Mapping of QTLs for Heat Tolerance at the Seedling Stage in Rice Based on a High-density Bin Map

doi:10.11983/CBB24047

Abstract

Abstract: 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.

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

Zhao Ling, Guan Ju, Liang Wenhua, Zhang Yong, Lu Kai, Zhao Chunfang, Li Yusheng, Zhang Yadong. Mapping of QTLs for Heat Tolerance at the Seedling Stage in Rice Based on a High-density Bin Map[J]. Chinese Bulletin of Botany, 2025, 60(3): 342-353.

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URL: https://www.chinbullbotany.com/EN/10.11983/CBB24047

https://www.chinbullbotany.com/EN/Y2025/V60/I3/342

Figures/Tables 6

References 60

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QTL	Chr.	Interval (Mb)	Genes	Annotation	Reference
qHTSR1.1	1	1.90-1.95	Os01g0134800*	Glycosyl hydrolase family
			Os01g0134900*	Glycosyl hydrolase family
			Os01g0135000	Similar to 1,4-beta-D xylan xylanohydrolase
			Os01g0135700*	OsCML16, calmodulin, calcium signaling during abiotic stress	Yang et al., 2018
			Os01g0135800*	HSP20, heat shock protein
			Os01g0135900*	HSP20, heat shock protein	Sarkar et al., 2020
			Os01g0136000*	OsHSP16.9C, HSP17.5 heat shock protein	Sarkar et al., 2020
			Os01g0136050	16.9 kDa heat shock protein
qHTSR4.1	4	15.72-15.92	Os04g0336600	Peptidase aspartic, catalytic domain containing protein
			Os04g0337000*	Aspartyl protease domain containing protein
			Os04g0337201*	SAD2, sensitive to ABA and drought2
			Os04g0337300	SAD2, sensitive to ABA and drought2
			Os04g0337500	Oxidoreductase
			Os04g0337800*	IN2-2 protein
			Os04g0338000*	Aldo/keto reductase family protein	Kim et al., 2019
qHTSR5.1	5	20.41-20.48	Os05g0417000*	DUF260 domain containing protein
qHTSR5.1	5	20.41-20.48	Os05g0417100*	Deg Protease Protein, chloroplast development and maintenance of PSII function under high temperatures	Zheng et al., 2016
			Os05g0417800*	ulp1 protease family
qHTSR5.2	5	26.25-26.39	Os05g0418000*	GDP-dissociation inhibitor	Shad et al., 2023
			Os05g0528500	OsWRKY58, WRKY transcription factor
			Os05g0528600	OsYUCCA2, flavin monooxygenase-like enzyme, auxin biosynthesis	Yamamoto et al., 2007
			Os05g0528900	Ribosomal protein
			Os05g0529000*	OsCOLE1, regulation of intracellular auxin transport	Liu et al., 2016a
			Os05g0529200	Enoyl-CoA hydratase/isomerase family protein
			Os05g0529300	ER lumen protein retaining receptor
			Os05g0529400*	Ubiquitin domain-containing protein
			Os05g0529600*	ATP binding protein
			Os05g0529700	Electron transporter/heat shock protein binding protein
			Os05g0529900	Cell cycle control protein, OsHsfA4d; Heat stress transcription factor	Mittal et al., 2009
			Os05g0530400*	Plant growth and balancing reactive oxygen species du- ring biotic and abiotic stress	Mittal et al., 2009
			Os05g0530500	Snf1 protein kinase; sucrose non-fermenting-1 related protein kinase 1	Kanegae et al., 2005
			Os05g0530701	Leucine-rich repeat
			Os05g0531000*	A member of S40 gene family, regulation of crosstalk among abiotic and biotic and developmental senescence
			Os05g0531100	A member of S40 gene family, regulation of crosstalk among abiotic and biotic and developmental senescence
			Os05g0531200	Pollen Ole e I allergen and extensin family protein precursor
			Os05g0531400	Pollen Ole e I allergen and extensin family protein precursor
			Os05g0531500	Hydrolase

