Over the past decades, numerous efforts were made towards the improvement of cereal crops mostly employing traditional or molecular breeding approaches. The current scenario made it possible to efficiently explore molecular understanding by targeting different genes to achieve desirable plants. To provide guaranteed food security for the rising world population particularly under vulnerable climatic condition, development of high yielding stress tolerant crops is needed. In this regard, technologies upgradation in the field of genome editing looks promising. Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 is a rapidly growing genome editing technique being effectively applied in different organisms, that includes both model and crop plants. In recent times CRISPR/Cas9 is being considered as a technology which revolutionized fundamental as well as applied research in plant breeding. Genome editing using CRISPR/Cas9 system has been successfully demonstrated in many cereal crops including rice, wheat, maize, and barley. Availability of whole genome sequence information for number of crops along with the advancement in genome-editing techniques provides several possibilities to achieve desirable traits. In this review, the options available for crop improvement by implementing CRISPR/Cas9 based genome-editing techniques with special emphasis on cereal crops have been summarized. Recent advances providing opportunities to simultaneously edit many target genes were also discussed. The review also addressed recent advancements enabling precise base editing and gene expression modifications. In addition, the article also highlighted limitations such as transformation efficiency, specific promoters and most importantly the ethical and regulatory issues related to commercial release of novel crop varieties developed through genome editing.

RNA-Seq technology was used to analyze the transcriptome of two rice hybrids, Ajay (based on wild-abortive (WA)-cytoplasm) and Rajalaxmi (based on Kalinga-cytoplasm), and their respective parents at the panicle initiation (PI) and grain filling (GF) stages. Around 293 and 302 million high quality paired-end reads of Ajay and Rajalaxmi, respectively, were generated and aligned against the Nipponbare reference genome. Transcriptome profiling of Ajay revealed 2814 and 4819 differentially expressed genes (DEGs) at the PI and GF stages, respectively, as compared to its parents. In the case of Rajalaxmi, 660 and 5264 DEGs were identified at PI and GF stages, respectively. Functionally relevant DEGs were selected for validation through qRT-PCR, which were found to be co-related with the expression patterns to RNA-seq. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated significant DEGs enriched for energy metabolism pathways, such as photosynthesis, oxidative phosphorylation, and carbon fixation, at the PI stage, while carbohydrate metabolism-related pathways, such as glycolysis and starch and sucrose metabolism, were significantly involved at the GF stage. Many genes involved in energy metabolism exhibited upregulation at the PI stage, whereas the genes involved in carbohydrate biosynthesis had higher expression at the GF stage. The majority of the DEGs were successfully mapped to know yield related rice quantitative trait loci (QTLs). A set of important transcription factors (TFs) was found to be encoded by the identified DEGs. Our results indicated that a complex interplay of several genes in different pathways contributes to higher yield and vigor in rice hybrids.

An immense increase in human population along with diminished lands necessitates the increase of rice production since, it serves the human population as a staple food. Though rice hybrids (RH) are showing considerable yield enhancement over inbreds in terms of both quality and quantity, farmers’ adoption of hybrid rice technology has been much slower than expected because of several constraints such as seed cost and quality. Doubled haploid (DH) technology was considered useful for the development of inbred lines from rice hybrids in a single generation. Androgenesis shows its significance in development of DHs in rice which requires an efficient method to establish the production of large population. To start the anther culture, anthers are the main component of androgenesis to be isolated from unopened spikes. However, the duration of spikes availability for anther culture coupled with the segregation of rice hybrids in the next generation requires the main crop be ratooned to reduce the cost of cultivation. Therefore, the efficiency of the androgenic method was tested in main crop using a quality indica rice hybrid, 27P63 and its ratooned ones. The effects of various factors such as cold temperature pre-treatment of boots, treatment duration, and different combination of plant growth regulators (PGR) on callus response along with shoot regeneration were tested for development of DHs from both ratooned and non-ratooned plants. The N6 medium supplemented with 2.0 mg/L 2,4-D (2,4-dichlrophenoxy acetic acid), 0.5 mg/L BAP (6-benzylamino purine), and 30 g/L maltose was found to be most effective for callusing as compared to MS (Murashige and Skoog) medium. The N6 media inducted calli showed maximum response rate for green shoot regeneration in MS media supplemented with 0.5 mg/L NAA (1-napthaleneacetic acid), 0.5 mg/L Kn (Kinetin; 6-furfurylaminopurine), 1.5 mg/L BAP and 30 g/L sucrose after 2 weeks of culture. The pre-treatment of spikes at 10 °C for 2 d followed by a 7th and 8th d were found to be most effective for callusing as well as for regeneration, producing a total of 343 green plants from ratooned and main rice hybrid, 27P63. Morpho-agronomic trait-based assessment of ploidy status revealed 94.46% diploids, 3.49% polyploids, 0.58% mixploids, and 1.45% haploids. Microsatellite markers could authenticate all 324 fertile diploids as true DHs. Though this study shows a reduction in generation of DHs from ratooned plants as compared to the main crop, manipulation of chemical factors could optimize the method to enhance the production of considerable number of DHs. Utilization of ratooned of hybrid rice in androgenesis would save time and cost of cultivation.

