Welcome to Acta Agronomica Sinica，

Acta Agronomica Sinica ›› 2023, Vol. 49 ›› Issue (10): 2633-2642.doi: 10.3724/SP.J.1006.2023.32007

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

QTL identification and favorable allele mining of cold tolerance at seedling stage by reciprocal introgression and recombinant inbred line populations in rice

CAO Hui-Min1,2(), YANG Xian-Li3(), WANG Li-Zhi3, LI Ping-Ping1, ZHAI Lai-Yuan2, JIANG Shu-Kun3, ZHENG Tian-Qing2, QIU Xian-Jin1(), XU Jian-Long2,4,5()   

  1. 1Key Laboratory of Sustainable Crop Production in the Middle Researches of the Yangtze River, Ministry of Agriculture and Rural Affairs (Co-construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou 434025, Hubei, China
    2Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
    3Institute of Crop Cultivation and Tillage, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, Heilongjiang, China
    4Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, Guangdong, China
    5Hainan Yazhou Bay Seed Laboratory, Sanya 572024, Hainan, China
  • Received:2023-02-16 Accepted:2023-04-17 Online:2023-10-12 Published:2023-04-24
  • Contact: E-mail: xjqiu216@yangtzeu.edu.cn; E-mail: xujianlong@caas.cn
  • About author:**Contributed equally to this work
  • Supported by:
    Shenzhen Basic Research Special Project(JCYJ20200109150713553);Hainan Yazhou Bay Seed Lab Project(B21HJ0216)

RichHTML415

21

PDF

821

Abstract:

Cold damage often hinders rice growth, affects its morphogenesis and leads finally to serious yield loss. Identifying favorable genes tolerant to cold, and breeding elite rice varieties with cold tolerance is an effective way to solve this problem. In this study, two sets of reciprocal introgression lines and a set of recombinant inbred line derived from xian variety Minghui 63 and geng variety 02428 were evaluated for cold tolerance in climate chamber using cold tolerance-related traits such as wilting degree and survival rate after recovered growth. Combined with the available Bin genotype data generated by previous re-sequencing, 13 QTLs for cold tolerance at seedling stage were identified on chromosomes 1, 4, 5, 7, and 12, which explained 0.36% to 13.63% of phenotypic variation. No QTL was stably detected in different genetic backgrounds, whereas five QTLs were simultaneously detected for both wilting degree and survival rate on chromosomes 1, 5, 7, and 12. Among them, QTLs in the regions of 12,732,139-13,202,097 bp and 14,445,778-14,585,009 bp on chromosome 1, and 14,658,891-15,684,510 bp on chromosome 5 had high LOD values above 25 and were considered as reliable main-effect QTLs. Combined with gene annotation, gene expression profile and phenotyping data of cold tolerance of 3K germplasms, the previously cloned gene OsWKRY45 for cold tolerance was regarded as the responsible gene for the QTL in the region of 14,658,891-15,684,510 bp on chromosome 5, while the two candidate genes, LOC_Os01g25540 and LOC_Os01g25560 in the two regions on chromosome 1, were the new candidate genes for both wilting degree and survival rate. Haplotype analysis indicated that Hap2, Hap4, and Hap9 of LOC_Os01g25540 and Hap1, Hap8, and Hap10 of LOC_Os01g25560 were favorable haplotypes for cold tolerance. The results provide the novel germplasms and favorable genes for molecular improvement of cold tolerance in rice.

Key words: rice, cold tolerance at seedling stage, wilting degree, QTL mapping, haplotype

Fig. 1

Frequency distribution of MH63 genome in the reciprocal introgression line and recombinant inbred line populations"

Table 1

Performance of cold tolerance at seedling stage of the parents, reciprocal introgression lines and recombinant inbred lines"

