Genome-wide Characterization of Far-Red Impaired Response 1 (FAR1) Transcription Factor Gene Family in Wild Rice Oryza brachyantha

Abstract

The wild rice variety, Oryza brachyantha, is categorized as having the F genome type and is a member of the primitive Oryza lineage. The O. brachyantha is particularly noteworthy because of its genetic variability and applications in rice breeding, especially for increasing traits like disease resistance and tolerance to abiotic stimuli. Bisexual spikelets, two almost completely developed sterile lemmas, acuminate entire lemmas that are occasionally setiform, herbaceous to crustaceous leaves, and herbaceous margins are the characteristics of Oryza species. The FAR1 gene family is a crucial part of the far-red light signal pathway regulated by phyA. With estimated sizes ranging from 531 to 851 amino acids, these proteins have commonalities in amino acid composition between 12.0% and 82.4% over their whole lengths. The light signaling pathways that impact photomorphogenesis and the general development of plants are influenced by the FAR1 gene family. In the present study, 32 genes encoding potential FAR1 TFs were found in the O. brachyantha genome.  We retrieved these genes based on the presence of the FAR1 domain in the protein sequence. The map chart indicates that chromosomes 1 and 8 have one gene on them. Similarly, seven genes are present on both chromosomes 2 and 3. There are four genes on chromosomes 4 and 7. Two genes are present on Chromosome 6. Chromosomes 11 and 12 contain two genes. Using the Molecular Evolutionary Genetics Analysis (MEGA 11) program, a phylogenetic analysis was carried out which divided 32 FAR1 genes into 3 clades. The location and pattern of intron-exon distribution within the genomic regions of the FAR1 gene served as evidence for the expansion and its evolutionary connection with its progenitors. O. brachyantha FAR1 genes showed variation in the number of introns ranging from 2 to 10. The motif analysis of FAR1 genes demonstrated the conservation of different motifs among the members of the same clades. Synteny analysis between O. brachyantha and Arabidopsis showed conservation and evolutionary relationships of the 5 O. brachyantha FAR1 genes in Arabidopsis. This study provides the basic characterization of FAR1 genes in O. brachyantha and their relationship with the Arabidopsis genes.