Scientia Agricultura Sinica ›› 2022, Vol. 55 ›› Issue (22): 4327-4341.doi: 10.3864/j.issn.0578-1752.2022.22.001


Construction of High Density Genetic Map for RIL Population and QTL Analysis of Heat Tolerance at Seedling Stage in Rice (Oryza sativa L.)

LIU Jin1,2(),HU JiaXiao1,MA XiaoDing2,CHEN Wu1,LE Si1,JO Sumin3,CUI Di2,ZHOU HuiYing1,ZHANG LiNa1,SHIN Dongjin3,LI MaoMao1,HAN LongZhi2(),YU LiQin1()   

  1. 1Rice Research Institute, Jiangxi Academy of Agricultural Sciences/Research Center of Jiangxi Crop Germplasm Resources, Nanchang 330200, China
    2Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
    3Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Milyang 627-803, South Korea
  • Received:2022-07-04 Accepted:2022-08-12 Online:2022-11-16 Published:2022-12-14
  • Contact: LongZhi HAN,LiQin YU;;


【Objective】 With global warming, high temperature has an increasing impact on food crop safe. Excavation of heat tolerance gene resources is the most direct green ecological method to cultivate new varieties of heat resistance and eliminate the harm of high temperature, which also the basis for clarifying the physiological, biochemical and molecular genetic mechanism of heat tolerance.【Method】Establishing the identification and evaluation method of heat tolerance at seedling stage, a set of RIL populations was structured from the extreme heat-tolerance Ganzaoxian58(GZX58) and heat-sensitive Junambyeo (JNB), and then the high density genetic map was constructed using genotyping by resequencing technology. To converting SNP information into Bin genotype of the RIL population using sliding window method, which predicting the recombination breakpoints on the chromosomes, finally a high density BinMap genetic map was constructed. Based on the genotype and phenotype data of the 171 lines, QTL mapping of the high temperature seedling survival rate (HTSR) and heat tolerance class (HTC) was performed by ICIM method of the QTL IciMapping software.【Result】A high-density genetic map containing 3 321 Bin markers was constructed, the number of Bin markers for each chromosome between 159 and 400, the average physical distance two markers was about to 106 kb; heat tolerance of the parents and RIL populations was identified by stepwise heat stress at seedlings stage, there have a significant negative correlation between HTSR and HTC, in addition, there has a significant positive correlation between HTSR and indica gene frequency (Fi), which the higher of the Fi, the heat tolerance is better; the bi-modal continuous distribution of phenotype traits from the RIL population showed that the heat tolerance is regulated by few major QTL. A total of 12 QTL controlling with heat tolerance at seedling stage, there have 8 and 4 QTL regulating for HTSR and HTC, respectively. There has a significant genetic overlap from HTSR and HTC, qHTS2, qHTS7 and qHTS8, three major QTL cluster play an important role in regulating the heat tolerance at seedling stage. Among these QTL, qHTS7 was a novel major QTL cluster, which has a strong effect on enhancing the heat resistance at seedling stage. 【Conclusion】 We constructed a high density genetic linkage map containing 3 321 Bin markers, which be used to analyzed the heat tolerance gene from the GZX58 at seedling stage, there have three key QTL cluster identified associated with the heat tolerance, a novel QTL cluster qHTS7 was discovered, efficient acquisition of target segments and candidate genes based on high-density genetic mapping, eight key candidate genes were selected by bioinformatics for regulation of the heat tolerance.

Key words: rice, high-density genetic map, seedling stage, heat tolerance, QTL mapping

Table 1

Identification and evaluation standard of heat tolerance class (HTC) at the seedling stage"