性状
Trait		 明恢63
MH63		 02428 明恢63背景导入系 MH63-ILs 02428背景导入系 02428-ILs 重组自交系 RIL
平均值±标准差
Mean ± SD		 峰度
Kurtosis		 偏度
Skewness		 变幅
Range		 平均值±标准差
Mean ± SD		 峰度
Kurtosis		 偏度
Skewness		 变幅
Range		 平均值±标准差
Mean ± SD		 峰度
Kurtosis		 偏度
Skewness		 变幅
Range
枯萎度
Wilting degree		 8.00 1.00** 8.40±
1.60		 10.07 -3.17 1.00-
9.00		 6.15±
2.91		 -1.30 -0.48 1.00-
9.00		 8.20±
1.80		 6.78 -2.65 1.00-
9.00
存活率
Survival rate (%)		 15.69 81.90** 6.00±
17.00		 12.63 3.53 0-
100.00		 35.00±
36.00		 -1.19 0.58 0-
100.00		 8.00±
20.00		 7.91 2.87 0-
100.00

Fig. 2

Frequency distribution of cold tolerance at seedling stage in the three populations derived from MH63 and 02428"

Table 2

QTLs for cold tolerance at seedling stage in the three populations derived from MH63 and 02428"

群体
Population		 性状
Trait		 染色体
Chr.		 QTL 区间
Interval (bp)		 LOD 加性效应
A		 贡献率
PVE (%)
明恢63背景导入系
MH63-ILs		 枯萎度WD 5 qWD5 14,658,891-15,684,510 28.72 -1.65 8.17
存活率SR 5 qSR5 14,658,891-15,684,510 29.43 0.18 5.86
12 qSR12.1 24,001,167-24,472,105 3.95 0.20 3.28
02428背景导入系
02428-ILs		 枯萎度WD 4 qWD4 1,048,077-1,157,529 7.20 1.15 12.92
12 qWD12 26,529,940-26,660,385 3.03 -0.67 5.20
存活率SR 4 qSR4 764,097-963,403 7.42 −0.15 13.63
12 qSR12.2 26,529,940-26,660,385 2.73 0.08 4.75
重组自交系
RIL		 枯萎度WD 1 qWD1.1 12,732,139-13,202,097 44.95 1.57 9.58
1 qWD1.2 14,445,778-14,585,009 31.63 -1.25 5.91
7 qWD7 16,793,414-17,068,785 2.64 -0.28 0.36
存活率SR 1 qSR1.1 12,732,139-13,202,097 49.88 -0.19 10.67
1 qSR1.2 14,445,778-14,585,009 36.09 0.15 6.71
7 qSR7 16,793,414-17,068,785 3.08 0.03 0.40

Fig. 3

Distribution of QTLs detected for cold tolerance at seedling stage in the three populations derived from MH63 and 02428 WD: wilting degree; SR: survival rate."

Fig. 4

Haplotype analysis of two candidate genes A, D: phenotypic difference between different haplotypes of the two cold tolerance traits, the different lowercase letters indicate significant differences among different haplotypes at the 0.01 probability level; B, E: frequency distribution of five subpopulations in the different haplotypes; C: the relative expression level of LOC_os01g22540 of leaf of Kongyu 131 at seedling stage under cold and normal conditions (data reported by Yu et al. [18]); F: the relative expression level of LOC_os01g22560 of root of Nipponbare at seedling stage under cold and normal conditions (data reported by Yu et al. [18]); ** and *** represent significant difference at the 0.01 and 0.001 probability levels, respectively."

Table S1

Haplotype information of the two candidate genes"

