| Plants will encounter various environmental stress during their growth stage,among whice low temperature stress is one of the major adverse environmental factors that affect crop growth,yield and limitation of crop geographical distribution.Rice is one of the most important food crops in the world,and half of the world’s population live on it.As rice originated from tropical and subtropical areas,compared with barley,wheat and other crops,it is more sensitive to low temperature stress,and is also more vulnerable to chilling injury at high latitude and high altitude areas.Continuous low temperature will also have an important effect on the rice growth and yield,even if rice is grown in the temperate zone.Therefore,it is helpful to identify cold tolerance of rice germplasms and explor their low temperature resistance mechanism to guide the rational design of cold tolerance rice breeding.In this study,a major QTL for cold tolerance at seedling stage was identified by genome-wide association analysis（GWAS）method,and qCT11 was fine mapped by map-based cloning method.The main results were as follows:1.We identified the cold tolerance of 550 rice from 53 countries at seedling stage,which was helpful for rice breeding and other research.The results showed that most indica rice varieties were sensitive to low temperature,while most japonica varieties were more resistant to cold.2.There were 20,000 SNPs for GWAS analysis.The average SNP interval was 18.6 kb,far less than the LD decay value of rice.The Kinship analisis showed that most of the 550 rice germplasms had a distant relationship with each other.Group structure had little effect on GWAS analysis.3.An association site related to the cold tolerance at seedling stage was detected on chromosome 11 by the mixed linear model analysis method in EMMAX,containing 52 extremely significant SNPs,ranged from23,863,396 bp to 24,281,415 bp.4.A major QTL for cold tolerance at seedling stage was detected on chromosome 11 by a F2 populations derived from a cross between Mimghui86 and SL11-2.The interval distance of qCT11 was 3.1 Mb between marker C11-2 and C11-4,which was consistent with the locus detected by GWAS.The LOD value of qCT11 was 25.2,which could explain 46.3%of the phenotypic variation with the additive effect value of 18.9%.5.The qCT11 was mapped within 30.0 kb between the markers CT11-120 and CT11-66 containing 5ORFs（Open Reading Frames）by map-based cloning method.All the five candidate genes differed between two parents on the coding sequence and the amino acid sequence of LOCOs11g40140,LOCOs11g40150,LOCOs11g40160 and LOCOs11g40170 were different between two parents.6.Transcriptome analysis found that a total of 1,673 genes were expressed differently,including 916 up-regulated genes and 757 down-regulated genes,compared with different expression genes in NIL-3442with low temperature treatment for 0h and 2h.Moreocer,there were 1501 different expression genes,including 778 up-regulated genes and 723 down-regulated genes,compared with different expression genes in NIL-MH86 with low temperature treatment for 0h and 2h.Plant hormone signal transduction and phenylalanine metabolism pathway play an important role in the low temperature tolerance of NIL-3442.7.Cold tolerance of PA64s and hybrid rice 2YP9 at seedling stage could be significantly improved by qCT11 with the 3442 genotype.qCT11 was a major QTL for cold tolerance at seedling stage and had important application value for improving the cold tolerance of indica rice sterile lines at seedling stage. |
