Identification of a genomic region controlling thermotolerance at flowering in maize using a combination of whole genomic re-sequencing and bulked segregant analysis

Abstract

Key message

A novel genomic region controlling thermotolerance at flowering was identified by the combination of whole genomic re-sequencing and bulked segregant analysis in maize.

Abstract

The increasing frequency of extreme high temperature has brought a great threat to the development of maize throughout its life cycle, especially during the flowering phase. However, the genetic basis of thermotolerance at flowering in maize remains poorly understood. Here, we characterized a thermotolerant maize ecotype Abe2 and dissected its genetic basis using a F2:8 recombinant inbred line (RIL) population generated from a cross between Abe2 and B73. After continuous high temperature stress above 35 °C for 17 days, Abe2 and B73 show distinct leaf scorching phenotype under field conditions. To identify the genomic regions associated with the phenotypic variation, we applied a combination of whole genomic re-sequencing and bulked segregant analysis, and revealed 10,316,744 SNPs and 1,488,302 InDels between the two parental lines, and 2,693,054 SNPs and 313,757 InDels between the two DNA pools generated from the thermos-tolerant and the sensitive individuals of the RIL, of which, 108,655 and 17,853 SNPs may cause nonsynonymous variations. Finally, a 7.41 Mb genomic region on chromosome 1 was identified, and 7 candidate genes were annotated to participate in high temperature-related stress response. A candidate gene Zm00001d033339 encoding a serine/threonine protein kinase was proposed to be the most likely causative gene contributing to the thermotolerance at flowering by involving in stomatal movement (GO: 0010119) via Abscisic acid (ABA) pathway (KO04075). This work could provide an opportunity for gene cloning and pyramiding breeding to improve thermotolerance at flowering in maize.

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Data availability

The raw sequence data reported in this paper have been deposited in the Genome Sequence Archive (Wang et al. 2017) in BIG Data Center (BIG et al. 2019), Beijing Institute of Genomics (BIG), Chinese Academy of Sciences, under accession numbers CRA002322, CRA002322 that are publicly accessible at https://bigd.big.ac.cn/gsa. The raw data supporting the conclusions of this manuscript will be made available by the authors, without undue reservation, to any qualified researcher.

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Acknowledgements

We thank Dr. Chuanxiao Xie from the Institute of Crop Science, Chinese Academy of Agricultural Sciences for providing the maize ecotype Abe2. This work was supported by The National Key Research and Development Program of China (2016YFD0101803), the National Key Research and Development Program of China (2017YFD0301301) and the National Natural Science Foundation of China (31670264). No conflict of interest declared.

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PL, WZ, JS and CQ contributed conception and designed the study. WZ, JS, CQ, SY, SH, CH, YW, WW, HC, SR, CC, ZT and CW performed the field experiments. WZ assayed the plant phenotype under controlled growth conditions, assembled and analyzed the data. WZ and PL wrote the manuscript. All authors contributed to manuscript revision.

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Correspondence to Peijin Li.

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Zeng, W., Shi, J., Qiu, C. et al. Identification of a genomic region controlling thermotolerance at flowering in maize using a combination of whole genomic re-sequencing and bulked segregant analysis. Theor Appl Genet 133, 2797–2810 (2020). https://doi.org/10.1007/s00122-020-03632-x

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