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Genetic analysis and molecular mapping of a high threshold and low temperature-sensitive mutant in rice (Oryza sativa L.) at the seedling stage

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Abstract

Cold stress is one of the most severe abiotic adverse factors limiting the growth, productivity, and spatial distribution of rice. We identified a high threshold and low temperature-sensitive mutant (lts) in our breeding program. This mutant displays severe cold sensitive phenotypes when the temperature is maintained below 20 °C for 3–5 days. Other abiotic stress responses tend to share common signal reception and gene regulation pathways, such as ABA-dependent pathways; however, the lts mutant only appears to be sensitive to cold stress. Genetic analysis indicates that this lts mutant is controlled by two major recessive loci linked within the same chromosome. The recombination value between these two loci in an indica × japonica cross of Longjing20 × lts is 12.65 %, and in an indica × indica cross of Newbonnet × lts, the recombination value is 13.93 %. Molecular mapping revealed that one of these two loci is co-segregated with RM5344 in chromosome 7. The candidate gene for this specific locus was determined by sequencing analysis, which showed that it encodes a functionally unknown protein with a transmembrane domain. The detected mutations take place not only in its coding region, including a terminal codon, but also in its promoter region, which results in polymorphism of RM5344. Thus, the recessive allele of this locus is referred to as Oslts a, and that of the other locus is referred to as Oslts b. The precise mapping of the Oslts b-associated locus is underway. These findings provide a solid base for further investigations on the molecular mechanism underlying the responses to cold stress in rice.

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Acknowledgments

This work was supported by the National Natural Science Foundation of China (31171166).

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  1. Institute of Crop Sciences, College of Agriculture and Biotechnology, Zhejiang University, Yuhangtang Road 866, Hangzhou, 310058, China

    Mengyun Xu, Xiufen Ye, Wenyi Wang, Chuchu Wei, Jiwen Zhang & Jumin Tu

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  1. Mengyun Xu
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  3. Wenyi Wang
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  5. Jiwen Zhang
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Correspondence to Jumin Tu.

Electronic supplementary material

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10681_2014_1260_MOESM1_ESM.tif

Supplementary Fig. 1 Introgression of Oslts a from lts mutant into NB via backcrossing, and maker-assisted foreground selection to obtain BC2F2 and BC2F3 lines (TIFF 52 kb)

10681_2014_1260_MOESM2_ESM.tif

Supplementary Fig. 2 Cold damage symptoms in lts mutant. Cold damage occurred at the tillering stage (a) and the maturing stage (b) when the temperature drops below 20°C for 3 to 5 days. Plants in (a) and (b) include the breeding line control (left) and the lts mutant (right) (TIFF 6025 kb)

10681_2014_1260_MOESM3_ESM.tif

Supplementary Fig. 3 Response of LJ20 (top row), NB (middle row), and lts (bottom row) seedlings to abiotic stress: (a) PEG6000; (b) NaCl; (c) ABA. The photos were taken 48 h after treatment (TIFF 11259 kb)

10681_2014_1260_MOESM4_ESM.tif

Supplementary Fig. 4 Marker analysis of mapping population derived from the cross between LJ20 (P2) and lts mutants (P1). (a) RM5344; (b) RM5752; (c) RM20916. The figure shows that the SSR marker RM5344 detected no recombinant segregants (TIFF 3134 kb)

10681_2014_1260_MOESM5_ESM.tif

Supplementary Fig. 5 (a) Indel04310 maker-assisted foreground selection of the BC2F2 segregating population derived from the backcross between lts mutants (P1) and NB (P3), with NB as recurrent parent. (b) and (c) are the phenotype identified as sensitive (S1 to S5) and insensitive (R1 to R5) in the BC2F3 line (TIFF 4543 kb)

10681_2014_1260_MOESM6_ESM.tif

Supplementary Fig. 6 RNAi plasmid construction in this study. To construct the RNAi vector, the PCR products of 5′UTR, exon3, and 3′UTR segment amplified from LJ20 genome DNA were digested with 2 pairs of restriction enzymes: KpnI/BamHI and SpeI/SacI. The differently digested fragments were then successively cloned into pTCK303 to produce the OsLTS a-5′UTR-RNAi plasmid (a), OsLTS a-exon3-RNAi plasmid (b), and OsLTS a-3′UTR-RNAi plasmid (c) (TIFF 82 kb)

Supplementary material 7 (DOCX 16 kb)

Supplementary material 8 (DOCX 13 kb)

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Xu, M., Ye, X., Wang, W. et al. Genetic analysis and molecular mapping of a high threshold and low temperature-sensitive mutant in rice (Oryza sativa L.) at the seedling stage. Euphytica 203, 71–82 (2015). https://doi.org/10.1007/s10681-014-1260-8

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