Allele mining of Badh1 gene in aromatic rice germplasm

Abstract

In this study, we explored the allelic diversity of the Badh1 gene in rice using a core set of 99+2 allele sequences. Phylogenetic analysis revealed seven distinct clusters, which were compared with haplogroups based on whole gene sequences of synonymous (Syn) and non-synonymous (non-Syn) SNPs. Detailed SNP and indel (insertion-deletion) analyses were conducted on alleles from six different categories of rice, highlighting significant variations in the exonic and intronic regions. These findings provide insights into the genetic diversity and evolutionary patterns of the Badh1 gene in rice. We also discovered the glutamic acid and cysteine active sites, as well as the N- and C-terminals, in the reference protein. All 99+2 genotypes were also found at these places. In certain accessions, the active sites for cysteine, glutamic acid, and C-terminal were not detected. Additionally, those genotypes lack 2-AP.