Following the milestone success of the Human Genome Project, the ‘Encyclopedia of DNA Elements (ENCODE)’ initiative was launched in 2003 to unearth information about the numerous functional elements within the genome. This endeavor coincided with the emergence of numerous novel technologies, accompanied by the provision of vast amounts of whole-genome sequences, high-throughput data such as ChIP-Seq and RNA-Seq. Extracting biologically meaningful information from this massive dataset has become a critical aspect of many recent studies, particularly in annotating and predicting the functions of unknown genes. The core idea behind genome annotation is to identify genes and various functional elements within the genome sequence and infer their biological functions. Traditional wet-lab experimental methods still rely on extensive efforts for functional verification. However, early bioinformatics algorithms and software primarily employed shallow learning techniques; thus, the ability to characterize data and features learning was limited. With the widespread adoption of RNA-Seq technology, scientists from the biological community began to harness the potential of machine learning and deep learning approaches for gene structure prediction and functional annotation. In this context, we reviewed both conventional methods and contemporary deep learning frameworks, and highlighted novel perspectives on the challenges arising during annotation underscoring the dynamic nature of this evolving scientific landscape.

The plant-specific SHI-related sequence (SRS) family of transcription factors plays a vital role in growth regulation, plant development, phytohormone biosynthesis, and stress response. However, the genome-wide identification and role in the abiotic stress-related functions of the SRS gene family were not reported in white sweet clover (Melilotus albus). In this study, nine M. albus SRS genes (named MaSRS01-MaSRS09) were identified via a genome-wide search method. All nine genes were located on six out of eight chromosomes in the genome of M. albus and duplication analysis indicated eight segmentally duplicated genes in the MaSRS family. These MaSRS genes were classified into six groups based on their phylogenetic relationships. The gene structure and motif composition results indicated that MaSRS members in the same group contained analogous intron/exon and motif organizations. Further, promoter region analysis of MaSRS genes uncovered various growth, development, and stress-responsive cis-acting elements. Protein interaction networks showed that each gene has both functions of interacting with other genes and members within the family. Moreover, real-time quantitative PCR was also performed to verify the expression patterns of nine MaSRS genes in the leaves of M. albus. The results showed that nine MaSRSs were up- and down-regulated at different time points after various stress treatments, such as salinity, low-temperature, salicylic acid (SA), and methyl jasmonate (MeJA). This is the first systematic study of the M. albus SRS gene family, and it can serve as a strong foundation for further elucidation of the stress response and physiological improvement of the growth functions in M. albus.

Canola crop has the potential for both seeds and grazing. Optimal planting density, time of nitrogen (N) fertilizer application and rates are the major aspects for successful qualitative traits and canola yield formation. In this content, optimization of planting density, N levels and its time of application in dual purpose canola are needed. This study was carried out in RCB design with split pot arrangement having three repeats during winter 2012–2013 and 2013–2014. The study evaluated N levels (120 and 80 kg N ha⁻¹), cutting treatment, N application timings and planting density (20 and 40 plants m⁻²) effects on qualitative traits and yield of canola. No-cut treatment had 7.02%, 2.46%, and 4.26% higher, glucosinolates, oil, and protein content with 31.3% and 30.5% higher biological and grain yield respectively, compared with grazed canola. Compared with no-cut canola, grazed canola resulted in 7.74% of higher erucic acid. Further, application of N at 120 kg N ha⁻¹ had 8.81%, 5.52%, and 6.06% higher glucosinolates, percent protein, and seed yield, respectively than 80 kg N ha⁻¹. In-addition, the application of N into two splits was most beneficial than the rest application timings. Cutting had 15% reduction in grain yield of canola and fetched additional income of 143.6 USD compared with no-cut. Grazing resulted in a 23% reduction in grain yield while had additional income of 117.7 USD from fodder yield. Conclusively, the application of N in two splits at 120 kg N ha⁻¹ combined with 20 plants m⁻² is a promising strategy to achieve good qualitative attributes and canola yield under dual purpose system.

Mulching and nitrogen (N) fertilization are the main drivers for sustainable crop production. The sole use of nitrogen fertilizer threatened both the physiology and production of maize in rain-fed areas. Therefore, we proposed that wheat straw mulching with N fertilization would increase maize yield by improving soil fertility, physiology, and nitrogen use efficiency. A two-year field study evaluated the effects of CK (control), N (nitrogen application at 172 kg ha⁻¹), HS (half wheat straw mulch, 2500 kg ha⁻¹), HS+N (half wheat straw, 2500 kg ha⁻¹ plus 172 kg N ha⁻¹), FS (full wheat straw, 5000 kg ha⁻¹), and FS+N (full wheat straw, 5000 kg ha⁻¹ plus 172 kg N ha⁻¹) on maize growth, physiology, and biochemistry. Compared with the control, the FS+N treatment resulted in the increase of 56% photosynthetic efficiency, 9.6% nitrogen use efficiency, 60% nitrogen uptake, 80% soluble sugar, 59% starches, 48% biomass, and 29% grain yield of maize. In addition, the FS+N regime increased 47%, 42%, and 106% of soil organic carbon and available P and N content in comparison with the control. Maize grain and biomass yields were positively correlated with N uptake, photosynthesis, soil organic carbon, and soil available N and P contents. Conclusively, the use of wheat straw at 5000 kg ha⁻¹, along with 172 kg N ha⁻¹, is a promising option for building a sustainable wheat–maize cropping system to achieve optimal crop yield and improved plant and soil health in a semi-arid region of China.

With the rapidly increasing world population and escalating food demand in the face of changing weather patterns, it is imperative to improve our understanding of how root functional traits enhance water acquisition and nutrient foraging for improved crop yields. Phosphorous (P) is poorly bioavailable element and essential for plant growth and development. Natural P reserves are very limited, and its availability is greatly influenced by several environmental factors, e.g., due to finite natural resources, soil pH, organic matter, and soluble complexes with cations (Al, Fe, and Ca); therefore, P limitation is a major factor that adversely affects crop production. To ensure an efficient and stable agricultural system, the establishment of P efficient crop production is inevitable. Plants have evolved different adaptability mechanisms to overcome these nutrient stresses. Low P adapted responses in plants are considered as an important trait for developing new lines with improved P acquisition, water uptake efficiency, and eventually protect roots from physical impedance. Previous studies showed that, modification in root architecture is potentially correlated with water, nutrient and phosphorus uptake. During P deficit condition, plant root undergoes several phenotypic (root hair density, cluster root, and lateral root) and biochemical modifications (citrate, malate, and acid phosphates secretion) leading to the solubilization and acquisition of unavailable P complexes in soil. This chapter reveals the biochemical, physiological, and molecular mechanisms of plant adaptive responses to low P availability. Moreover, this chapter proposes how plant competes with various abiotic stresses such as P deficiency, drought, and salinity. Screening of plants with superior root hair traits would be an important approach toward the development of P efficient crop varieties.