Abstract
Key message
Ten stable loci for freezing tolerance (FT) in wheat were detected by genome-wide association analysis. The putative candidate gene TaRPM1-7BL underlying the major locus QFT.ahau-7B.2 was identified and validated.
Abstract
Frost damage restricts wheat growth, development, and geographical distribution. However, the genetic mechanism of freezing tolerance (FT) remains unclear. Here, we evaluated FT phenotypes of 245 wheat varieties and lines, and genotyped them using a Wheat 90 K array. The association analysis showed that ten stable loci were significantly associated with FT (P < 1 × 10–4), and explained 6.45–26.33% of the phenotypic variation. In particular, the major locus QFT.ahau-7B.2 was consistently related to all nine sets of FT phenotypic data. Based on five cleaved amplified polymorphic sequence (CAPS) markers closely linked to QFT.ahau-7B.2, we narrowed down the target region to the 570.67–571.16 Mb interval (0.49 Mb) on chromosome 7B, in which four candidate genes were annotated. Of these, only TaRPM1-7BL exhibited consistent differential expression after low temperature treatment between freezing-tolerant and freezing-sensitive varieties. The results of cloning and whole-exome capture sequencing indicated that there were two main haplotypes for TaRPM1-7BL, including freezing-tolerant Hap1 and freezing-sensitive Hap2. Based on the representative SNP (+1956, A/G), leading to an amino acid change in the NBS domain, a CAPS marker (CAPS-TaRPM1-7BL) was developed and validated in 431 wheat varieties (including the above 245 materials) and 318 F2 lines derived from the cross of ‘Annong 9267’ (freezing-tolerant) × ‘Yumai 9’ (freezing-sensitive). Subsequently, the TaRPM1-7BL gene was silenced in ‘Yumai 9’ by virus-induced gene silencing (VIGS), and these silenced wheat seedlings exhibited enhanced FT phenotypes, suggesting that TaRPM1-7BL negatively regulates FT. These findings are valuable for understanding the complex genetic basis of FT in wheat.
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Funding
This work was supported by grants from the University Synergy Innovation Program of Anhui Province (GXXT-2021-058), Key Scientific and Technological Breakthroughs of Anhui Province “Innovation of Excellent Wheat Germplasm Resources, Discovery of Important New Genes and Application in Wheat Molecular Design Breeding” (2021d06050003), the Joint Key Project of Improved Wheat Variety of Anhui Province (22805001), the Agriculture Research System of Anhui Province (AHCYTX-02), and Jiangsu Collaborative Innovation Center for Modern Crop Production (JCIC-MCP).
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HPZ, CC, and CXM initiated the project, designed the study, and revised the paper; XP and XLN completed the experiment, and prepared the manuscript; WG, SNY, HSF, JJC, JL, and HS assisted in the cultivation, management, and phenotyping of experimental materials. All authors read the manuscript and approved it for publication.
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Pan, X., Nie, X., Gao, W. et al. Identification of genetic loci and candidate genes underlying freezing tolerance in wheat seedlings. Theor Appl Genet 137, 57 (2024). https://doi.org/10.1007/s00122-024-04564-6
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DOI: https://doi.org/10.1007/s00122-024-04564-6