候选基因
Candidate gene		 单倍型编号
Hap ID		 单倍型
Haplotype (5′-3′)		 种质资源数目 No. of accessions
籼稻
xian		 粳稻
geng		 Aus Bas 中间型
Admix
LOC_Os01g25540 Hap1 GCTATTGGACCAGAACCCGTAGGAGGCCACCTGCAGCCACTGCAGCGAAGCGAG 110 4 37 9 4
Hap2 GAGACTGGATCGGATCCCGTGGGGGGCTGCCTATAGCCACTGTGGCAAAGCGGA 1 138 0 1 3
Hap3 TCGATTAGACCAGAACTAGTAGGAGGCCACCTGCAGCCACTGTGGCGAAGCGGA 123 0 0 0 2
Hap4 TCGATTAGGCCAGAACCAGTAGGAGGTCACCTGCAGCCACTGTGGAGAAGCGGA 96 0 0 0 1
Hap5 GAGGCCGGATTAAACCCCGTGGAGGGCCACCTATAGCCACTGTGTAGAAGCGGG 37 0 40 1 4
Hap6 TCGATTGAACCAGAACCCGTAGGGGGCCACTTGCAGCCACAGTGGAGAAACGGA 57 0 0 0 1
Hap7 GAGGCTGGATTAGACCCCATGGGGGGTCATCTATGGCTACTGTAGCGAAGCGGG 49 0 0 0 2
Hap8 GCTATTGGACCAGAACCCGTAGGAGGCCACCTGCAGCCACTGTAGCGAAGCGAG 42 0 0 0 0
Hap9 GAGACTGGATCGGATCCCGTGGGGGACTGCCTATAGCCACTGTGGCAAAGCGGA 0 28 0 0 2
LOC_Os01g25560 Hap1 ACCAGCGCGCGATCGGGAGCTTCAGTGGCCCTTCCAAG 5 344 0 8 14
Hap2 TCCGGTGCAGAGCTGGGAGCGTTAGCGTTCCTATCAGG 155 0 0 0 3
Hap3 TTCGGCGCAGAGCTGGGGGCGCTGGCGGCCCTATCAGG 136 3 12 0 3
Hap4 TCAGGCGCAGAGCTGGGAGCGTTAGCGGCCCTATCAGG 109 0 0 0 0
Hap5 TCCGGCGCAGAGCTGGAAGCGTTAGCGGCCCTATCAGG 89 0 0 0 0
Hap6 TCCGGCGCAGAGCTAAGAGCGTTAACGGCCCGATCAGA 29 0 52 0 5
Hap7 TCCGACGCAGAGCTGGGAGCGTTAGCCGCCCTATCAGG 41 0 33 7 2
Hap8 ACCAGCGCGCGATCGGGAGCTTCAGTGGCCCTTCCMAG 1 76 0 0 2
Hap9 TCCGGCGCAGAGCTGAGATCGTTAGCGGCTCTATTAGG 60 0 1 0 1
Hap10 ACCAGCGCGCGATCGGGAGCTTCAGTGGCCCTTCC-AG 1 37 0 3 6
Hap11 TTCGGCGCAGAGCTGGGGGCGCTGGCGGCCCTATC-GG 31 0 3 0 0
[1] Li T G, Visperas R M, Vergara B S. Correlation of cold tolerance at different growth stages in rice. Acta Bot Sin, 1981, 23: 203-207.
[2] 李霞, 戴传超, 程睿, 陈婷, 焦德茂. 不同生育期水稻耐冷性的鉴定及耐冷性差异的生理机制. 作物学报, 2006, 32: 76-83.
Li X, Dai C C, Cheng R, Chen T, Jiao D M. Identification for cold tolerance at different growth stages in rice (Oryza sativa L.) and physiological mechanism of differential cold tolerance. Acta Agron Sin, 2006, 32: 76-83. (in Chinese with English abstract)
[3] Lou Q J, Chen L, Sun Z X, Xing Y Z, Li J, Xu X Y, Mei H W, Luo L J. A major QTL associated with cold tolerance at seedling stage in rice (Oryza sativa L.). Euphytica, 2007, 158: 87-94.
doi: 10.1007/s10681-007-9431-5
[4] Zhao J L, Zhang S H, Dong J F, Yang T F, Mao X X, Liu Q, Wang X F, Liu B. A novel functional gene associated with cold tolerance at the seedling stage in rice. Plant Biotechnol J, 2017, 15: 1141-1148.
doi: 10.1111/pbi.12704 pmid: 28173633
[5] Kim S, Suh J, Lee C, Lee J, Kim Y, Jena K K. QTL mapping and development of candidate gene-derived DNA markers associated with seedling cold tolerance in rice (Oryza sativa L.). Mol Genet Genomics, 2014, 289: 333-343.
doi: 10.1007/s00438-014-0813-9
[6] Ma Y, Dai X Y, Xu Y Y, Luo W, Zheng X M, Zeng D L, Pan Y J, Lin X L, Liu H H, Zhang D J, Xiao J, Guo X Y, Xu S J, Niu Y D, Jin J B, Zhang H, Xu X, Li L G, Wang W, Qian Q, Ge S, Chong K. COLD1 confers chilling tolerance in rice. Cell, 2015, 160: 1209-1221.
doi: 10.1016/j.cell.2015.01.046 pmid: 25728666
