Uncovering natural allelic and structural variants of OsCENH3 gene by targeted resequencing and in silico mining in genus Oryza

Abstract

Plant breeding efforts to boost rice productivity have focused on developing a haploid development pipeline. CENH3 gene has emerged as a leading player that can be manipulated to engineer haploid induction system. Currently, allele mining for the OsCENH3 gene was done by PCR-based resequencing of 33 wild species accessions of genus Oryza and in silico mining of alleles from pre-existing data. We have identified and characterized CENH3 variants in genus Oryza. Our results indicated that the majority CENH3 alleles present in the Oryza gene pool carry synonymous substitutions. A few non-synonymous substitutions occur in the N-terminal Tail domain (NTT). SNP A/G at position 69 was found in accessions of AA genome and non-AA genome species. Phylogenetic analysis revealed that non-synonymous substitutions carrying alleles follow pre-determined evolutionary patterns. O. longistaminata accessions carry SNPs in four codons along with indels in introns 3 and 6. Fifteen haplotypes were mined from our panel; representative mutant alleles exhibited structural variations upon modeling. Structural analysis indicated that more than one structural variant may be exhibited by different accessions of single species (Oryza barthii). NTT allelic mutants, though not directly implicated in HI, may show variable interactions. HI and interactive behavior could be ascertained in future investigations.

Progress in Rice Breeding Based on Genomic Research

“…A comparison of the sequence data from these two varieties identified eight candidate genes carrying nonsynonymous SNPs, providing valuable insights for identifying the gene associated with qFfR9 [20]. Through the analysis of resequencing data from 33 wild species of rice, different alleles of the haploid induction gene OsCENH3 were identified [21]. Han et al, utilized high-throughput resequencing technology to analyze genes associated with drought tolerance in wild rice, revealing the evolutionary history and selection pressure acting on these genes [22].…”

Haploid Induction in Indica Rice: Exploring New Opportunities

“…Kalinowska et al ( 2019), in their review, have identified a patent describing the development of three haploid-inducing rice lines by the substitution of single amino acids in the Nterminal region of CENH3, resulting in up to 1% haploid progeny [104]. In a recent study, several CENH3 variants were identified and characterized in the genus Oryza [105]. In silico analysis of sequence variation at the OsCENH3 locus identified many synonymous substitutions, while a few non-synonymous substitutions affected the protein conformation to some extent.…”