J Integr Plant Biol. ›› 2019, Vol. 61 ›› Issue (6): 658-674.DOI: 10.1111/jipb.12797

• Research Articles • Previous Articles     Next Articles

Genome-wide association study dissects the genetic bases of salt tolerance in maize seedlings

Xi Luo1†, Bingcai Wang1†, Shan Gao2†, Fei Zhang1, William Terzaghi3 and Mingqiu Dai1*   

  1. 1 National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
    2 College of Plant Science, Tarim University, Alaer 843300, China
    3 Department of Biology, Wilkes University, Wilkes-Barre, Pennsylvania 18766, USA

    These authors contributed equally to this work.
    *Correspondence:

    Email: Mingqiu Dai(mingqiudai@mail.hzau.edu.cn)
  • Received:2018-11-27 Accepted:2019-02-19 Online:2019-02-25 Published:2019-06-01

Abstract: Excess salinity is a natural stress that causes crop yield losses worldwide. The genetic bases of maize salt tolerance remain largely unknown. Here we investigated the survival rates of 445 maize natural accessions after salt treatments. A skewed distribution of the salt-tolerant phenotypes was observed in this population. Genome-wide association studies (GWAS) revealed 57 loci significantly associated with salt tolerance. Forty-nine candidate genes were detected from these loci. About 10% of these genes were co-localized with loci from QTL mapping. Forty four percent of the candidate genes were involved in stress responses, ABA signaling, stomata division, DNA binding/transcription regulation and auxin signaling, suggesting that they are key genetic mechanisms of maize salt tolerance. Transgenic studies showed that two genes, the salt-tolerance-associated-gene 4 (SAG4, GRMZM2G077295) and SAG6 (GRMZM2G106056), which encode a protein transport protein and the double-strand break repair protein MRE11, respectively, had positive roles in plant salt tolerance, and their salt-tolerant haplotypes were revealed. The genes we identified in this study provide a list of candidate targets for further study of maize salt tolerance, and of genetic markers and materials that may be used for breeding salt-tolerance in maize.

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