QTL	Chr.	Interval (Mb)	Genes	Annotation	Reference
qHTSR1.1	1	1.90-1.95	Os01g0134800*	Glycosyl hydrolase family
			Os01g0134900*	Glycosyl hydrolase family
			Os01g0135000	Similar to 1,4-beta-D xylan xylanohydrolase
			Os01g0135700*	OsCML16, calmodulin, calcium signaling during abiotic stress	Yang et al., 2018
			Os01g0135800*	HSP20, heat shock protein
			Os01g0135900*	HSP20, heat shock protein	Sarkar et al., 2020
			Os01g0136000*	OsHSP16.9C, HSP17.5 heat shock protein	Sarkar et al., 2020
			Os01g0136050	16.9 kDa heat shock protein
qHTSR4.1	4	15.72-15.92	Os04g0336600	Peptidase aspartic, catalytic domain containing protein
			Os04g0337000*	Aspartyl protease domain containing protein
			Os04g0337201*	SAD2, sensitive to ABA and drought2
			Os04g0337300	SAD2, sensitive to ABA and drought2
			Os04g0337500	Oxidoreductase
			Os04g0337800*	IN2-2 protein
			Os04g0338000*	Aldo/keto reductase family protein	Kim et al., 2019
qHTSR5.1	5	20.41-20.48	Os05g0417000*	DUF260 domain containing protein
qHTSR5.1	5	20.41-20.48	Os05g0417100*	Deg Protease Protein, chloroplast development and maintenance of PSII function under high temperatures	Zheng et al., 2016
			Os05g0417800*	ulp1 protease family
qHTSR5.2	5	26.25-26.39	Os05g0418000*	GDP-dissociation inhibitor	Shad et al., 2023
			Os05g0528500	OsWRKY58, WRKY transcription factor
			Os05g0528600	OsYUCCA2, flavin monooxygenase-like enzyme, auxin biosynthesis	Yamamoto et al., 2007
			Os05g0528900	Ribosomal protein
			Os05g0529000*	OsCOLE1, regulation of intracellular auxin transport	Liu et al., 2016a
			Os05g0529200	Enoyl-CoA hydratase/isomerase family protein
			Os05g0529300	ER lumen protein retaining receptor
			Os05g0529400*	Ubiquitin domain-containing protein
			Os05g0529600*	ATP binding protein
			Os05g0529700	Electron transporter/heat shock protein binding protein
			Os05g0529900	Cell cycle control protein, OsHsfA4d; Heat stress transcription factor	Mittal et al., 2009
			Os05g0530400*	Plant growth and balancing reactive oxygen species du- ring biotic and abiotic stress	Mittal et al., 2009
			Os05g0530500	Snf1 protein kinase; sucrose non-fermenting-1 related protein kinase 1	Kanegae et al., 2005
			Os05g0530701	Leucine-rich repeat
			Os05g0531000*	A member of S40 gene family, regulation of crosstalk among abiotic and biotic and developmental senescence
			Os05g0531100	A member of S40 gene family, regulation of crosstalk among abiotic and biotic and developmental senescence
			Os05g0531200	Pollen Ole e I allergen and extensin family protein precursor
			Os05g0531400	Pollen Ole e I allergen and extensin family protein precursor
			Os05g0531500	Hydrolase

