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Molecular Dissection of a Genomic Region Governing Root Traits Associated with Drought Tolerance Employing a Combinatorial Approach of QTL Mapping and RNA-seq in Rice

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Abstract

Drought is considered as one of the major obstacles for progressive yield enhancement and stability in rice, especially in rain-fed conditions. Being a complex trait, drought is regulated by numerous quantitative trait loci (QTL), of which, however, very few underlying genes have been cloned. In the present investigation, we made an attempt to uncover the candidate gene(s) behind a major QTL, rdw8.1 governing drought tolerance traits viz., root dry weight and root length. The targeted QTL has been delimited to 366.75 kb from 10.17 Mb by QTL mapping in BC1F2 population. Further, the targeted region was delineated employing next-generation sequencing based RNA-seq. Based on the QTL mapping and RNA-seq approaches, the plausible candidate gene underlying the QTL region was identified as a wound inducible protein (LOC_Os08g08090). This gene can be of potential value to enhance the drought tolerance of the elite rice varieties through molecular breeding.

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Abbreviations

NPT:

Number of productive tillers per plant

NTP:

Number of tillers per plant

RWC:

Relative water content

PH:

Plant height

NPP:

Number of panicles per plant

GNP:

Grain number per plant

SFP:

Spikelet fertility percentage

GW:

100 seeds grain weight

GY:

Grain yield

LRS:

Leaf rolling score

PL:

Panicle length

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Acknowledgments

LRV acknowledges Acharya NG Ranga Agricultural University (ANGRAU) for providing financial support under Rashtriya Krishi Vikas Yojana (RKVY), Govt. Andhra Pradesh. S.P. acknowledges Indian Council of Agricultural Research (ICAR) for providing Senior Research Fellowship.

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Author notes

  1. Santosh Patil, A Srividhya, Roja Veeraghattapu, D A K Deborah have equally contributed.

Authors and Affiliations

  1. Institute of Biotechnology, Acharya N G Ranga Agricultural University, Rajendranagar, Hyderabad, India

    Santosh Patil, A Srividhya, Roja Veeraghattapu, D A K Deborah, Gopalakrishna Murty Kadambari, Ranjitkumar Nagireddy, E A Siddiq & Lakshminarayana R Vemireddy

Authors
  1. Santosh Patil
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  2. A Srividhya
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  3. Roja Veeraghattapu
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  4. D A K Deborah
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  5. Gopalakrishna Murty Kadambari
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  6. Ranjitkumar Nagireddy
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  7. E A Siddiq
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  8. Lakshminarayana R Vemireddy
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Contributions

S.P. conducted all experiments and drafted the manuscript. S.P., R.V., D.A.K.D. involved in phenotyping, genotyping and data analysis. L.R.V., R.V., S.P., A.S. involved in sequencing and data interpretation. G.M. and R.N. helped in the constitution of mapping population and field trials. E.A.S., L.R.V., A.S. designed the study and participated in drafting and correcting the manuscript critically and gave final approval of version for publication.

Corresponding author

Correspondence to Lakshminarayana R Vemireddy.

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Conflict of Interest

The authors declare that they have no conflict of interest.

Electronic supplementary material

Supplementary Figure 1

Soil moisture content at 30 cm depth of the soil during the drought stress period. (JPEG 380 kb)

Supplementary Figure 2

Drought screening of backcross population along with parents in college farm. During panicle initiation stage the irrigation was completely stopped for 21 days til severe leaf rolling observed. A & B- Drought Imposed field (College farm, ANGRAU, Rajendranagar). (JPEG 1464 kb)

Supplementary Figure 3

Genotyping of BC1F2 population with RM7080 marker. (JPEG 270 kb)

Supplementary Table 1

Polymorphic markers within the QTL interval of RM38-RM331 (DOC 50 kb)

Supplementary Table 2

List of polymorphic markers used for background selection in BC1F1 population (DOC 87 kb)

Supplementary Table 3

Recovery of recurrent parent allele in BC1F1 plants through background selection (DOC 28 kb)

Supplementary Table 4

List of differentially expressed genes between the INRC10192 and IR64 in the target QTL (DOC 35 kb)

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Patil, S., Srividhya, A., Veeraghattapu, R. et al. Molecular Dissection of a Genomic Region Governing Root Traits Associated with Drought Tolerance Employing a Combinatorial Approach of QTL Mapping and RNA-seq in Rice. Plant Mol Biol Rep 35, 457–468 (2017). https://doi.org/10.1007/s11105-017-1037-z

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  • DOI: https://doi.org/10.1007/s11105-017-1037-z

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