Analysis of QTL Controlling Cold Tolerance at Seedling Stage by Using a High-Density SNP Linkage Map in japonica Rice

doi:10.16819/j.1001-7216.2025.240111

Chinese Journal OF Rice Science ›› 2025, Vol. 39 ›› Issue (1): 82-91.DOI: 10.16819/j.1001-7216.2025.240111

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Analysis of QTL Controlling Cold Tolerance at Seedling Stage by Using a High-Density SNP Linkage Map in japonica Rice

YANG Chuanming¹^,²^,⁴, WANG Lizhi²^,⁴, ZHANG Xijuan²^,⁴, YANG Xianli²^,⁴, WANG Yangyang¹^,²^,⁴, HOU Benfu¹^,²^,⁴, CUI Shize²^,⁴, LI Qingchao³, LIU Kai⁴, MA Rui⁵, FENG Yanjiang⁶, LAI Yongcai⁴, LI Hongyu¹^,^*(), JIANG Shukun²^,³^,⁴^,^*()

¹Agricultural College, Heilongjiang Bayi Agricultural University, Daqing 163319, China
²Crop Cultivation and Tillage Institute, Heilongjiang Academy of Agricultural Sciences/Heilongjiang Provincial Key Laboratory of Crop Physiology and Ecology in Cold Region/Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin 150086, China
³Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences/Heilongjiang Provincial Engineering Technology Research Center of Crop Germplasm Resources Innovation and Utilization in Songnen Plain, Qiqihar 161006, China
⁴Northeast Center of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin 150086, China
⁵Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi 154007, China
⁶Rice Research Institute of Heilongjiang Academy of Agricultural Sciences, Jiamusi 154005, China

Received:2024-01-29 Revised:2024-04-20 Online:2025-01-10 Published:2025-01-14
Contact: LI Hongyu, JIANG Shukun

基于高密度遗传图谱的粳稻苗期耐冷QTL分析

杨传铭¹^,²^,⁴, 王立志²^,⁴, 张喜娟²^,⁴, 杨贤莉²^,⁴, 王洋洋¹^,²^,⁴, 侯本福¹^,²^,⁴, 崔士泽²^,⁴, 李青超³, 刘凯⁴, 马瑞⁵, 冯延江⁶, 来永才⁴, 李红宇¹^,^*(), 姜树坤²^,³^,⁴^,^*()

¹黑龙江八一农垦大学农学院, 黑龙江大庆 163319
²黑龙江省农业科学院耕作栽培研究所/黑龙江省寒地作物生理生态重点实验室/黑龙江省农作物低温冷害工程技术研究中心, 哈尔滨 150086
³黑龙江省农业科学院齐齐哈尔分院/黑龙江省松嫩平原西部作物种质资源创新与利用工程技术研究中心, 黑龙江齐齐哈尔 161006
⁴国家耐盐碱水稻技术创新中心东北中心, 哈尔滨 150086
⁵黑龙江省农业科学院佳木斯分院, 黑龙江佳木斯 154007
⁶黑龙江省农业科学院水稻研究所, 黑龙江佳木斯 154005

通讯作者: 李红宇,姜树坤
基金资助:
黑龙江省农业科技创新跨越工程重大需求科技创新攻关计划资助项目(CX23ZD01);黑龙江省自然基金杰出青年基金资助项目(JQ2023C009);国家自然科学基金资助项目(32071889)

Abstract

Abstract:

【Objective】Low temperature is a primary abiotic stress that inhibits rice development and growth, ultimately reducing its yield. Identifying and utilizing cold tolerance genes to breed cold tolerant cultivars is a simple and effective way to address this issue.【Method】A recombinant inbred line (RIL) population consisting of 144 lines derived from the cross between ‘Lijiang Xintuan Heigu’ (LTH) and ‘Shennong 265’ (SN265) was used to evaluate cold tolerance at the seedling stage in a phytotron. Quantitative trait loci (QTL) for cold tolerance at the seedling stage were detected using a high-density linkage map comprising 2818 markers.【Result】A total of four cold tolerance QTLs at the seedling stage were identified on chromosomes 1, 8, 10, and 12 using the composite interval mapping (CIM) method. The phenotypic variations of these QTL ranged from 5.33% to 19.86%. Among them, the cold tolerance alleles of qCTS1, qCTS10, and qCTS12 were derived from the cold-tolerant parent LTH, while the cold tolerance allele of qCTS8 was from SN265. The major QTL, qCTS12, was located in a 396.67 kb interval from 15.98 Mb to 16.37 Mb on chromosome 12. The qCTS1 was located in a 299.85 kb interval from 9.20 Mb to 9.50 Mb on chromosome 1. The qCTS8 was located in a 55.05 kb interval from 26.09 Mb to 26.15 Mb on chromosome 8. The qCTS10 was located in an 85.82 kb interval from 11.13 Mb to 11.21 Mb on chromosome 10. Further analysis indicated that most interactions between QTLs are additive, except for the negative interaction between qCTS1 and qCTS8. 【Conclusion】Four cold tolerance QTLs were identified using the LTH/SN265 RIL population and its linkage map of 2818 markers at the seedling stage. Three cold tolerance alleles were derived from the cold-tolerant parent LTH. These results not only provide valuable genetic resources for breeding cold-tolerant rice but also offer references for elucidating the genetic and molecular mechanisms of cold tolerance in rice seedlings.