QTL	This study		Known QTLs or genes
QTL	Chr.	Position (Mb)	Population	Traits	Position (Mb)	Reference
qHTSR1.1	1	1.90-1.95	Nipponbare/Kasalath backcross inbred lines (BILs)	HT during grain filling	0.64-3.44	朱昌兰等, 2005
			Teqin/Yuanjiang Common Wild Rice BILs	HT at flowering stage	0.38-2.18	奎丽梅等, 2008
			N22/IR64 recombinant inbred lines (RILs)	Shoot length under heat stress	1.86-2.31	Kilasi et al., 2018
qHTSR1.2	1	39.82-39.86	Longdao 5/Zhongyouzao 8RILs	HTSR	37.6-39.08	刘进等, 2022a
qHTSR1.2	1	39.82-39.86	Bala/Azucena RILs	HT at flowering stage	38.35-40.66	Jagadish et al., 2010
qHTSR2.2	2	24.58-24.72	255 core materials	HTSR	24.66	魏昭然, 2020
qHTSR4.1	4	15.71-15.92	996/4628 RILs	HT at flowering stage	15.74-18.82	Xiao et al., 2011; 盘毅等, 2011
qHTSR4.1	4	15.71-15.92	Bala/Azucena RILs	HT at flowering stage	14.19-16.86	Jagadish et al., 2010
qHTSR 5.2	5	26.25-26.39	Zhongyouzao 8/Fengjin RILs	HT at flowering stage	3.08-26.85	张涛等, 2008
			Longdao 5/Zhongyouzao 8 RILs	HTSR	25.78-26.28	刘进等, 2022a; 李林浩, 2023
			R498/R3551 RILs	HT at flowering stage	26.69-27.69	陶磊, 2020
qHTSR9.1	9	9.42-9.46	Nipponbare/Kasalath bils	Thermo-tolerance of amylose content	5.27-21.85	朱昌兰等, 2006
qHTSR10	10	22.57-22.63	Bala/Azucena RILs	HT at flowering stage	20.84-23.45	Jagadish et al., 2010
			233 core materials	HT during grain filling	22.62	杨飞, 2020
			Sasanishiki/Habataki CSSLs	Pollen fertility under high temperature	19.89-23.01	Zhu et al., 2017

QTL	This study		Known QTLs or genes
QTL	Chr.	Position (Mb)	Population	Traits	Position (Mb)	Reference
qHTSR1.1	1	1.90-1.95	Nipponbare/Kasalath backcross inbred lines (BILs)	HT during grain filling	0.64-3.44	朱昌兰等, 2005
			Teqin/Yuanjiang Common Wild Rice BILs	HT at flowering stage	0.38-2.18	奎丽梅等, 2008
			N22/IR64 recombinant inbred lines (RILs)	Shoot length under heat stress	1.86-2.31	Kilasi et al., 2018
qHTSR1.2	1	39.82-39.86	Longdao 5/Zhongyouzao 8RILs	HTSR	37.6-39.08	刘进等, 2022a
qHTSR1.2	1	39.82-39.86	Bala/Azucena RILs	HT at flowering stage	38.35-40.66	Jagadish et al., 2010
qHTSR2.2	2	24.58-24.72	255 core materials	HTSR	24.66	魏昭然, 2020
qHTSR4.1	4	15.71-15.92	996/4628 RILs	HT at flowering stage	15.74-18.82	Xiao et al., 2011; 盘毅等, 2011
qHTSR4.1	4	15.71-15.92	Bala/Azucena RILs	HT at flowering stage	14.19-16.86	Jagadish et al., 2010
qHTSR 5.2	5	26.25-26.39	Zhongyouzao 8/Fengjin RILs	HT at flowering stage	3.08-26.85	张涛等, 2008
			Longdao 5/Zhongyouzao 8 RILs	HTSR	25.78-26.28	刘进等, 2022a; 李林浩, 2023
			R498/R3551 RILs	HT at flowering stage	26.69-27.69	陶磊, 2020
qHTSR9.1	9	9.42-9.46	Nipponbare/Kasalath bils	Thermo-tolerance of amylose content	5.27-21.85	朱昌兰等, 2006
qHTSR10	10	22.57-22.63	Bala/Azucena RILs	HT at flowering stage	20.84-23.45	Jagadish et al., 2010
			233 core materials	HT during grain filling	22.62	杨飞, 2020
			Sasanishiki/Habataki CSSLs	Pollen fertility under high temperature	19.89-23.01	Zhu et al., 2017