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INTRODUCTION: As the main grain crop, rice plays an important role in ensuring food security of China. Rise in global average temperature is detrimental to crop yield and heat stress is currently one of the major abiotic threats on rice production. There are significant variations in heat tolerance among different rice varieties. As a typical quantitative trait, heat tolerance of rice is controlled by multiple genes. Identification of new QTLs and genes related to heat tolerance is very important for the genetic research and the breeding of new heat-tolerant rice varieties.
RATIONALE:In recent years, many heat tolerant QTLs had been identified with different genetic populations and evaluation indicators at different growth stages. Most of those QTLs were mapped in large intervals due to the limited population sizes, simplified experimental designs and inaccurately controlled environments. The heat tolerance level identification in a population is very difficult for mature plants. Therefore, we developed a population of recombinant inbred lines (RILs) with 186 lines derived from japonica rice TD70 and indica rice Kasalath, which showed large variations in seedling survival rates under high temperature stress (HTSR). QTLs associated with HTSR were mapped by the high-density linkage Bin-map and candidate genes were identified.
RESULTS: Twenty-six QTLs related to the HTSR were mapped on 11 of the 12 chromosomes, with the exception of 3. The LOD values of single QTL ranged from 2.59-16.15, four of which with LOD values greater than 10. Seven QTLs were located within the same interval or adjacent to known heat tolerance QTLs. The major locus of qHTSR5.2 was located in the 26.25-26.38 Mb region of Chr. 5 with an LOD value of 12.07, which explained 7.18% of the total phenotypic variation in the HTSR. According to the annotation and sequence analysis of the genes located in the region of four major QTLs,we found that twenty-seven annotated genes with non-synonymous mutations in the coding regions between TD70 and Kasalath. Five of them were identified as potential candidate genes because the RILs sharing each of the distinct haplotypes of their parents for each gene exhibited significant different HTSR resistance level. Among them, three candidate genes encode heat shock proteins HSP20 or HSP17.5.
CONCLUSION: We detected 26 QTLs controlling seedling heat tolerance based on a high-density Bin map in a RIL population. Some of the QTLs were overlapped with known heat tolerance loci, indicating their strong effects on regulating heat tolerance of rice. Five candidate genes were identified through gene annotation, parental sequence comparison, effect analysis of heat tolerance between RILs with different haplotypes. The candidate genes identified in our study could be used for molecular mechanism research on high temperature tolerance of rice in the future.
Mapping of QTL for heat tolerance at seedling stage in rice based on a high-density Bin map. Heat tolerance of parents and RILs population during seedling stage. Location of QTLs contributing to heat tolerance at seedling stage.
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| 科 Family | 属数 Number of genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) | 属 Genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) |
|---|---|---|---|---|---|---|
| 鹅膏菌科Amanitaceae | 2 | 11 | 5.26 | 鹅膏菌属 Amanita | 10 | 4.78 |
| 小菇科 Mycenaceae | 2 | 12 | 5.74 | 丝盖伞属 Inocybe | 5 | 2.39 |
| 多孔菌科 Polyporaceae | 8 | 14 | 6.70 | 蜡蘑属 Laccaria | 5 | 2.39 |
| 红菇科 Russulaceae | 3 | 23 | 11.00 | 小皮伞属 Marasmius | 6 | 2.87 |
| 小菇属 Mycena | 11 | 5.26 | ||||
| 光柄菇属 Pluteus | 5 | 2.39 | ||||
| 红菇属 Russula | 17 | 8.13 | ||||
| 栓菌属 Trametes | 5 | 2.39 |
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