[7] Tao Z, Kou Y J, Liu H B, Li X H, Xiao J H, Wang S P. OsWRKY45 alleles play different roles in abscisic acid signalling and salt stress tolerance but similar roles in drought and cold tolerance in rice. J Exp Bot, 2011, 62: 4863-4874.
doi: 10.1093/jxb/err144
[8] Chen L P, Zhao Y, Xu S J, Zhang Z Y, Xu Y Y, Zhang J Y, Chong K. OsMADS57 together with OsTB1 coordinates transcription of its target OsWRKY94 and D14 to switch its organogenesis to defense for cold adaptation in rice. New Phytol, 2018, 218: 219-231.
doi: 10.1111/nph.14977
[9] Ryu H S, Han M, Lee S K, Cho J I, Ryoo N, Heu S, Lee Y H, Bhoo S H, Wang G L, Hahn T R, Jeon J S. A comprehensive expression analysis of the WRKY gene superfamily in rice plants during defense response. Plant Cell Rep, 2006, 25: 836-847.
doi: 10.1007/s00299-006-0138-1
[10] Li J, Brader G, Palva E T. The WRKY70 transcription factor: a node of convergence for jasmonate-mediated and salicylate-mediated signals in plant defense. Plant Cell, 2004, 16: 319-331.
doi: 10.1105/tpc.016980 pmid: 14742872
[11] Yang C C, Li D Y, Mao D H, Liu X, Ji C J, Li X B, Zhao X F, Cheng Z K, Chen C Y, Zhu L H. Overexpression of microRNA319 impacts leaf morphogenesis and leads to enhanced cold tolerance in rice (Oryza sativa L.). Plant Cell Environ, 2013, 36: 2207-2218.
doi: 10.1111/pce.12130
[12] Liu H, Soomro A, Zhu Y J, Qiu X J, Chen K, Zheng T Q, Yang L W, Xing D Y, Xu J L. QTL underlying iron and zinc toxicity tolerances at seedling stage revealed by two sets of reciprocal introgression populations of rice (Oryza sativa L.). Crop J, 2016, 4: 280-289.
doi: 10.1016/j.cj.2016.05.007
[13] Xie W B, Feng Q, Yu H H, Huang X H, Zhao Q, Xing Y Z, Yu S B, Han B, Zhang Q. Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing. Proc Natl Acad Sci USA, 2010, 107: 10578-10583.
doi: 10.1073/pnas.1005931107 pmid: 20498060
[14] 韩龙植, 张三元. 水稻耐冷性鉴定评价方法. 植物遗传资源学报, 2004, 5: 75-80.
Han L Z, Zhang S Y. Methods of characterization and evaluation of cold tolerance in rice. J Plant Genet Resour, 2004, 5: 75-80.
[15] Morsy M R, Jouve L, Hausman J, Hoffmann L, Stewart J M. Alteration of oxidative and carbohydrate metabolism under abiotic stress in two rice (Oryza sativa L.) genotypes contrasting in chilling tolerance. J Plant Physiol, 2007, 164: 157-167.<br
doi: 10.1016/j.jplph.2005.12.004
[16] Meng L, Li H H, Zhang L Y, Wang J K. QTL IciMapping: integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations. Crop J, 2015, 3: 269-283.
doi: 10.1016/j.cj.2015.01.001
[17] Zhang F, Wang C C, Li M, Cui Y R, Shi Y Y, Wu Z C, Hu Z Q, Wang W S, Xu J L, Li Z K. The landscape of gene- CDS-haplotype diversity in rice: Properties, population organization, footprints of domestication and breeding, and implications for genetic improvement. Mol Plant, 2021, 14: 787-804.
doi: 10.1016/j.molp.2021.02.003 pmid: 33578043
