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Abstract
BackgroundRice is a crop that is very sensitive to low temperature, and its morphological development and production are greatly affected by low temperature. Therefore, understanding the genetic basis of cold tolerance in rice is of great significance for mining favorable genes and cultivating excellent rice varieties. However, there have been limited studies focusing on cold tolerance at the bud burst stage; therefore, considerable attention should be given to the genetic basis of cold tolerance at this stage.ResultsIn this study, a natural population consisting of 211 rice landraces collected from 15 provinces in China and other countries was used for the first time to evaluate cold tolerance at the bud burst stage. Population structure analysis showed that this population was divided into two groups and was rich in genetic diversity. Our evaluation results confirmed that japonica rice was more tolerant to cold at the bud burst stage than indica rice. A genome-wide association study (GWAS) was performed with the phenotypic data of 211 rice landraces and a 36,727 SNP dataset under a mixed linear model. Twelve QTLs (P < 0.0001) were identified for the seedling survival rate (SR) after treatment at 4 °C, in which there were five QTLs (qSR2–2, qSR3–1, qSR3–2, qSR3–3 and qSR9) that were colocalized with those from previous studies and seven QTLs (qSR2–1, qSR3–4, qSR3–5, qSR3–6, qSR3–7, qSR4 and qSR7) that were reported for the first time. Among these QTLs, qSR9, harboring the most significant SNP, explained the most phenotypic variation. Through bioinformatics analysis, five genes (LOC_Os09g12440, LOC_Os09g12470, LOC_Os09g12520, LOC_Os09g12580 and LOC_Os09g12720) were identified as candidates for qSR9.ConclusionThis natural population consisting of 211 rice landraces combined with high-density SNPs will serve as a better choice for identifying rice QTLs/genes in the future, and the detected QTLs associated with cold tolerance at the bud burst stage in rice will be conducive to further mining favorable genes and breeding rice varieties under cold stress.
Highlights
Rice is a crop that is very sensitive to low temperature, and its morphological development and production are greatly affected by low temperature
A natural population consisting of 211 rice landraces (130 indica rice and 81 japonica rice) was used to assess cold tolerance in rice at the bud burst stage
The results show that the survival rate (SR) ranged from 0 to 100% (Table S2); indica rice is extremely sensitive to temperature, and its SR is low after cold treatment
Summary
Rice is a crop that is very sensitive to low temperature, and its morphological development and production are greatly affected by low temperature. Low temperature has a large impact on rice growth and cultivation. More than 15 million hectares of rice cultivated area worldwide have been affected by low temperatures. Li et al BMC Plant Biology (2021) 21:542 large area in China, ranging from 53°27′ to 18° 90′ north latitude, especially in the provinces of the Yangtze River basin, and from 1951 to 1980, rice in the Yangtze River basin suffered from severe cold injury, with losses of 5 to 10 billion kilograms of rice every year [1]. Rice in the Yangtze River basin in China is often affected by cold injury at the bud burst stage, resulting in a low germination rate and failure to emerge. It is necessary to study cold tolerance in rice at the bud burst stage
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