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OsWRKY115 on qCT7 links to cold tolerance in rice

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Abstract

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qCT7, a novel QTL for increasing seedling cold tolerance in rice, was fine-mapped to a 70.9-kb region on chromosome 7, and key OsWRKY115 was identified in transgenic plants.

Abstract

Cold stress caused by underground cold-water irrigation seriously limits rice productivity. We systemically measured the cold-responsive traits of 2,570 F2 individuals derived from two widely cultivated rice cultivars, Kong-Yu-131 and Dong-Nong-422, to identify the major genomic regions associated with cold tolerance. A novel major QTL, qCT7, was mapped on chromosome 7 associated with the cold tolerance and survival, using whole-genome re-sequencing with bulked segregant analysis. Local QTL linkage analysis with F2 and fine mapping with recombinant plant revealed a 70.9-kb core region on qCT7 encoding 13 protein-coding genes. Only the LOC_Os07g27670 expression level encoding the OsWRKY115 transcription factor on the locus was specifically induced by cold stress in the cold-tolerant cultivar. Moreover, haplotype analysis and the KASP8 marker indicated that OsWRKY115 was significantly associated with cold tolerance. Overexpression and knockout of OsWRKY115 significantly affected cold tolerance in seedlings. Our experiments identified OsWRKY115 as a novel regulatory gene associated with cold response in rice, and the Kong-Yu-131 allele with specific cold-induced expression may be an important molecular variant.

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Funding

This research was financially supported by the major science and technology project of Heilongjiang Province, China (Grant No. 2020ZX16B01) and the China Postdoctoral Science Foundation (Grant No. 2019M651249).

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  1. Hualong Liu, Luomiao Yang, Shanbin Xu and Ming-Jie Lyu these authors have contributed equally to the article.

Authors and Affiliations

  1. Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China

    Hualong Liu, Luomiao Yang, Shanbin Xu, Jingguo Wang, Hongliang Zheng, Wei Xin & Detang Zou

  2. National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China

    Ming-Jie Lyu & Jun Liu

  3. Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China

    Huan Wang

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  1. Hualong Liu
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Contributions

HLL, JL, and DTZ conceived and designed the research. LMY, SBX, and MJL participated in data analysis. JGW, SB, X, HLZ, JML, and WX performed material development, sample preparation, and data analysis. LMY, JL, and DTZ wrote the manuscript. JL and DTZ corrected the manuscript. The final manuscript was read and approved by all authors.

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Correspondence to Jun Liu or Detang Zou.

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The authors declare that there are no conflicts of interest.

Data availability

The raw sequencing data were uploaded to the NCBI Sequence Read Archive database under the accession numbers SRR10896964, SRR10896965, SRR10896966, and SRR10896967.

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Communicated by Matthias Wissuwa.

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Fig. S1

SNP and Indel statistics. (A) Venn diagram of SNP in the four DNA pools. (B) Venn diagram of InDel in the four DNA pools.

Supplementary file1 (PNG 919 kb)

Fig. S2

Expression levels of the 13 candidate genes in DN422 and KY131 under the normal measured by qRT-PCR. The results were statistically analysed using Student’s t-test (*, P<0.05; **, P<0.01).

Supplementary file2 (PNG 338 kb)

Fig S3

Phylogenetic relationships among 15 WRKY-associated proteins with cold response function in Oryza sativa, Arabidopsis thaliana, Vitis vinifera, and Cucumis sativus. The maximum likelihood tree was created using MEGA v. 7.0 (bootstrap value = 1,000).

Supplementary file3 (TIF 6260 kb)

Fig. S4

Segregation of OsWRKY115 alleles in the 179 BC2F4 populations.

Supplementary file4 (TIF 90 kb)

Fig. S5

179 BC2F4 populations were genotyped with KASP8. The genotypes of KY131, DN422 and, Heterozygote were represented by yellow fluorescence, red fluorescence, and green fluorescence. The T, S, and M on the fluorescence marker represent cold tolerance (T), cold sensitivity (S), and moderate cold resistance (M), respectively.

Supplementary file6 (JPG 698 kb)

Supplementary file7 (JPG 15872 kb)

Supplementary file8 (XLSX 53 kb)

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Liu, H., Yang, L., Xu, S. et al. OsWRKY115 on qCT7 links to cold tolerance in rice. Theor Appl Genet 135, 2353–2367 (2022). https://doi.org/10.1007/s00122-022-04117-9

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