[18] Yu Y M, Zhang H, Long Y P, Shu Y, Zhai J X. Plant public RNA-seq database: a comprehensice online database for expression analysis of -45000 plant public RNA-seq libraries. Plant Biotechnol J, 2022, 20: 806-808.
[19] Li J L, Zeng Y W, Pan Y H, Zhou L, Zhang Z Y, Guo H F, Lou Q J, Shui G H, Huang H G, Tian H, Guo Y M, Yuan P R, Yang H, Pan G J, Wang R Y, Zhang H L, Yang S H, Guo Y, Ge S, Li J J, Li Z C. Stepwise selection of natural variations at CTB2and CTB4a improves cold adaptation during domestication of japonica rice. New Phytol, 2021, 231: 1056-1072.
doi: 10.1111/nph.v231.3
[20] 王韵, 程立锐, 孙勇, 周政, 朱苓华, 徐正进, 徐建龙, 黎志康. 利用双向导入系解析水稻抽穗期和株高QTL及其与环境互作表达的遗传背景效应. 作物学报, 2009, 35: 1386-1394.
Wang Y, Cheng L R, Sun Y, Zhou Z, Zhu L H, Xu Z J, Xu J L, Li Z K. Genetic background effect on QTL expression of heading date and plant height and their interaction with environment in reciprocal introgression lines of rice. Acta Agron Sin, 2009, 35: 1386-1394. (in Chinese with English abstract)
[21] Wang Y, Zhang Q, Zheng T Q, Cui Y R, Zhang W Z, Xu J L, Li Z K. Drought-tolerance QTLs commonly detected in two sets of reciprocal introgression lines in rice. Crop Past Sci, 2014, 65: 171.
doi: 10.1071/CP13344
[22] 张帆, 郝宪彬, 高用明, 华泽田, 马秀芳, 陈温福, 徐正进, 朱苓华, 黎志康. 利用籼稻资源中的“隐蔽有利基因”提高粳稻苗期耐冷性. 作物学报, 2007, 33: 1618-1624.
Zhang F, Hao X B, Gao Y M, Hua Z T, Ma X F, Chen W F, Xu Z J, Zhu L H, Li Z K. Improving seedling cold tolerance of japonica rice by using the “Hidden Diversity” in indica rice germplasm in backcross breeding program. Acta Agron Sin, 2007, 33: 1618-1624. (in Chinese with English abstract)
[1] Peng Jia-Luo, Li Ying, Li Dan-Dan, Yang Jun-Ning, Guo Xue-Feng, Zhang Wen-Jiao, Yu Xiao-Xue, Zhou Ya-Rong, Wang Zhen-Yu, Wang Cai-Xiang, Ma Xiong-Feng, Su Jun-Ji. Identification of class I LBD family members in upland cotton and function and haplotype analyses of GhLBD6 in regulating flowering period [J]. Acta Agronomica Sinica, 2026, 52(6): 1682-1697.
[2] Tang Kuan-Qiang, Li Gong-Yun, Song Mei-Yi, Zhao Xue, Chang Chun-Ling. Genome-wide association analysis and prediction model construction for soybean plant height [J]. Acta Agronomica Sinica, 2026, 52(6): 1743-1756.
[3] Zheng Yu-Zhen, Qi Fei-Yan, Sun Zi-Qi, Liu Hua, Qin Li, Shi Lei, Wang Juan, Wang Meng-Meng, Han Suo-Yi, Xu Jing, Miao Li-Juan, Huang Bing-Yan, Dong Wen-Zhao, Zheng Zheng, Zhang Xin-You. QTL mapping of total very long-chain fatty acids and seven fatty acid components in peanut seeds [J]. Acta Agronomica Sinica, 2026, 52(6): 1646-1657.
[4] Hu Zhao, Qian Run, Xie Feng-Pu, Ying Su-Ping. Genome-wide identification and expression analysis of the SPX gene family in rice under phosphorus treatment [J]. Acta Agronomica Sinica, 2026, 52(6): 1902-1912.
[5] Zou Yi-Mei, Xu Min, Wang Hai-Yang, Yao Hui, Wang Jia-Feng, Liu Hao, Ren Dai-Sheng. Analysis of transcription factor regulatory networks in two-line male sterile rice seedling roots in response to salt stress [J]. Acta Agronomica Sinica, 2026, 52(6): 1728-1742.
