GWAS elucidated grain yield genetics in Indian spring wheat under diverse water conditions.

KEY MESSAGE: Underpinned natural variations and key genes associated with yield under different water regimes, and identified genomic signatures of genetic gain in the Indian wheat breeding program. A novel KASP marker for TKW under water stress was developed and validated. A comprehensive genome-wide association study was conducted on 300 spring wheat genotypes to elucidate the natural variations associated with grain yield and its eleven contributing traits under fully irrigated, restricted water, and simulated no water conditions. Utilizing the 35K Wheat Breeders' Array, we identified 1155 quantitative trait nucleotides (QTNs), with 207 QTNs exhibiting stability across diverse conditions. These QTNs were further delimited into 539 genomic regions using a genome-wide LD value of 3.0 Mbp, revealing pleiotropic control across traits and conditions. Sub-genome A was significantly associated with traits under irrigated conditions, while sub-genome B showed more QTNs under water stressed conditions. Favourable alleles with significantly associated QTNs were delineated, with a notable pyramiding effect for enhancing trait performance. Additionally, allele of only 921 QTNs significantly affected the population mean. Allele profiling highlighted C-306 as a most potential source of drought tolerance. Moreover, 762 genes overlapping significant QTNs were identified, narrowing down to 27 putative candidate genes overlapping 29 novel and functional SNPs expressing (≥ 0.5 tpm) relevance across various growth conditions. A new KASP assay was developed, targeting a gene TraesCS2A03G1123700 regulating thousand kernel weight under severe drought condition. Genomic selection models (GBLUP, BayesB, MxE, and R-Norm) demonstrated an average prediction accuracy of 0.06-0.58 across environments, indicating potential for trait selection. Retrospective analysis of the Indian wheat breeding program supported a genetic gain in GY at the rate of ca. 0.56% per breeding cycle, since 1960, supporting the identification of genomic signatures driving trait selection and genetic gain. These findings offer insight into improving the rate of genetic gain in wheat breeding programs globally.

Genome-wide association study identifies novel loci and candidate genes for rust resistance in wheat (Triticum aestivum L.).

BACKGROUND: Wheat rusts are important biotic stresses, development of rust resistant cultivars through molecular approaches is both economical and sustainable. Extensive phenotyping of large mapping populations under diverse production conditions and high-density genotyping would be the ideal strategy to identify major genomic regions for rust resistance in wheat. The genome-wide association study (GWAS) population of 280 genotypes was genotyped using a 35 K Axiom single nucleotide polymorphism (SNP) array and phenotyped at eight, 10, and, 10 environments, respectively for stem/black rust (SR), stripe/yellow rust (YR), and leaf/brown rust (LR). RESULTS: Forty-one Bonferroni corrected marker-trait associations (MTAs) were identified, including 17 for SR and 24 for YR. Ten stable MTAs and their best combinations were also identified. For YR, AX-94990952 on 1A + AX-95203560 on 4A + AX-94723806 on 3D + AX-95172478 on 1A showed the best combination with an average co-efficient of infection (ACI) score of 1.36. Similarly, for SR, AX-94883961 on 7B + AX-94843704 on 1B and AX-94883961 on 7B + AX-94580041 on 3D + AX-94843704 on 1B showed the best combination with an ACI score of around 9.0. The genotype PBW827 have the best MTA combinations for both YR and SR resistance. In silico study identifies key prospective candidate genes that are located within MTA regions. Further, the expression analysis revealed that 18 transcripts were upregulated to the tune of more than 1.5 folds including 19.36 folds (TraesCS3D02G519600) and 7.23 folds (TraesCS2D02G038900) under stress conditions compared to the control conditions. Furthermore, highly expressed genes in silico under stress conditions were analyzed to find out the potential links to the rust phenotype, and all four genes were found to be associated with the rust phenotype. CONCLUSION: The identified novel MTAs, particularly stable and highly expressed MTAs are valuable for further validation and subsequent application in wheat rust resistance breeding. The genotypes with favorable MTA combinations can be used as prospective donors to develop elite cultivars with YR and SR resistance.

Genome-wide identification of DCL, AGO, and RDR gene families in wheat (Triticum aestivum L.) and their expression analysis in response to heat stress.

