The molecular evolution of Ghd7 orthologs is not in line with the speciation events in genus Oryza

Under long day conditions, the grain number, plant height, and heading date7 (Ghd7) is a key regulatory gene in the rice specific flowering pathway, with significant pleotropic effects on yield related traits such as the number of spikelets per panicle, and heading date. The Ghd7 codes for a CO, COLIKE and TIMING OF CAB1 (CCT) domain, which is unique from the other CCT family proteins. In the current study, the evolutionary relationships of putative orthologs of Ghd7 within the genus Oryza is assessed via computational approaches. The relationships were deduced based on the nucleotide diversity, gene tree and synteny of Ghd7 orthologs of nine Oryza species using genomic, coding, and polypeptide sequences of the putative Ghd7 orthologs and adjacent genes retrieved from the Gramene database. The coding sequences (CDS) were found to be highly conserved (> 95 %) across the Oryza species, including the CCT domain. The length and the composition of the exons were not conserved between species. The exonintron boundaries depicted an intron phase where codons in exons were not interrupted by introns. The reconstructed gene tree revealed earlier divergence of Oryza brachyantha (diploid F genome) and Oryza punctata (diploid B genome) from the diploid species carrying an A genome. The A genome carriers were grouped into two strongly supported monophyletic clades, with clear separation of the Asian-origin species from the African-origin species. The movement of the syntenic blocks comprising putative orthologs of Ghd7 and its adjacent genes in 0.5 Mbp region revealed complex relationships, especially in ancestral species and species with African descent as the 1:1 putative orthologs were found in non-predictor chromosomes. Hence, the evolutionary pathway of Ghd7 was found to be complex and was governed by geographic origins, and gene movement across syntenic and non-syntenic regions.