APBN New Site

APBN Developing Site

Researchers Discover Key Codon Repeats Controlling Rice’s Tolerance to Cold

A possible strategy to finely manipulate key genes in rice genomes and effectively improve chilling tolerance through molecular designing.

In recent years, abnormal environmental temperatures (like chilling) brought on by global climate change have jeopardised the cultivation of rice, one of the most important food crops feeding roughly half of the world’s population. Thus, to yield consistent harvests, crops must be able to withstand extreme temperatures. Although plants have developed complicated and delicate protections to withstand chilling stress, DNA damage still occurs, weakening plants’ defences. Furthermore, not much is known about the underlying regulatory mechanisms.

A recent study conducted by a research team led by Professor Chong Kang from the Institute of Botany of the Chinese Academy of Sciences (CAS) has revealed a novel cold domesticated repair mechanism for DNA in rice, providing corresponding elite modules for the improvement of chilling tolerance in rice with the codon repeats at a single site.

Using a method that combines population genetics, genomics, cell and evolutionary biology, Prof. Chong’s group, in collaboration with Prof. Li Qizhai’s group from the Academy of Mathematics and Systems Science of CAS, and Prof. Cheng Zhukuan’s group from the Institute of Genetics and Developmental Biology of CAS, explored the novel module for chilling tolerance in this study.

The researchers carried out data-merging genome-wide association studies (DM-GWAS) based on multidimensional scaling. Using merged phenotypic data, the GWAS found a number of loci, one of which was qCTS11-1 on chromosome 11, which makes a clear contribution to increasing rice’s ability to withstand chilling. COLD11 was a key gene that was identified with fine-scale mapping. The researchers found that loss-of-function mutations of COLD11 resulted in reduced chilling tolerance.

Different types of GCG codon repeats encoding alanine in the first exon of COLD11 were observed for chilling-sensitive indica varieties and chilling-tolerant japonica varieties. The GCG codon repeat numbers correlated strongly and favourably with the ability to withstand cold. Additionally, a genome evolution analysis of representative rice germplasms revealed that a large number of GCG sequence repeats were subjected to strong domestication selection during the northern expansion of rice planting.

Furthermore, the DNA repair protein encoded by COLD11 is crucial for the restoration of DNA double-strand breaks. The GCG repeat numbers in its first exon showed a positive correlation with its biochemical activity. This is the first report of a domestication-selected DNA damage repair mechanism and its corresponding elite modules involving chilling stress.

Using DM-GWAS of japonica and indica—two rice subspecies with significant differences in their ability to withstand cold temperatures—this work shows that COLD11 is a key quantitative trait loci gene for chilling tolerance.

Rice chilling tolerance can now be finely regulated with a single site thanks to the identification of the essential codon repeats in the first exon of COLD11 as confirmed by phylogenetic and regional distribution analyses. It is a potentially helpful molecular module for enhancing the chilling tolerance trait in rice through molecular design. [APBN]

Source: Li et al. (2023). Natural variation of codon repeats in COLD11 endows rice with chilling resilience. Science Advances.