Journal Article

Genetics of chilling response at early growth stage in rice: a recessive gene for tolerance and importance of acclimation

Koide, Yohei, Bannai, Hiroaki, Meija, Yan, Ueno, Haruka, Kasuga, Jun, Baruah, Akhil Ranjan, Palta, Jiwan, Kimura, Ayumi, Yamamoto, Masayuki P, Onishi, Kazumitsu, Kishima, Yuji

2023

Overview

Abstract Low-temperature adaptation in rice is mediated by the ability of a genotype to tolerate chilling temperatures. A genetic locus on chromosome 11 was analysed for chilling tolerance at the plumule stage in rice. The tolerant allele of A58, a japonica landrace in Japan, was inherited as a recessive gene (ctp-1A58), whereas the susceptible alleles from wild rice (Ctp-1W107) and modern variety (Ctp-1HY) were the dominant genes. Another recessive tolerant allele (ctp-1Silewah) was found in a tropical japonica variety (Silewah). Fine-mapping revealed that a candidate gene for the ctp-1 locus encoded a protein similar to the nucleotide-binding domain and leucine-rich repeat (NLR) protein, in which frameshift mutation by a 73 bp-deletion might confer chilling tolerance in ctp-1A58. Analysis of near-isogenic lines demonstrated that ctp-1A58 imparted tolerance effects only at severe chilling temperatures of 0.5 °C and 2 °C, both at plumule and seedling stages. Chilling acclimation treatments at a wide range of temperatures (8 °C–16 °C) for 72 h concealed the susceptible phenotype of Ctp-1W107 and Ctp-1HY. Furthermore, short-term acclimation treatment of 12 h at 8 °C was enough to be fully acclimated. These results suggest that the NLR gene induces a susceptible response upon exposure to severe chilling stress, however, another interacting gene(s) for acclimation response could suppress the maladaptive phenotype caused by the Ctp-1 allele. This study provides new insights for the adaptation and breeding of rice in a low-temperature environment. This paper showed that a recessive gene (ctp-1) conferred tolerance to severe chilling stress and its candidate gene was nucleotide-binding domain and leucine-rich repeat (NLR) gene, known as disease resistance gene. The role of acclimation response, which enhances chilling tolerance by pre-exposure to mild stress temperature before severe stress, has been mostly ignored in rice breeding; however, we demonstrated that gene(s) other than the intrinsic tolerance gene (the ctp-1 locus) could contribute to improvement of chilling tolerance.

• Publisher: Oxford University Press
• Subject: Acclimation / Acclimatization / Adaptation / Agriculture / Alleles / Chromosome 11 / Cold / Cooling / Flowers & plants / Frameshift mutation / Gene deletion / Gene mapping / Genes / Genetic analysis / Genetics / Genotype & phenotype / Genotypes / Growth stage / Leucine / Low temperature / Low temperature environments / Mutation / Nucleotides / Peptide mapping / Phenotypes / Physiology / Plant breeding / Proteins / Rice / Seedlings / Temperature / Temperature tolerance