstrated that an α-helix located in zinc-binding domain potentially interacts with residues of WH domain, which plays a significant role in strand annealing activity. We have shown that deletion of the α-helix or mutation of specific residues on it restores strand annealing activity of annealing deficient constructs of RECQ1. Our results also demonstrate that mutations on the α-helix induce conformational changes and affects DNA stimulated ATP hydrolysis and unwinding activity of RECQ1. Our study, for the first time, provides insight into the conformational requirements of the WH domain for efficient strand annealing by human RECQ1.

Genome-wide association mapping in maize: status and prospects.

Genome-wide association study (GWAS) provides a robust and potent tool to retrieve complex phenotypic traits back to their underlying genetics. Maize is an excellent crop for performing GWAS due to diverse genetic variability, rapid decay of linkage disequilibrium, availability of distinct sub-populations and abundant SNP information. The application of GWAS in maize has resulted in successful identification of thousands of genomic regions associated with many abiotic and biotic stresses. Many agronomic and quality traits of maize are severely affected by such stresses and, significantly affecting its growth and productivity. To improve productivity of maize crop in countries like India which contribute only 2% to the world's total production in 2019-2020, it is essential to understand genetic complexity of underlying traits. Various DNA markers and trait associations have been revealed using conventional linkage mapping methods. However, it has achieved limited success in improving polygenic complex traits due to lower resolution of trait mapping. The present review explores the prospects of GWAS in improving yield, quality and stress tolerance in maize besides, strengths and challenges of using GWAS for molecular breeding and genomic selection. The information gathered will facilitate elucidation of genetic mechanisms of complex traits and improve efficiency of marker-assisted selection in maize breeding. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-021-02799-4.

Potential and safe utilization of Fly ash as fertilizer for Pisum sativum L. Grown in phytoremediated and non-phytoremediated amendments.

The present study focuses on the possibility of applying fly ash to agricultural fields for enhancing the production of agricultural crops. In this study, Pisum sativum L. was grown from germination stage to maturation stage in phytoremediated and non-phytoremediated or raw fly ash-amended soil. All the morphological (height, biomass, number of leaf, and leaf size) and physiological parameters like, protein content, chlorophyll content, nitrate reductase activity, and peroxidase activity were monitored to understand the effects of fly ash or its usefulness for using it as a fertilizer for facilitating micronutrients. Major finding of this study is that 40% (w/w) of non-phytoremediated fly ash amendment could be used for field application. Percentage increase of toxic metals in below ground organs was 6% for Cd, 6% for Cr, 5% for Cu, 15% for Mn, and 7% for Pb when compared with the control. In the non-phytoremediated fly ash-amended set, heavy metals and metalloids were present in the grains only at higher amendments T3 (60%) and T4 (80%). However, except Cd, all the metals were below the permissible limits suggested by the WHO. Phytoremediated fly ash could be used as a fertilizer up to 100% for the cultivation of pea plant as metals concentrations were found either below detection limit or below the WHO permissible limit.

Repulsive interaction induces fibril formation and their growth.

In a type-II diabetes disease, amylin protein takes an incorrect structure that leads to the formation of the amyloid fibril. The conversion mechanism of amyloid fibril is not well understood. We have observed a repulsive interaction, in terms of second virial co-efficient (A2), between protein molecules in their native state in the PBS buffer through laser light scattering technique. The A2 switches from repulsive (positive A2) to attractive (negative A2) interactions with elapsed time favoring the formation and growth of the fibril. We report aggregation and fibril growth kinetics of amylin protein in different environmental conditions. The measurement of shape factor (ρ) through light scattering experiment shows a transition from coil-like structure to rod-like growth. In addition to rod-like growth, sheet-like growth of fibril is also observed through analytical and high-resolution TEM imaging techniques. The nucleation leading to elongation of fibrils as well as stacking of individual fibril perpendicular to the fibril axis is held by hydrogen bonding observed through high-resolution TEM.

Effect of two biodegradable chelates on metals uptake, translocation and biochemical changes of Lantana Camara growing in fly ash amended soil.

The present work had two purposes firstly to evaluate the potential of Lantana Camara for phytoextraction of heavy metals from fly ash amended soil and to assess the suitability of a proper biodegradable chelating agent for chelate assisted phytoextraction. Plants were grown in manure mixed soil amended with various concentration of fly ash. Two biodegradable chelating agents were added (EDDS and MGDA) in the same dose separately before maturation stage. Sampling was done at different growing stages. The plant took up metal in different plant parts in the following order: for Cu, and Zn leaf >root >stem, for Cr and Mn leaf>stem >root, for Ni root >leaf>stem and for Pb root≈leaf>stem respectively. For Cu, Zn, Cr and Mn Lantana camara acted as phytoextractor. Translocation factor and bioaccumulation coefficient was>1 signifying enrichment and translocation of metals in the plant. Morphological studies showed no toxicity symptom in the plant. Among biochemical parameters protein and nitrate reductase activity decreased, whereas, chlorophyll and peroxidise activity increased with the growth stages. Finally, it was evident from the results that Lantana Camara can be used as efficient phytoextractor of metals, with proper harvesting cycle and both chelate were proved as effective chelators for phytoextraction of metals.

Metal phytoremediation potential of naturally growing plants on fly ash dumpsite of Patratu thermal power station, Jharkhand, India.

Three naturally growing plants Ipomoea carnea, Lantana camara, and Solanum surattense were found in fly ash dumpsite of Patratu thermal power station, Jharkhand, India. They were assessed for their metal uptake potential. The fly ash was slightly alkaline with very less nitrogen and organic carbon but enriched with phosphorus and heavy metals. Lantana camara and Ipomoea carnea showed good translocation from root to shoot for most of the metals except Mn and Pb. The order of metal accumulation in stem of both the plants were Fe(205mg/kg)>Mn(65mg/kg)>Cu(22.35mg/kg)>Pb(6.6mg/kg)>Cr(3.05mg/kg)>Ni(1 mg/kg)>Cd(0.5 mg/kg) and Fe(741 mg/kg)>Mn(154.05 mg/kg)>Cu(20.75 mg/kg)>Pb(6.75 mg/kg)>Ni(4.0 mg/kg)>Cr(3.3mg/kg)>Cd(0.05mg/kg), respectively. But Solanum surattense accumulated most of the metals in roots. The order was in the following order, Mn (382.2mg/kg) >Fe (264.1mg/kg) > Cu (25.35mg/kg) >Pb (5.95 mg/kg) > Ni (1.9 mg/kg) > Cr (1.8mg/kg) > Cd (0.55 mg/kg). The order of Bioconcentration factor (BCF) in root and shoot followed almost the same order as, Mn>Fe>Ni>Pb>Cu>Cr≈ Cd in all the three species. ANOVA showed significant variation in metal accumulation by root and stem between the species. Finally, it can be concluded that Solanum surattense can be used as phytostabilizer and other two species as phytoextractor of metal for fly ash dumpsite reclamation.