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

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

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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.

Item Type:	Article
Divisions:	Genebank
CRP:	UNSPECIFIED
Uncontrolled Keywords:	Biotechnology, Genetics, Plant sciences
Subjects:	Others > Biotechnology Others > Rice Others > Genetics and Genomics
Depositing User:	Mr Nagaraju T
Date Deposited:	03 Nov 2023 06:44
Last Modified:	03 Nov 2023 06:44
URI:	http://oar.icrisat.org/id/eprint/12267
Official URL:	https://www.nature.com/articles/s41598-023-28053-w
Projects:	UNSPECIFIED
Funders:	Bayer’s Beachell Borlaug International Scholars Program, CSIR-UGC joint Junior Research Fellowship
Acknowledgement:	The authors acknowledge that this study was carried out as part of doctoral thesis of Karminderbir Kaur. The authors are grateful to Bayer’s Beachell Borlaug International Scholars Program (earlier Monsanto’s Beachell Borlaug International Scholars Program) and Council of Scientific and Industrial Research and University Grants Commission administered joint Junior Research Fellowship for financial support. The authors are grateful to Dr. Anne Britt, Dr. Luca Comai, Dr. Nitzan Shabek and Dr. Sundaram Kuppu of University of California, Davis for their inputs and discussions that helped shape this manuscript. The authors also express their thanks to Dr. S.S.Banga, Dr. Parveen Chhuneja, Dr. Yogesh Vikal and Dr. Priti Sharma for their feedback.
Links:	Google Scholar

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