Publications

High-throughput sequencing technologies (HSTs) have revolutionized crop breeding. The advent of these technologies has enabled the identification of beneficial quantitative trait loci (QTL), genes, and alleles for crop improvement. Climate change have made a significant effect on the global maize yield. To date, the well-known omic approaches such as genomics, transcriptomics, proteomics, and metabolomics are being incorporated in maize breeding studies. These approaches have identified novel biological markers that are being utilized for maize improvement against various abiotic stresses. This review discusses the current information on the morpho-physiological and molecular mechanism of abiotic stress tolerance in maize. The utilization of omics approaches to improve abiotic stress tolerance in maize is highlighted. As compared to single approach, the integration of multi-omics offers a great potential in addressing the challenges of abiotic stresses of maize productivity.

The current pace of crop improvement is inadequate to feed the burgeoning human population by 2050. Higher, more stable, and sustainable crop production is required against a backdrop of drought stress, which causes significant losses in crop yields. Tailoring crops for drought adaptation may hold the key to address these challenges and provide resilient production systems for future harvests. Understanding the genetic and molecular landscape of the functionality of alleles associated with adaptive traits will make designer crop breeding the prospective approach for crop improvement. Here, we highlight the potential of genomics technologies combined with crop physiology for high-throughput identification of the genetic architecture of key drought-adaptive traits and explore innovative genomic breeding strategies for designing future crops.

Abstract Stable bacterial communities are essential for maintaining soil functions. However, the role of abundant and rare bacterial taxa in maintaining bacterial community stability remains controversial. To explore the relationship between abundant and rare taxa and bacterial community stability, we used high‐throughput sequencing technology and molecular ecological networks to characterize the distribution of abundant and rare bacterial taxa under different nitrogen (N) fertilization rates (0, 150, 200, and 250 kg N hm −2 ). Our findings revealed that rare taxa had much higher Simpson's diversity index values than abundant taxa. Moreover, rare taxa Simpson's diversity decreased with increasing N application, while bacterial community differences (Bray–Curtis distance dissimilarity) increased (i.e., bacterial community stability decreased with increasing N application). The network topology showed that rare sub‐communities had higher modularity and a greater proportion of positive links than abundant taxa. The rare bacterial Simpson's diversity was significantly and negatively correlated with bacterial community differences, no correlation occurred between abundant bacterial Simpson's diversity and bacterial community differences. This study underscores the importance of rare species in maintaining bacterial community stability. Consequently, when optimizing agricultural management practices to ensure the stability of bacterial communities and soil functions, it is crucial not only to concentrate consider the roles of abundant species involved in nutrient cycling but also to give greater consideration to the role of rare taxa.

The world population is expected to reach 9 billion by 2050 and food production to support this population needs to increase by at least 60% while maintaining the natural resource base and the environment (World Bank 2008). The decrease in productive arable land from urbanisation, the reduction in irrigable land due to water scarcity and groundwater salinisation, competition for use of crops for biofuels, and increasing cost of inputs (e.g. fertilizers, fuel, pesticides and herbicides) suggest that agriculture needs to be much more efficient in its use of land, water and energy in order to meet the food security requirements of the rising world population. This is true without the complicating factor of climate change. According to the World Development Report (World Bank 2010), food production will be required to increase by 1.8% per annum between 2005 and 2050 rather than 1% per annum if there were no impact of climate change. This puts tremendous pressure on dryland agriculture to increase the efficiency of use of precipitation and nutrients.

Summary Continuous rotation of rice with wheat in rice–wheat system has resulted in stagnant yields and reduced profit margins while deteriorating the soil health. Legume incorporation in existing rice–wheat rotations might be a viable option to improve soil health and productivity. We investigated the influence of puddled transplanted flooded rice and direct-seeded rice on weed dynamics, soil health, productivity, and profitability of post-rice wheat and chickpea grown under zero tillage and conventional tillage. The previous direct-seeded rice crop was either sown alone or intercropped with sesbania as brown manure. The experiment comprised different rice–wheat and rice–chickpea systems which had been in place for two years: with and without rice residue retention. The initial soil analysis indicated that the plots with sesbania brown manuring in direct-seeded rice had the lowest soil bulk density (17.2%) and highest soil porosity (19.3%). Zero tillage in wheat or chickpea in the plots previously cultivated with co-culture of sesbania and direct-seeded rice increased total soil organic carbon by 13–22% in both years. The plots with sesbania brown manuring in direct-seeded rice followed by zero till or conventional till wheat and the plots with direct-seeded rice followed by zero till wheat with rice residue retention recorded the greater concentrations of total nitrogen, available phosphorus, and exchangeable potassium. Zero tillage in wheat and chickpea in post-rice sesbania brown manuring plots produced 41% and 43% more grain yield than those in the puddled transplanted flooded rice with conventional tillage and had the highest profitability. Overall, the rice–chickpea systems had better soil health and profitability than rice–wheat cropping systems. In conclusion, direct-seeded rice intercropped with sesbania followed by wheat and chickpea under zero tillage suppressed weed flora and improved soil physical properties, nutrient availability, productivity, and profitability.

Tobacco (Nicotiana tabacum L.) plant height (PH) is a biologically important plant architecture trait linked to yield and controlled by polygenes. However, limited information is available on quantitative trait nucleotides (QTNs), alleles, and candidate genes. The plant height of 94 tobacco accessions and their 126,602 SNPs were measured to conduct a genome-wide association study (GWAS) using four multi-locus (ML) and two single-locus (SL) models to better understand its genetic basis. The ML and SL models detected 181 and 29 QTNs, respectively, across four environments/BLUP; LOD scores ranged from 3.01–13.45, and the phenotypic variance explained (PVE) ranged from 0.69–25.37%. Fifty-two novel, stable QTNs were detected across at least two methods and/or two environments/BLUP, with 0.64–24.76% PVE. Among these, 49 QTNs exhibited significant phenotypic differences between two alleles; the distribution of elite and alternative alleles for each accession ranged from 3–42 and 6–46, respectively, in the mapping population. Seven cross combinations in two directions were predicted using alleles of validated QTNs, including Qinggeng × KY14 for taller plants and RG112 × VA115 for shorter plants. We identified 27 candidate genes in the vicinity of 49 stable QTNs based on comparative genomics, gene ontology (GO), and KEGG enrichment analysis, including AP2, Nitab4.5_0000343g0250.1 (ROC1), Nitab4.5_0000197g0010.1 (VFB1), CDF3, AXR6, KUP8, and NPY2. This is the first study to use genotyping-by-sequencing (GBS) of SNPs to determine QTNs, potential candidate genes, and alleles associated with plant height. These findings could provide a new avenue for investigating the QTNs in tobacco by combining SL and ML association mapping and solid foundations for functional genomics, the genetic basis, and molecular breeding for PH in tobacco.

Plant growth and development is dependent on a plant’s ability to convert light energy into usable chemical energy during a process termed photosynthesis. However, temperatures above that optimum for growth (heat stress) may injure and/or irreversibly damage photosynthetic machinery, pigments, and metabolites including photosynthetic enzymes, as well as the stomata (Xu et al. 1995; Sairam et al. 2000; Farooq et al. 2011). Heat stress disrupts the integrity of thylakoid membranes, thus inhibiting the activities of membrane-associated electron carriers and enzymes (Rexroth et al. 2011), which reduces the rate of photosynthesis.