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QTL mapping and development of candidate gene-derived DNA markers associated with seedling cold tolerance in rice (Oryza sativa L.)

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Abstract

Cold stress at the seedling stage is a major threat to rice production. Cold tolerance is controlled by complex genetic factors. We used an F7 recombinant inbred line (RIL) population of 123 individuals derived from a cross of the cold-tolerant japonica cultivar Jinbu and the cold-susceptible indica cultivar BR29 for QTL mapping. Phenotypic evaluation of the parents and RILs in an 18/8 °C (day/night) cold stress regime revealed continuous variation for cold tolerance. Six QTLs including two on chromosome 1 and one each on chromosomes 2, 4, 10, and 11 for seedling cold tolerance were identified with phenotypic variation (R 2) ranging from 6.1 to 16.5 %. The QTL combinations (qSCT1 and qSCT11) were detected in all stable cold-tolerant RIL groups, which explained the critical threshold of 27.1 % for the R 2 value determining cold tolerance at the seedling stage. Two QTLs (qSCT1 and qSCT11) on chromosomes 1 and 11, respectively, were fine mapped. The markers In1-c3, derived from the open reading frame (ORF) LOC_Os01g69910 encoding calmodulin-binding transcription activator (CAMTA), and In11-d1, derived from ORF LOC_Os11g37720 (Duf6 gene), co-segregated with seedling cold tolerance. The result may provide useful information on seedling cold tolerance mechanism and provide DNA markers for a marker-assisted breeding program to improve seedling cold tolerance in indica rice varieties.

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Abbreviations

AFGP:

Antifreeze glycoprotein

BAC:

Bacterial artificial chromosome

CAMTA:

Calmodulin-binding transcription activator

CBF:

C-repeat binding factor

CBS:

Cystathionine β-synthase

CDS:

Cold damage score

CIM:

Composite interval mapping

CT:

Cold treatment

GST:

Glutathione S-transferase

InDel:

Insertion–deletion polymorphisms

LOD:

Logarithm of odds

R 2 :

Phenotypic variance

LTH:

Lijianxintuanheigu

ORF:

Open reading frame

QTL:

Quantitative trait loci

RIL:

Recombinant inbred line

RP:

Recovery period

SPV:

Sum of phenotypic variation

SSR:

Simple sequence repeat

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Acknowledgments

This research was supported in part by a grant to the Temperate Rice Research Consortium (TRRC) and Agenda Program (Code No. PJ0068272011) of the Rural Development Administration, Republic of Korea. We thank Dr. Benildo De Los Reyes, University of Maine, Orono, Maine, USA for a critical review and suggestions to improve the manuscript. We thank Bill Hardy, senior science editor of IRRI, for editing the manuscript.

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Authors and Affiliations

  1. Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, 7777, Metro Manila, Philippines

    Suk-Man Kim & Kshirod Kumar Jena

  2. C/o IRRI-Korea Office, National Institute of Crop Science, Rural Development Administration, Suwon, 441-857, Republic of Korea

    Suk-Man Kim

  3. Rice Research Division, National Institute of Crop Science, Rural Development Administration, Suwon, 441-857, Republic of Korea

    Jung-Pil Suh, Chung-Koon Lee, Jeong-Heui Lee & Yeong-Gyu Kim

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  1. Suk-Man Kim
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  2. Jung-Pil Suh
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Correspondence to Kshirod Kumar Jena.

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Communicated by B. Han.

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Kim, SM., Suh, JP., Lee, CK. et al. QTL mapping and development of candidate gene-derived DNA markers associated with seedling cold tolerance in rice (Oryza sativa L.). Mol Genet Genomics 289, 333–343 (2014). https://doi.org/10.1007/s00438-014-0813-9

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