Abstract
AbstractLow-temperature stress (LTS) is one of the major abiotic stresses that affect crop growth and ultimately decrease grain yield. The development of rice varieties with low-temperature stress tolerance has been a severe challenge for rice breeders for a long time. The lack of consistency of the quantitative trait loci (QTLs) governing LTS tolerance for any given growth stage over different genetic backgrounds of mapping populations under different low-temperature stress conditions remains a crucial barrier for adopting marker-assisted selection (MAS). In this review, we discuss the ideal location and phenotyping for agromorphological and physiological parameters as indicators for LTS tolerance and also the traits associated with QTLs that were identified from biparental mapping populations and diverse rice accessions. We highlight the progress made in the fields of genome editing, genetic transformation, transcriptomics, and metabolomics to elucidate the molecular mechanisms of cold tolerance in rice. The stage-specific QTLs and candidate genes for LTS tolerance brought out valuable information toward identifying and improving LTS tolerance in rice varieties. We showed 578 QTLs and 38 functionally characterized genes involved in LTS tolerance. Among these, 29 QTLs were found to be colocalized at different growth stages of rice. The combination of stage-specific QTLs and genes from biparental mapping populations and genome-wide association studies provide potential information for developing LTS-tolerant rice varieties. The identified colocalized stage-specific LTS-tolerance QTLs will be useful for MAS and QTL pyramiding and for accelerating mapping and cloning of the possible candidate genes, revealing the underlying LTS-tolerance mechanisms in rice.
Highlights
Rice (Oryza sativa L.) is an important cereal crop, being the staple food for more than half of the world’s population, providing 21% of global human per capita energy (Nalley et al 2017)
Selection based solely on genetic markers is highly biased because the environment profoundly influences most of the economic traits
The development of a metabolite quantitative trait locus and metabolome-wide association studies (MWAS) could be helpful in crop improvement by overcoming the problems emerging from differing environmental conditions during selection
Summary
Rice (Oryza sativa L.) is an important cereal crop, being the staple food for more than half of the world’s population, providing 21% of global human per capita energy (Nalley et al 2017). The rice crop is relatively sensitive to temperatures below 15 °C, which causes varying effects across different crop growth stages such as germination, seedling, vegetative, reproductive, and grain maturity (Andaya and Mackill 2003a, b). The effect of LTS on different plant growth stages (germination, seedling, and reproductive) is crucial. High-elevation areas with low air and water temperatures, especially in subtropical regions in Kunming, People’s Republic of China (subsequently “China”), and in regions of Kashmir and Himachal Pradesh, India, are ideal spots for screening for cold tolerance (Jiang et al 2012). The effects of LTS in different growth stages, such as germination stage (GS), seedling stage (SS), and reproductive stage (RS), have significant impacts on agromorphological changes and yield component losses, especially in tropical zones.
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