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Finding genomic regions and candidate genes governing water use efficiency in rice

  • Original Paper
  • Published:
Biologia Plantarum

Abstract

Water use efficiency (WUE) is an worth attempting trait to discover the genomic regions governing it, especially in view of the diminishing water resources for the crop plants in general and rice in particular. In order to address this, the present investigation was aimed at identification of genomic regions governing WUE employing a recombinant inbred line population derived from a cross between INRC10192, a high WUE landrace, and IR64, a high yielding cultivar. A total of 36 quantitative trait loci (QTLs) were detected under control as well as drought conditions on chromosomes 1, 2, 4, 8, 9, 10, and 11. Among all, the QTLs with the marker intervals RM486-RM6703, RM6703-RM11484, RM404-RM447, RM24879-RM171, and RM229-RM332 on chromosomes 1, 8, 10, and 11 were found to govern the water use efficiency related traits such as carbon isotope discrimination, specific leaf area, leaf width, and relative water content. Nine major QTL intervals were targeted for candidate gene identification using gene ontology (GO) and transcriptome-based analyses. Overrepresented GO terms in the targeted QTLs were found to be associated with the genes/pathways controlling stomatal regulatory mechanism, stress responsive genes or transcription factors, and saccharide biosynthesis pathways under stress situation. Hence, these genes or genomic regions are potential candidates for development of high WUE rice cultivars.

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Abbreviations

C:

control

CID:

carbon isotope discrimination

FPKM:

fragments per kilobase of exon per million fragments

GO:

gene ontology

LA:

leaf area

LLN:

leaf length

LOD:

maximum likelihood ratio of odds

LWD:

leaf width

NFG:

number of filled grains

nsSNPs:

non synonymous single nucleotide polymorphic regions

PNO:

total number of panicles

QTL:

quantitative trait locus

RIL:

recombinant inbred line

RTLN:

root length

RWC:

relative water content

SHLN:

shoot length

SLA:

specific leaf area

SPF:

spikelet fertility

T:

treatment

TYLD:

total yield per plant

WUE:

water use efficiency

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Authors and Affiliations

  1. Institute of Biotechnology, Acharya NG Ranga Agricultural University, Rajendranagar, Hyderabad, 500030, AP, India

    V. Roja, S. Patil, D. A. Deborah, A. Srividhya, N. Ranjitkumar, G. Kadambari, P. V. Ramanarao, E. A. Siddiq & L. R. Vemireddy

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  1. V. Roja
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  2. S. Patil
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  3. D. A. Deborah
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  4. A. Srividhya
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  5. N. Ranjitkumar
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  6. G. Kadambari
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  7. P. V. Ramanarao
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  8. E. A. Siddiq
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  9. L. R. Vemireddy
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Correspondence to L. R. Vemireddy.

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authors contributed equally to this work.

Acknowledgements: L.R. Vemireddy acknowledges the Acharya NG Ranga Agricultural University (ANGRAU) for providing financial support under Rashtriya Krishi Vikas Yojana (RKVY). V. Roja acknowledges the ANGRAU for offering the Senior Research Fellowship under the RKVY scheme.

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Roja, V., Patil, S., Deborah, D.A. et al. Finding genomic regions and candidate genes governing water use efficiency in rice. Biol Plant 60, 757–766 (2016). https://doi.org/10.1007/s10535-016-0651-1

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  • DOI: https://doi.org/10.1007/s10535-016-0651-1

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