Novel cis-acting regulatory elements in wild Oryza species impart improved rice bran quality by lowering the expression of phospholipase D alpha1 enzyme (OsPLDα1)

Kaur, Amandeep; Neelam, Kumari; Kitazumi, Ai; Kaur, Karminderbir; Sharma, Priti; Mangat, Gurjit Singh; Reyes, Benildo G. de los; Brar, D. S.; Singh, Kuldeep

doi:10.1007/s11033-019-05144-4

Cited by 9 publications

(8 citation statements)

References 71 publications

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“…While mining alleles for OsCENH3 in wild species germplasm of Oryza genus, not all accessions could be amplified uniformly. Similar problems were faced by other workers while mining alleles for specific genes from Oryza germplasm 36 , 37 . Transferability of the primer pairs between species belonging to the same genus, is not always 100% as observed in Passiflora and Allium 38 , 39 .…”

Section: Discussionmentioning

confidence: 69%

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

Kaur

Neelam

Singh

et al. 2023

Sci Rep

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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.

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Section: Discussionmentioning

confidence: 69%

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

Kaur

Neelam

Singh

et al. 2023

Sci Rep

Self Cite

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show abstract

“…While mining alleles for OsCENH3 in wild species germplasm of Oryza genus, not all accessions could be ampli ed uniformly and for all regions of the gene. Similar problems were faced by other workers while mining alleles for speci c genes from Oryza germplasm [37][38]. Transferability of the primer pairs between species belonging to the same genus, is not always 100% as observed in Passi ora and Allium [39][40].…”

Section: Wild Germplasm Presents Synonymous As As Non-synonymous Vari...mentioning

confidence: 71%

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

Kaur

Neelam

Singh

et al. 2022

Preprint

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Plant breeding efforts to boost 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.

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“…Therefore, genomics and epigenomics are used to identify and analyze CREs. For example, the alignment of the upstream sequences of OsPLD α 1 orthologs across 34 rice accessions revealed sequence variations and identified CREs involved in differential transcription of orthologs, which resulted in the low expression of OsPLD α 1 and reduced free fatty acid content in the oil, facilitating good quality bran oil (Kaur et al, 2020 ). A genome-wide association study (GWAS) screen of 45 natural accessions and the pif4 mutant in Arabidopsis identified CREs affecting SAUR26 gene expression (Wang et al, 2021 ).…”

Section: Cis -Regulatory Elements and Their Mining In Plantsmentioning

confidence: 99%

“…The ARFAT and SEBF elements have been identified as CREs that might act as repressors in regulating OsPLD α 1 expression, which lead to decreased free fatty acid content in oil and improve the flavor and quality of rice bran oil ( Table 1 ) (Kaur et al, 2020 ). Two common variations in the potential CREs of the OsAAP6 5′-untranslated region (5′-UTR) seem to be associated with grain protein content diversity and nutritional quality, mainly in indica cultivars (Peng et al, 2014 ).…”

Section: The Key Roles Of Cis -Regulatory Elements In the Improvement In Rice Qualitymentioning

confidence: 99%

Targeting Cis-Regulatory Elements for Rice Grain Quality Improvement

et al. 2021

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Rice is the most important source of food worldwide, providing energy, and nutrition for more than half of the population worldwide. Rice grain quality is a complex trait that is affected by several factors, such as the genotype and environment, and is a major target for rice breeders. Cis-regulatory elements (CREs) are the regions of non-coding DNA, which play a critical role in gene expression regulation. Compared with gene knockout, CRE modifications can fine-tune the expression levels of target genes. Genome editing has provided opportunities to modify the genomes of organisms in a precise and predictable way. Recently, the promoter modifications of coding genes using genome editing technologies in plant improvement have become popular. In this study, we reviewed the results of recent studies on the identification, characterization, and application of CREs involved in rice grain quality. We proposed CREs as preferred potential targets to create allelic diversity and to improve quality traits via genome editing strategies in rice. We also discussed potential challenges and experimental considerations for the improvement in grain quality in crop plants.

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Novel cis-acting regulatory elements in wild Oryza species impart improved rice bran quality by lowering the expression of phospholipase D alpha1 enzyme (OsPLDα1)

Cited by 9 publications

References 71 publications

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

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

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

Targeting Cis-Regulatory Elements for Rice Grain Quality Improvement

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