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Journal of Applied Genetics

, Volume 59, Issue 4, pp 377–389 | Cite as

An EMS-induced new sequence variant, TEMS5032, in the coding region of SRS3 gene leads to shorter grain length in rice (Oryza sativa L.)

  • Umakanta Ngangkham
  • Manoj Nath
  • Prasad Dokku
  • S. V. Amitha Mithra
  • Srinivasan Ramamurthy
  • Nagendra K. Singh
  • R. P. Sharma
  • Trilochan Mohapatra
Plant Genetics • Original Paper
  • 71 Downloads

Abstract

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.

Keywords

Kinesin 13 family gene Induced mutation Grain size QTL mapping EMS mutagenesis 

Abbreviations

EMS

ethyl methane sulfonate

QTL

quantitative trait locus

SMA

single marker analysis

CIM

composite interval mapping

LOD

logarithm of the odds

DAH

days after heading

GL

grain length

GB

grain breadth

GT

grain thickness

GW

grain weight

N22

Nagina 22

WT

wild type

CAPS

cleaved amplified polymorphic sequences

Notes

Acknowledgements

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.

Author contributions

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.

Funding information

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.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

13353_2018_455_Fig8_ESM.png (2.1 mb)
Fig. S1

Graphical genotyping of whole genome using polymorphic markers between the M40 and IR64. Genotyping is done using parent Mutant M40 and IR64 along with nine short grain F2 recombinants derived from the M40 × IR64 cross. 1–9: denoted the F2 recombinants with short grain mutant type. Red, violet, and light green vertical bars denoted allele of mutant, IR64, and heterozygote alleles, respectively. The numbers in the parenthesis on the right side of the markers are the physical position of the markers in Mb unit. Presence of M40 segment in all the nine short grain recombinants localized mutation site in the short arm of chromosome 5. This was not observed for any other chromosomes (JPG 172 kb)

13353_2018_455_Fig9_ESM.png (4.3 mb)
Fig. S2

Multiple sequence alignment of 88 rice accessions for the mutation site showing the absence of mutant allele in all the germplasm studied. GL: grain length in mm is given on the left (JPG 245 kb)

13353_2018_455_MOESM1_ESM.docx (19 kb)
ESM 1 (DOCX 18 kb)

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Copyright information

© Institute of Plant Genetics, Polish Academy of Sciences, Poznan 2018

Authors and Affiliations

  • Umakanta Ngangkham
    • 1
    • 2
  • Manoj Nath
    • 1
  • Prasad Dokku
    • 1
  • S. V. Amitha Mithra
    • 1
  • Srinivasan Ramamurthy
    • 1
  • Nagendra K. Singh
    • 1
  • R. P. Sharma
    • 1
  • Trilochan Mohapatra
    • 1
    • 3
  1. 1.National Research Centre on Plant BiotechnologyNew DelhiIndia
  2. 2.ICAR-National Rice Research InstituteCuttackIndia
  3. 3.Indian Council of Agricultural ResearchNew DelhiIndia

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