An EMS-induced new sequence variant, TEMS5032, in the coding region of SRS3 gene leads to shorter grain length in rice (Oryza sativa L.)
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Grain shape and size influence yield and consumer preferences in rice. In the present study, we characterized and mapped a short and bold grained mutant and named it as TEMS5032, as the mutant is a result of EMS-induced transition from C to T at the 5032nd bp of SRS3 gene, which is known to affect grain size in rice. The substitution led to creation of a stop codon in the motor domain of SRS3, a kinesin 13 family gene, translating into a truncated protein product. However, transcription of this gene remained unaffected in TEMS5032 compared to the wild type, N22. Further, the mutation was found to affect 13 of the 25 cell cycle-related genes as they showed differential expression with respect to N22. Based on rate of grain filling, dry matter accumulation in the endosperm and histological studies, the effect of mutation in TEMS5032 was found to be similar to a known variant, TCM758, but less severe than sar1 mutant. Sequencing of 88 rice germplasm lines in the kinesin motor domain region did not reveal the presence of this mutation, establishing it as a new variant of SRS3 gene.
KeywordsKinesin 13 family gene Induced mutation Grain size QTL mapping EMS mutagenesis
ethyl methane sulfonate
quantitative trait locus
single marker analysis
composite interval mapping
logarithm of the odds
days after heading
cleaved amplified polymorphic sequences
We acknowledge the Project Director, NRCPB, New Delhi for extending all support and the laboratory facility for this work. We also thank Dr. V. Ramamurthy, Division of Entomology, Indian Agricultural Research Institute, New Delhi for providing the facility of the scanning electron microscope.
TM and UN designed and conceived the research work. UN and MN performed histological work. UN and PD did phenotyping and genotyping. UN and SAM performed QTL analysis. UN, SR, NKS, and RPS contributed in drafting manuscript. TM, UN, and SAM contributed in editing the revised manuscript.
This work was partly supported by the Department of Biotechnology, Government of India, New Delhi, funded project “Generation, characterization, and use of EMS-induced mutants of upland variety nagina-22 functional genomics in rice.” The first author acknowledges the financial support in the form of fellowship from DST, Government of India.
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Conflict of interest
The authors declare that they have no conflict of interest.
- Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Window 95/98/NT. Nucleic Acids Symp Ser 41:95–98Google Scholar
- Rozen S, Skaletsky HJ (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics methods and protocols: methods in molecular biology. Humana Press, Totowa, pp 365–386Google Scholar
- Wang S, Basten CJ, Zeng ZB (2012b) Windows QTL cartographer 2.5. Department of Statistics, North Carolina State UniversityGoogle Scholar