Key components of the RNA interference (RNAi) pathway include the Dicer-like (DCL), Argonaute (AGO), and RNA-dependent RNA polymerase (RDR) gene families. While these components have been studied in various plant species, their functional validation in wheat remains unexplored particularly under heat stress. In this study, a comprehensive genome-wide analysis to identify, and characterize DCL, AGO, and RDR genes in wheat and their expression patterns was carried out. Using phylogenetic analysis with orthologous genes from Arabidopsis and rice, we identified a total of 82 AGO, 31 DCL, and 31 RDR genes distributed across the 21 chromosomes of wheat. To understand the regulatory network, a network analysis of miRNAs that target RNA-silencing genes was performed. Our analysis revealed that 13 miRNAs target AGO genes, 8 miRNAs target DCL genes, and 10 miRNAs target RDR genes at different sites, respectively. Additionally, promoter analysis of the RNA-silencing genes was done and identified the presence of 132 cis-elements responsive to stress and phytohormones. To examine their expression patterns, we performed RNA-seq analysis in the flag leaf samples of wheat exposed to both normal and heat stress conditions. To understand the regulation of RNA silencing, we experimentally analysed the transcriptional changes in response to gradient heat stress treatments. Our results showed constitutive expression of the AGO1, AGO9, and DCL2 gene families, indicating their importance in the overall biological processes of wheat. Notably, RDR1, known to be involved in small interfering RNA (siRNA) biogenesis, exhibited higher expression levels in wheat leaf tissues. These findings suggest that these genes may play a role in responses to stress in wheat, highlighting their significance in adapting to environmental challenges. Overall, our study provides additional knowledge to understand the mechanisms underlying heat stress responses and emphasizes the essential roles of these gene families in wheat. Supplementary Information: The online version contains supplementary material available at 10.1007/s12298-023-01362-0.

Influence of tillage and residue management practices on productivity, sustainability, and soil biological properties of rice-barley cropping systems in indo-gangetic plain of India.

Introduction: Conservation agriculture is a sustainable system of farming that safeguard and conserves natural resources besides enhancing crop production. The biological properties of soil are the most sensitive indicator to assess the short term impact of management practices such as tillage and residue incorporation. Methods: Nine treatments of tillage and residue management practices [Reduced till direct seeded rice-zero till barley (RTDSR-ZTB); RTDSR-ZTB-green gram residue (Gg); Zero till direct seeded rice-zero till barley-zero till green gram (ZTDSR-ZTB-ZTGg); RTDSR-ZTB + rice residue at 4 t ha 1 (RTDSR-ZTBRR4); RTDSR-ZTBRR6; un-puddled transplanted rice (UPTR)-ZTB-Gg; UPTR-ZTBRR4; UPTR-ZTBRR6, and puddled transplanted rice (PTR)-RTB] executed under fixed plot for five years on crop productivity and soil biological properties under rice-barley production system. Results: The shifting in either RTDSR or ZTDSR resulted in yield penalty in rice compared to PTR. The PTR recorded highest pooled grain yield of 3.61 ha-1. The rice grain yield reduced about 10.6% under DSR as compared to PTR. The ZTB along with residue treatments exhibited significantly higher grain yield over ZTB, and the RTDSR-ZTBRR6 registered highest pooled grain yield of barley. The system productivity (12.45 t ha-1) and sustainable yield index (0.87) were highest under UPTR-ZTBRR6. Biological parameters including microbial biomass carbon, soil respiration, microbial enzymes (Alkaline phosphatase, nitrate reductase and peroxidase), fluorescein diacetate hydrolysis, ergosterol, glomalin related soil proteins, microbial population (bacteria, fungi and actinobacteria) were found to be significantly (p < 0.05) effected by different nutrient management practices. Based on the PCA analysis, Fluorescein diacetate hydrolysis, microbial biomass carbon, soil respiration, nitrate reductase and fungi population were the important soil biological parameters indicating soil quality and productivity in present experiment. The results concluded that UPTR-ZTBRR6 was a more suitable practice for maintaining system productivity and soil biological health. Discussion: The understanding of the impact of different tillage and residue management practices on productivity, soil biological properties and soil quality index under rice-barley cropping system will help in determining the combination of best conservation agriculture practices for improved soil quality and sustainable production.

Unveiling the Wheat Microbiome under Varied Agricultural Field Conditions.

