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

Suk Man Kim, Jung Pil Suh, Chung Koon Lee, Jeong Heui Lee, Yeong Gyu Kim, Kshirod Kumar Jena

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53 Scopus citations

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 F 7 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 (R2) 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 R2 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.

Original languageEnglish
Pages (from-to)333-343
Number of pages11
JournalMolecular Genetics and Genomics
Volume289
Issue number3
DOIs
StatePublished - Jun 2014

Keywords

  • Candidate genes
  • DNA marker
  • QTL
  • Rice
  • Seedling cold tolerance

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