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. 2022 Mar 14;17(3):e0264478.
doi: 10.1371/journal.pone.0264478. eCollection 2022.

Identification of C-T novel polymorphism in 3rd exon of OsSPL14 gene governing seed sequence in rice

Muhammad Salah Ud Din  1 , Xiukang Wang  2 , Salman Alamery  3 , Sajid Fiaz  4 , Haroon Rasheed  5   6 , Muhammad Abid Khan  5 , Shahid Ullah Khan  7 , Sumbul Saeed  8 , Niaz Ali  1 , Kalim Ullah Marwat  9 , Kotb Attia  3 , Itoh Kimiko  10 , Shabir Hussain Wani  11
Affiliations

Identification of C-T novel polymorphism in 3rd exon of OsSPL14 gene governing seed sequence in rice

Muhammad Salah Ud Din et al. PLoS One. .

Retraction in

Abstract

Recently food shortage has become the major flagging scenario around the globe. To resolve this challenge, there is dire need to significantly increase crop productivity per unit area. In the present study, 24 genotypes of rice were grown in pots to assess their tillering number, number of primary and secondary branches per panicle, number of grains per panicle, number of grains per plant, and grain yield, respectively. In addition, the potential function of miR156 was analyzed, regulating seed sequence in rice. Furthermore, OsSPL14 gene for miR156 was sequenced to identify additional mutations within studied region. The results demonstrated Bas-370 and L-77 showed highest and lowest tillers, respectively. Bas-370, Rachna basmati, Bas-2000, and Kashmir Basmati showed high panicle branches whereas, L-77, L-46, Dilrosh, L-48, and L-20 displayed lowest panicle branches. Bas-370 and four other studied accessions contained C allele whereas, L-77 and 18 other investigated accessions had heterozygous (C and T) alleles in their promoter region. C-T allelic mutation was found in 3rd exon of the OsSPL14 gene. The sequence analysis of 12 accessions revealed a novel mutation (C-T) present ~2bp upstream and substitution of C-A allele. However, no significant correlation for novel mutation was found for tillering and panicle branches in studied rice accessions. Taken together present results suggested novel insight into the binding of miR156 to detected mutation found in 3rd exon of the OsSPL14 gene. Nevertheless, L-77, L-46, Dilrosh, L-48, and L-20 could be used as potential breeding resource for improving panicle architecture contributing yield improvement of rice crop.

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Depicted accession in study for C -T allele.
Fig 2
Fig 2. Depicted accession in study for C-A allele.
Fig 3
Fig 3. Aikawa1 and ST-12 are the two control sequences along reference genome (Nipponbare).
Fig 4
Fig 4. Amino acid alignment to missense mutation indicates from alanine to valine.
Fig 5
Fig 5
(A) Overall quality factor of wild type protein. (B) Overall quality factor of C-T substitution.
Fig 6
Fig 6. (A) Wild type (B) Alanine to Valine substitution.
Model generated by I-TASSER.
See this image and copyright information in PMC

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References

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Grants and funding

The publication of the present work is supported by the Natural Science Basic Research Program of Shaanxi Province (grant no. 2018JQ5218) and the National Natural Science Foundation of China (51809224), Top Young Talents of Shaanxi Special Support Program. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.