Wheat being the important staple food crop plays a significant role in nutritional security. A wide variety of microbial communities beneficial to plants and contributing to plant health and production are found in the rhizosphere. The wheat microbiome encompasses an extensive variety of microbial species playing a key role in sustaining the physiology of the crop, nutrient uptake, and biotic/abiotic stress resilience. This report presents wheat microbiome analysis under six different farm practices, namely, organic (Org), timely sown (TS), wheat after pulse crop (WAPC), temperature-controlled phenotyping facility (TCPF), maize-wheat cropping system (MW), and residue burnt field (Bur), using 16S rRNA sequencing methodology. The soil samples collected from either side of the wheat row were mixed to get a final sample set for DNA extraction under each condition. After the data preprocessing, microbial community analysis was performed, followed by functional analysis and annotation. An abundance of the phylum Proteobacteria was observed, followed by Acidobacteria, Actinobacteria, and Gemmatimonadetes in the majority of the samples, while relative abundance was found to vary at the genus level. Analysis against the Carbohydrate-Active Enzymes (CAZy) database showed a high number of glycoside hydrolase genes in the TS, TCPF, and WAPC samples, while the Org, MW, and Bur samples predominantly had glycosyltransferase genes and carbohydrate esterase genes were in the lowest numbers. Also, the Org and TCPF samples showed lower diversity, while rare and abundant species ranged from 12 to 25% and 20 to 32% of the total bacterial species in all the sets, respectively. These variations indicate that the different cropping sequence had a significant impact on soil microbial diversity and community composition, which characterizes its economic and environmental value as a sustainable agricultural approach to maintaining food security and ecosystem health. IMPORTANCE This investigation examined the wheat microbiome under six different agricultural field conditions to understand the role of cropping pattern on soil microbial diversity. This study also elaborated the community composition, which has importance in economic (role of beneficial community leading to higher production) and environmental (role of microbial diversity/community in safeguarding the soil health, etc.) arenas. This could lead to a sustainable farming approach for food security and improved ecosystem health. Also, the majority of the microbes are unculturable; hence, technology-based microcultivation will be a potential approach for harnessing other cultured microorganisms, leading to unique species for commercial production. The outcome of this research-accelerated work can provide an idea to the scientists/breeders/agronomists/pathologists under the mentioned field conditions regarding their influence over their crops.

Wheat endophytes and their potential role in managing abiotic stress under changing climate.

Wheat (Triticum aestivum L.) cultivation differs considerably in respect of soil type, temperature, pH, organic matter, moisture regime, etc. Among these, rising atmospheric temperature due to global warming is most important as it affects grain yield drastically. Studies have shown that for every 1°C rise in temperature above wheat's optimal growing temperature range of 20-25°C, there is a decrease in 2.8 days and 1.5 mg in the grain filling period and kernel weight, respectively, resulting in wheat yield reduction by 4-6 quintal per hectare. Growing demand for food and multidimensional issues of global warming may further push wheat crop to heat stress environments that can substantially affect heading duration, percent grain setting, maturity duration, grain growth rate and ultimately total grain yield. Considerable genetic variation exists in wheat gene pool with respect to various attributes associated with high temperature and stress tolerance; however, only about 15% of the genetic variability could be incorporated into cultivated wheat so far. Thus, alternative strategies have to be explored and implemented for sustainable, more productive and environment friendly agriculture. One of the feasible and environment friendly option is to look at micro-organisms that reside inside the plant without adversely affecting its growth, known as 'endophytes', and these colonize virtually all plant organs such as roots, stems, leaves, flowers and grains. The relationship between plant and endophytes is vital to the plant health, productivity and overall survival under abiotic stress conditions. Thus, it becomes imperative to enlist the endophytes (bacterial and fungal) isolated till date from wheat cultivars, their mechanism of ingression and establishment inside plant organs, genes involved in ingression, the survival advantages they confer to the plant under abiotic stress conditions and the potential benefits of their use in sustainable wheat cultivation.

Screening of biological, morphological, and molecular characteristics of single-spore isolate collections of the straw mushroom, Volvariella volvacea (higher Basidiomycetes) from India.

Of the 2 parent strains and 6 single-spore isolates (SSIs) used in this study, the SSIs BBSR-007 and BBSR-002 of the culinary-medicinal straw mushroom Volvariella volvacea exhibited superior growth characteristics on different growth media. These also took less time until first harvest (days after spawning), gave higher numbers of fruiting bodies per unit weight of substrate, and provided a higher mushroom yield on composted substrate. The fruiting body weight of isolate BBSR-007 was significantly higher compared to BBSR-002. On pasteurized paddy straw, the SSI BBSR-007 had a higher mushroom yield than BBSR-002. The contents of dry matter, protein, and other elements (sodium, potassium, and calcium) were on par in both the parent strains and different SSIs, except SSI OE-55-08, which had highest dry matter, protein content, and potassium/-to-odium ratio. In amplified ribosomal DNA restriction analysis, the SSIs did not show any distinctness, whereas in amplified fragment length polymorphism, the SSI OE-55-08 of parent strain OE-55 formed a separate clade; of 4 SSIs of strain OE-274, the SSI BBSR-003 formed a separate clade than other SSIs. The genetically distinct SSI OE-55-08 produced the highest numbers of fruit bodies per unit weight of substrate and exhibited the highest amounts of dry matter and protein in its fruit bodies. Another slightly distinct SSI, BBSR-003, formed white aerial mycelia on growth substrate, and its fruit bodies exhibited the highest levels of sodium and calcium.