Chinese Journal OF Rice Science >
Analysis of QTL Controlling Cold Tolerance at Seedling Stage by Using a High-Density SNP Linkage Map in japonica Rice
Received date: 2024-01-29
Revised date: 2024-04-20
Online published: 2025-01-14
【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
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 . DOI: 10.16819/j.1001-7216.2025.240111
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