Heat stress phenotype
Heat tolerance
1 植株叶片、根系无损害症状,生长势较好,高温胁迫幼苗存活率高于80%
The plant leaves and roots showed no damage symptoms, the growth potential was good, and then heat stress seedling survival rate was higher than 80%
Extreme heat tolerance
3 部分植株叶片卷曲、黄化失绿,根系受损变黄,高温胁迫幼苗存活率明显下降
The leaves of some plants were curled, yellowing and lost green, the roots were damaged and turned yellow, and then heat stress seedling survival rate have a significantly decreased
Heat tolerance
5 植株整株或部分叶片黄化、枯死,生长受抑,高温胁迫幼苗存活率低于50%
The whole or part of the plant leaves were yellowing and dead, the growth was inhibited, and then heat stress seedling survival rate was less than 50%
Moderate resistance
7 植株叶片和茎秆脱水、生长停止,幼苗枯死或新叶死亡,高温胁迫幼苗存活率较低
Plant leaves and stalks were dehydrated, growth stopped, and then seedlings died or new leaves died, which heat stress seedling survival rate was lower
Heat sensitive
9 幼苗植株全部枯死或接近死亡,高温胁迫幼苗存活率低于10%
All seedling plants died or were nearly death, and then heat stress seedlings survival rate was less than 10%
Extreme heat sensitive

Fig. 1

Evaluation of heat tolerance at the seedling stage for the parents and RIL population under heat stress condition A: Phenotype of RIL population lines from the control; B: Phenotype of RIL population lines from heat stress treatment; C: The parents’ phenotype under heat stress; D: The typical phenotype of different heat tolerance class in the RIL population, respectively"

Fig. 2

Phenotype distribution of the HTSR and HTC for the RIL populations A: Distribution of the high temperature seedling survival rate (HTSR); B: Distribution of heat tolerance class (HTC)"

Fig. 3

Heat tolerance correlation analysis and the distribution of indica gene frequency (Fi) A: The correlation analysis between HTC and HTSR; B: Distribution of Fi in the parents and RIL populations; C: The correlation analysis between HTSR and Fi, ** means extremely significant correlation"

Fig. 4

Construction of the high-density genetic map of the RIL-ZG population A: The high-density Bin marker genotype of the RIL populations; B: The distribution of the high density Bin marker on the chromosome; C: The correlation between the linkage marker on the genetic map and the physical map, respectively"

Table 2

Distribution of the markers in the genetic linkage map of the RIL population"

Bin marker
Distance (cM)
Average distance (cM)
Max gap (cM)
Chr.1 306 160.62 0.52 3.29
Chr.2 332 115.86 0.35 3.11
Chr.3 400 152.91 0.38 3.34
Chr.4 325 155.75 0.48 3.44
Chr.5 342 141.71 0.41 3.62
Chr.6 192 99.60 0.52 4.77
Chr.7 190 147.96 0.78 4.18
Chr.8 255 142.60 0.56 3.97
Chr.9 225 160.73 0.71 3.79
Chr.10 332 154.57 0.47 5.42
Chr.11 263 155.00 0.59 4.18
Chr.12 159 115.78 0.73 3.80
总计Total 3321 1703.09 0.51 5.42

Table 3

Putative QTLs for heat tolerance were detected at seedling stage"

LOD value
PVE (%)
Additive effect
Position(bp) and distance (kb)
qHTSR2 Block4364-4396 3.89 5.25 6.33 34029923—34439386 (409)
qHTSR3 Block4512-4513 2.95 7.20 9.44 2137—105390 (103)
qHTSR4 Block6417-6435 2.89 5.80 4.99 4868070—5212956 (345)
qHTSR6 Block9309-9325 2.68 5.25 6.33 1814778—1992782 (178)
qHTSR7 Block11026-11067 4.55 15.89 -17.86 2023438—2912508 (889)
qHTSR8 Block12594-12597 2.67 6.31 8.34 5289371—5860658 (571)
qHTSR9 Block14481-14488 2.52 6.72 -9.10 22679210—22800304 (121)
qHTSR12 Block18068-18081 3.22 8.51 3.53 3003771—3304029 (300)
qHTC2.1 Block3098-3136 3.39 8.52 0.66 9969848—10850583 (880)
qHTC2.2 Block4364-4396 3.44 9.93 1.55 34029923—34439386 (409)
qHTC7 Block11026-11067 6.52 18.88 -2.56 2023438—2912508 (889)
qHTC8 Block12456-12597 3.67 7.80 0.88 5289371—5860658 (571)


Location of QTL detected for heat tolerance at seedling stage on RILs populations genetic map QTL Red solid and green box indicate the QTL for HTSR and HTC, respectively"

Table 4

Analysis for the important candidate genes from the major QTL cluster"

