A Comprehensive Genome-Wide Investigation of the Cytochrome 71 () Gene Family: Revealing the Impact of Promoter and Gene Variants (Ser33Leu) of on Yield-Related Traits in Indica Rice ( L.).

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 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 genes were distributed across 11 chromosomes, and 36 pairs of involved in gene duplication events. Within the promoter region of , 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 gene is involved in insect resistance, senescence, and yield-related traits in rice. Hence, understanding the association between 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 was found to be linked to spikelet fertility. Additionally, different alleles of the 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 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 -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 gene could potentially impact traits related to rice yield. Therefore, the identified promoter variants in the gene could be harnessed to amplify rice yields.