[6] Zhang Xian-Feng, Guo Li-Jian, Li Kang-Chun, Kong Bin-Xue, Liu Yu-Fang, Che Zhuo, Yang De-Long. Identification of the ABHD6 gene family and development of functional markers for grain weight in wheat [J]. Acta Agronomica Sinica, 2026, 52(6): 1711-1727.
[7] Yan An, Jiang Kun-Wei, Wang Rong-Yuan, Tian Lin, Zhang Lu, Wang Yun, Xu Jian-Long. Identification and cloning of SVN7 controlling small vascular bundle number in the rice flag leaf [J]. Acta Agronomica Sinica, 2026, 52(5): 1364-1372.
[8] Chen Wei, Wei Wan-Juan, Zhao Qi-Bing, Chang Dong-Wei, Yu Ling-Bo, Zhai Peng-Fei, Feng Zhi-Ming, Chen Zong-Xiang, Ren Yang-Tao, Yang Peng, Liu Hai-Lang, Li Zhen-Fu, Yang Yong-Le, Jin Yan-Gang, Zuo Shi-Min. Developing new germplasm of high-quality and early-maturing rice by editing Hd6 via CRISPR/Cas9 [J]. Acta Agronomica Sinica, 2026, 52(4): 1046-1056.
[9] Shi Shao-Jie, Liu Kai, Chen Zi-Yi, Wang Hui-Ying, Li San-He, Zhou Lei, You Ai-Qing. Cloning and functional analysis of the dwarf and multi-tiller gene DMT1 in rice [J]. Acta Agronomica Sinica, 2026, 52(4): 1022-1034.
[10] Liu Chang-You, Wang Shen, Shi Hui-Ying, Shen Ying-Chao, Sun Lei, Wang Yan, Zhang Zhi-Xiao, Su Qiu-Zhu, Tian Jing, Fan Bao-Jie. QTL mapping for bruchid resistance in an adzuki bean distant hybridization population using rice bean genetic resources [J]. Acta Agronomica Sinica, 2026, 52(3): 936-944.
[11] Ye Fan, Li Shuai, Li Si-Yu, Chen Yun, Dou Chao-Yin, Liu Li-Jun. Effects of water-saving irrigation on rice yield and population quality in Northeast China [J]. Acta Agronomica Sinica, 2026, 52(3): 895-907.
[12] Liu Ning, Fan Ping, Wang Cheng, Chen Qi-Qi, Cheng Qing-Yue, Tie Xia-Na, Tang Jing-Sha, Liu Bin-Bin, Xie Hong-Kun, Wang Jia-Yue, Shi Yuan-Qing, Ma Jun. Effects of reduced nitrogen application combined with organic fertilizer on yield formation and nitrogen utilization in mechanically transplanted rice [J]. Acta Agronomica Sinica, 2026, 52(3): 866-880.
[13] Qin Yi-Yan, Fu Yao, Su Chang, Li Na, Xu Jing-Ru, Cheng Xiao-Ran, Zhang Qi, Zhao Ming-Hui. Functional analysis of OsST41 regulating salt tolerance in rice seedlings [J]. Acta Agronomica Sinica, 2026, 52(3): 802-812.
[14] Li Shi-Qing, Wang Qian, Wang Su-Hua, Zhang Yao-Wen, Wang Li-Xia. Evaluation of salt tolerance at the seedling stage and related gene mining in mung bean germplasm resources [J]. Acta Agronomica Sinica, 2026, 52(2): 376-388.
[15] Zhu Jin-Juan, Wang Hui-Ping, Yang Guo-Dong, Wang Yu-Cheng, Yang Chen, Wang Bin, Agustiani Nurwulan, Tu Jun-Ming, Bi Jun-Guo, Cui Ke-Hui, Huang Jian-Liang, Peng Shao-Bing, Yuan Shen. Effects of water management and variety type on grain yield and quality in ratoon rice [J]. Acta Agronomica Sinica, 2026, 52(1): 295-315.
Viewed
Full text


Abstract

Cited
  Shared   
  Discussed   
No Suggested Reading articles found!
Add: No. 80 Xueyuan South Rd, Beijing 100081, P. R. China E-mail: zwxb301@caas.cn
Supported by Beijing Magtech Co.Ltd