Record Details

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

OAR@ICRISAT

View Archive Info
 
 
Field Value
 
Relation http://oar.icrisat.org/12267/
https://www.nature.com/articles/s41598-023-28053-w
https://doi.org/10.1038/s41598-023-28053-w
 
Title Uncovering natural allelic and structural variants of OsCENH3 gene by targeted resequencing and in silico mining in genus Oryza
 
Creator Kaur, K
Neelam, K
Singh, J
Malik, P
Singh, K
 
Subject Biotechnology
Rice
Genetics and Genomics
 
Description 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.
 
Publisher Nature Publishing Group
 
Date 2023-01-16
 
Type Article
PeerReviewed
 
Format application/pdf
 
Language en
 
Rights cc_attribution
 
Identifier http://oar.icrisat.org/12267/1/Scientific%20Reports_13_01-14_2023.pdf
Kaur, K and Neelam, K and Singh, J and Malik, P and Singh, K (2023) Uncovering natural allelic and structural variants of OsCENH3 gene by targeted resequencing and in silico mining in genus Oryza. Scientific Reports (TSI), 13. pp. 1-14. ISSN 2045-2322