The cytochrome P450 (CYP450) gene family plays a critical role in plant growth and developmental processes, nutrition, and detoxification of xenobiotics in plants. In the present research, a comprehensive set of 105 OsCYP71 family genes was pinpointed within the genome of indica rice. These genes were categorized into twelve distinct subfamilies, where members within the same subgroup exhibited comparable gene structures and conserved motifs. In addition, 105 OsCYP71 genes were distributed across 11 chromosomes, and 36 pairs of OsCYP71 involved in gene duplication events. Within the promoter region of OsCYP71, there exists an extensive array of cis-elements that are associated with light responsiveness, hormonal regulation, and stress-related signaling. Further, transcriptome profiling revealed that a majority of the genes exhibited responsiveness to hormones and were activated across diverse tissues and developmental stages in rice. The OsCYP71P6 gene is involved in insect resistance, senescence, and yield-related traits in rice. Hence, understanding the association between OsCYP71P6 genetic variants and yield-related traits in rice varieties could provide novel insights for rice improvement. Through the utilization of linear regression models, a total of eight promoters were identified, and a specific gene variant (Ser33Leu) within OsCYP71P6 was found to be linked to spikelet fertility. Additionally, different alleles of the OsCYP71P6 gene identified through in/dels polymorphism in 131 rice varieties were validated for their allelic effects on yield-related traits. Furthermore, the single-plant yield, spikelet number, panicle length, panicle weight, and unfilled grain per panicle for the OsCYP71P6-1 promoter insertion variant were found to contribute 20.19%, 13.65%, 5.637%, 8.79%, and 36.86% more than the deletion variant, respectively. These findings establish a robust groundwork for delving deeper into the functions of OsCYP71-family genes across a range of biological processes. Moreover, these findings provide evidence that allelic variation in the promoter and amino acid substitution of Ser33Leu in the OsCYP71P6 gene could potentially impact traits related to rice yield. Therefore, the identified promoter variants in the OsCYP71P6 gene could be harnessed to amplify rice yields.

Amino acid transporters (AATs) play a crucial role in facilitating the movement of amino acids across cellular membranes, which is vital for the growth and development of plants. Amino acid permease (AAP), which belongs to the AAT family, has been the subject of extensive functional research in plants. Although its importance is recognized, a comprehensive grasp of this family’s dynamics in indica rice remains lacking. In this investigation, a total of 27 AAP genes were identified in the genome of indica rice. Further, the phylogenetic analysis unveiled that the 69 AAP genes from both the model species and other plant species could be classified into 16 distinct subfamilies. The analysis of chromosomal mapping revealed an uneven distribution of the 27 OsAAP genes across the 12 rice chromosomes. Notably, the OsAAP family displayed a total of 10 duplicated gene pairs, along with the identification of numerous conserved motifs. The examination of cis-elements within OsAAP genes unveiled that their promoters contain cis-elements related to phytohormones, plant growth and development, as well as stress responses. Additionally, transcriptome profiling demonstrated that a substantial portion of these genes exhibited responsiveness to various hormones, with their activation spanning multiple tissues and developmental stages in rice. The study identified miRNAs with a specific affinity for OsAAP genes. Out of the 27 OsAAP genes investigated, seventeen were discovered to be targeted by a total of forty-three miRNAs. Furthermore, the aus allele of OsAAP3 that we named OsAAP17 was validated for its effect on productive tillers and yield, and seventeen genetic variants of OsAAP17 were found to be associated with a culm number in indica rice. In addition, indica rice varieties were monomorphic, while aus genotypes displayed polymorphism for OsAAP17 gene-specific in/dels. Moreover, in Season II (rabi season), it was found that the aus allele of OsAAP17 increased the number of productive tillers and the single plant yield by 22.55% and 9.67%, respectively, in a recombinant inbred population created by crossing N22 and JR 201. Remarkably, this enhancement was more pronounced during the dry cultivation season, highlighting the influence of environmental factors in the regulation of tiller numbers mediated by OsAAP17. The discoveries presented here lay a strong foundation for further exploration into the roles of OsAAP family genes across a range of developmental processes. Therefore, the identified allelic variations in the utilization of OsAAP17 has the potential to enhance rice crop production via molecular breeding in the changing climate scenario.