Candidate gene
Gene function
ORF2-1 Os02g0801700 锌指蛋白,BED型预测结构域 Zinc finger, BED-type predicted domain containing protein
ORF2-2 Os02g0802700* 单半乳糖基二酰基甘油合酶,调控植物生长发育 Monogalactosyldiacylglycerol synthase, plant growth and development
ORF2-3 Os02g0804500* 热休克蛋白Hsp40,含有DnaJ结构域蛋白 Heat shock protein, Hsp40, DnaJ domain containing protein
ORF2-4 Os02g0804900* 核糖核苷酸还原酶,叶绿体生物合成 Ribonucleotide reductase, chloroplast biogenesis
ORF2-5 Os02g0805100 生长素反应蛋白IAA12 Auxin-responsive protein IAA12
ORF2-6 Os02g0806400 锌指家族蛋白 Zine finger family protein
ORF7-1 Os07g0138200* NAC转录因子,ABA诱导的叶片衰老和分蘖 NAC transcription factor, ABA-induced leaf senescence and tillering
ORF7-2 Os07g0138400 CCCH型锌指蛋白,调控耐旱性 CCCH-type zinc finger protein, drought tolerance
ORF7-3 Os07g0139000 预测的含锌指 CCCH 结构域蛋白48 Putative zinc finger CCCH domain-containing protein 48
ORF7-4 Os07g0141500 含有SWIM型结构域锌指蛋白 Zinc finger, SWIM-type domain containing protein
ORF7-5 Os07g0143200* 光敏色素互作 bHLH 因子,冷诱导OsPIF14可变剪接体,光力信号传导
Phytochrome-interacting bHLH factor, cold-induced alternative splicing variant of OsPIF14, cross-talk between light and stress signaling
ORF7-6 Os07g0148900 特色光系统I蛋白 Photosystem I protein-like protein
ORF7-7 Os07g0150500 含C3HC结构域的锌指蛋白 Zinc finger, C3HC-like domain containing protein
ORF7-8 Os07g0152000* 转录因子,调控耐冷性 Transcription factor, cold tolerance
ORF8-1 Os08g0191100* 乌头酸酶,参与热激响应 Aconitase, response to heat stress
ORF8-2 Os08g0191200 叶绿体发育、叶绿素代谢和细胞分裂调节 Regulation of chloroplast development, chlorophyll metabolism and cell division
ORF8-3 Os08g0191900 低温条件下调控叶绿体发育 Regulation of chloroplast development under low-temperature condition
ORF8-4 Os08g0191700* 乙二醛酶I,非生物逆境应激反应 Glyoxalase I, abiotic stress response
ORF8-5 Os08g0196700 核因子Y转录因子,干旱胁迫耐受性 Nuclear Factor Y transcription factor, drought stress tolerance
ORF8-6 Os08g0198100 锌指蛋白,BED型预测结构域 Zinc finger, BED-type predicted domain containing protein
ORF8-7 Os08g0199300 特异G蛋白,参与植物防御及耐盐胁迫反应 Unconventional G protein, plant defense response, salinity stress tolerance
ORF8-8 Os08g0200600* NAC转录因子,调控耐旱性 NAC transcription factor, negative regulation of drought tolerance

Fig. 6

Validating heat tolerance QTL and analyzing pyramiding effect at seedling stage *: P<0.05; **: P<0.01,ns: indicate there have no significant different. n: The number of lines of the some genotype from the RIL population (total 171 lines), nine lines genotype were heterozygous or missing not list, respectively"

Fig. 7

Comparison of the heat tolerance phenotype from different lines carrying major QTL at seedling stage in RIL population A and C indicate the parents from the high temperature stress phenotypes at seedling stage, GZX58 have been three major QTL cluster qHTS2, qHTS7 and qHTS8, JNB no positive QTL cluster; B and D indicate for the aggregation effect of different genotypes from the RIL populations, and then R162, R93, R102, R61, R67, and R20 cluster effect qHTS7+qHTS8, qHTS2+qHTS7, qHTS7, qHTS8, qHTS2, and -; A and B phenotypic of the lines at water plant and high temperature stress environments, C and D phenotypic of the lines at soil plant and high temperature stress environments, respectively"

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