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Identification of a gene controlling variation in the salt tolerance of rapeseed (Brassica napus L.)

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Abstract

Main conclusion

By genome-wide association study, QTLs for salt tolerance in rapeseed were detected, and a TSN1 ortholog was identified as a candidate gene responsible for genetic variation in cultivars.

Dissecting the genomic regions governing abiotic stress tolerance is necessary for marker-assisted breeding to produce elite breeding lines. In this study, a world-wide collection of rapeseed was evaluated for salt tolerance. These rapeseed accessions showed a large variation for salt tolerance index ranging from 0.311 to 0.999. Although no significant correlation between salt tolerance and Na+ content was observed, there was a significant negative correlation between shoot biomass production under a control condition and salt tolerance. These rapeseed accessions were genotyped by DArTseq for a total of 51,109 genetic markers, which were aligned with ‘pseudomolecules’ representative of the genome of rapeseed to locate their hypothetical order for association mapping. A total of 62 QTLs for salt tolerance, shoot biomass, and ion-homeostasis-related traits were identified by association mapping using both the P and Q+K models. Candidate genes located within the QTL regions were also shortlisted. Sequence analysis showed many polymorphisms for BnaaTSN1. Three of them in the coding region resulting in a premature stop codon or frameshift were found in most of the sensitive lines. Loss-of-function mutations showed a significant association with salt tolerance in B. napus.

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Acknowledgments

We are grateful to Dr. Tadashi Takahashi for his guidance about measurement of ion contents. This work was supported in part by the Japan–China Joint Research Program of the Japan Science and Technology Agency (J120000331) and the Rapeseed Project for Restoring Tsunami-Salt-Damaged Farmland. Hui-Yee Yong is a recipient of a Japanese government (Monbukagakusho: MEXT) scholarship from the Ministry of Education, Culture, Sports, Science and Technology, Japan. Construction of the genome pseudomolecules was supported by UK Department for Environment, Food and Rural Affairs (Defra IF0144).

Conflict of interest

The authors declare that they have no competing interests.

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Author notes

  1. Hui-Yee Yong

    Present address: ACGT Sdn. Bhd., Lot L3-I-1, Enterprise 4, Technology Park Malaysia, Bukit Jalil, Kuala Lumpur, 57000, Malaysia

  2. Chunlei Wang

    Present address: College of Horticulture and Plant Protection, Yangzhou University, 48 Wenhuidonglu, Yangzhou, 225009, Peoples Republic of China

  3. Feng Li

    Present address: Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori Amamiyamachi, Aoba-ku, Sendai, Miyagi, 981-8555, Japan

Authors and Affiliations

  1. Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori Amamiyamachi, Aoba-ku, Sendai, Miyagi, 981-8555, Japan

    Hui-Yee Yong, Chunlei Wang, Hiroyasu Kitashiba & Takeshi Nishio

  2. Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China

    Feng Li & Xiaoming Wu

  3. Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK

    Ian Bancroft

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Electronic supplementary material

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425_2015_2310_MOESM1_ESM.pptx

Supplementary Fig. S1 Population structure of B. napus accessions. (a) Estimated L(K) of possible clusters k from 1 to 10; (b) Δk based on the rate of change of L(K) between successive k; (c) Bar plot population structure based on k=2; blue color represents Group 1, red color represents Group 2 (PPTX 73 kb)

425_2015_2310_MOESM2_ESM.png

Supplementary Fig. S2 Quantile–quantile plots for all eight traits for six models: naïve (a), Q (b), P (c), K (d), Q+K (e), P+K (f) (PNG 131 kb)

425_2015_2310_MOESM3_ESM.pdf

Supplementary Fig. S3 Manhattan plots of association analysis using the P model and Q + K model for shoot fresh weight of control plants (a), shoot fresh weight of salt-treated plants (b), shoot dry weight of control plants (c), shoot dry weight of salt-treated plants (d), leaf K+ content of control plants (e), leaf K+ content of salt-treated plants (f), leaf Ca2+ content of control plants (g), leaf Ca2+ content of salt-treated plants (h), leaf Na+ content of salt-treated plants (i), leaf ratio of Na+:K+ of salt-treated plants (j) and leaf ratio of Na+:Ca2+ of salt-treated plants (k). Candidate genes previously shown to be associated with traits near peak SNPs are shown along the top. The horizontal red line represents the significance threshold −log10(p) = 4. The x-axis represents chromosome (PDF 1370 kb)

Supplementary Fig. S4 Expression fold change of BnaaTSN1 genes in response to salt stress (PDF 254 kb)

Supplementary Table S1. Detail of B. napus accessions (XLSX 13 kb)

Supplementary Table S2. Tag sequences of DArT markers (Sheet 1) and SNP markers (Sheet 2) (2157 21 kb)

Supplementary Table S3. Unigene-based map of the B. napus A genome (XLSX 5363 kb)

Supplementary Table S4. Unigene-based map of the B. napus A genome (XLSX 6193 kb)

Supplementary Table S5. Primer sequences for qRT-PCR analysis (XLSX 11 kb)

425_2015_2310_MOESM10_ESM.xlsx

Supplementary Table S6. F test following analysis of variance for shoot FW, DW, leaf K+ and leaf Ca2+ content under control and salt stress (XLSX 11 kb)

425_2015_2310_MOESM11_ESM.xlsx

Supplementary Table S7. F test following analysis of variance for leaf Na+, Na+:K+ and Na+:Ca2+ under salt stress (XLSX 11 kb)

Supplementary Table S8 Phenotype scoring of B. napus accessions (XLSX 29 kb)

Supplementary Table S9. Kinship matrix of 85 B. napus accessions (XLSX 52 kb)

425_2015_2310_MOESM14_ESM.xlsx

Supplementary Table S10. Significant marker associations (p < 1.0x10−4) with the mean of biomass and ion accumulation traits (XLSX 22 kb)

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Yong, HY., Wang, C., Bancroft, I. et al. Identification of a gene controlling variation in the salt tolerance of rapeseed (Brassica napus L.). Planta 242, 313–326 (2015). https://doi.org/10.1007/s00425-015-2310-8

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