Key words: japonica rice, high-density linkage map, cold tolerance, seedling stage, QTL

摘要：

【目的】低温冷害是影响水稻生长发育，进而造成不同程度减产的主要气象灾害之一。挖掘鉴定耐冷基因，选育耐冷品种，是解决水稻低温冷害最简单、直接和有效的手段之一。【方法】利用丽江新团黑谷/沈农265衍生的包含144个株系的重组自交系群体，通过人工气候室进行苗期耐冷性鉴定。结合全基因组重测序构建的包含2828个bin标记的高密度遗传图谱，进行苗期耐冷性QTL定位和互作分析。【结果】利用完备区间作图法共检测到4个苗期耐冷QTL，分别定位于水稻的1、8、10和12号染色体上，单个QTL的表型贡献率为5.33%~19.86%。其中，qCTS1、qCTS10和qCTS12的增效等位基因来源于强耐冷亲本丽江新团黑谷，qCTS8的增效等位基因来源于沈农265。主效QTL qCTS12定位在12号染色体的15.98 Mb－16.37 Mb之间，物理图谱区间为396.67 Kb。qCTS1定位在1号染色体的9.20 Mb－9.50 Mb间，物理图谱区间为299.85 kb。qCTS8定位在8号染色体的26.09 Mb－26.15 Mb之间，物理图谱区间为55.05 Kb。qCTS10定位在10号染色体的11.13 Mb－11.21 Mb间，物理图谱区间为85.82 kb。进一步分析发现，除qCTS1-qCTS8之间存在负向互作外，其余QTL间的互作表现为加性效应。【结论】利用丽江新团黑谷和沈农265的重组自交系群体，结合包含2818个bin标记的遗传图谱，共检测到4个苗期耐冷QTL，其中3个QTL的增效等位基因来自强耐冷地方品种丽江新团黑谷。可为耐冷分子设计育种提供有用的基因资源，同时为阐明水稻苗期耐冷的遗传和分子机制提供参考。

关键词: 粳稻, 高密度连锁图谱, 苗期, 耐冷, 数量性状位点

YANG Chuanming, WANG Lizhi, ZHANG Xijuan, YANG Xianli, WANG Yangyang, HOU Benfu, CUI Shize, LI Qingchao, LIU Kai, MA Rui, FENG Yanjiang, LAI Yongcai, LI Hongyu, JIANG Shukun. Analysis of QTL Controlling Cold Tolerance at Seedling Stage by Using a High-Density SNP Linkage Map in japonica Rice[J]. Chinese Journal OF Rice Science, 2025, 39(1): 82-91.

杨传铭, 王立志, 张喜娟, 杨贤莉, 王洋洋, 侯本福, 崔士泽, 李青超, 刘凯, 马瑞, 冯延江, 来永才, 李红宇, 姜树坤. 基于高密度遗传图谱的粳稻苗期耐冷QTL分析[J]. 中国水稻科学, 2025, 39(1): 82-91.

Figures/Tables 6

Fig. 1. Evaluation criteria for chilling injury during rice seedling stage

Fig. 2. Cold tolerant phenotypes of LTH and SN265 and distribution of cold tolerance scales in LTH/SN265 RILs at seedling stage A, Comparison of phenotypes between LTH and SN265 after cold treatment after 7 days of recovery at the seedling stage; B, Distribution of cold tolerance scales at the seedling stage in LTH/SN265 RILs; C, Phenotypes of LTH/SN265 RILs after cold treatment at seedling stage (after 7 days of recovery). LTH, Lijiang Xintuan Heigu; SN265, Shennong 265.

Table 1. QTL controlling cold tolerance at seedling stage identified in LTH/SN265 RILs

QTL	Chr.	峰值位置^a Peak position ^a (Mb)	峰值标记 Peak marker	QTL区间 QTL interval		LOD值 LOD value	表型贡献率 Phenotypic variation explained (%)	加性效应 Additive effect	增效等位基因来源 Positive allele donor
QTL	Chr.	峰值位置^a Peak position ^a (Mb)	峰值标记 Peak marker	物理图谱 Physical location (Mb)	定位区间 Location interval(kb)	LOD值 LOD value	表型贡献率 Phenotypic variation explained (%)	加性效应 Additive effect	增效等位基因来源 Positive allele donor
qCTS1	1	9.23	Bin01-072	9.20－9.50	299.85	4.35	5.33	−0.37	LTH
qCTS8	8	26.10	Bin08-220	26.05－26.15	55.05	4.42	5.59	0.36	SN265
qCTS10	10	11.20	Bin10-149	11.13－11.21	85.82	7.07	9.04	−0.46	LTH
qCTS12	12	16.02	Bin12-103	15.98－16.37	396.67	13.82	19.86	−0.69	LTH

Fig. 3. Chromosome location of the four cold tolerance QTLs at seedling stage in LTH-SN265 RILs

Fig. 4. Interaction analysis of four QTLs for cold tolerance at seedling stage CTS denotes cold tolerant allele genotype; cts denotes the cold susceptible allelic genotype.

Fig. 5. Epistasis effect estimation for cold tolerance QTLs at the seedling stage

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Analysis of QTL Controlling Cold Tolerance at Seedling Stage by Using a High-Density SNP Linkage Map in japonica Rice

基于高密度遗传图谱的粳稻苗期耐冷QTL分析

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