Characterization of natural genetic variation identifies multiple genes involved in salt tolerance in maize

  • Devinder SandhuEmail author
  • Manju V. Pudussery
  • Rohit Kumar
  • Andrew Pallete
  • Paul Markley
  • William C. Bridges
  • Rajandeep S. SekhonEmail author
Original Article


Progressive decline in irrigation water is forcing farmers to use brackish water which increases soil salinity and exposes the crop plants to salinity. Maize, one of the most important crops, is sensitive to salinity. Salt tolerance is a complex trait controlled by a number of physiological and biochemical processes. Scant information is available on the genetic architecture of salt tolerance in maize. We evaluated 399 inbred lines for six early vigor shoot and root traits upon exposure of 18-day seedlings to salinity (ECiw = 16 dS m-1) stress. Contrasting response of shoot and root growth to salinity indicated a meticulous reprogramming of resource partitioning by the plants to cope with the stress. The genomic analysis identified 57 single nucleotide polymorphisms (SNP) associated with early vigor traits. Candidate genes systematically associated with each SNP include both previously known and novel genes. Important candidates include a late embryogenesis protein, a divalent ion symporter, a proton extrusion protein, an RNA-binding protein, a casein kinase 1, and an AP2/EREBP transcription factor. The late embryogenesis protein is associated with both shoot and root length, indicating a coordinated change in resource allocation upon salt stress. Identification of a casein kinase 1 indicates an important role for Ser/Thr kinases in salt tolerance. Validation of eight candidates based on expression in a salt-tolerant and a salt-sensitive inbred line supported their role in salt tolerance. The candidate genes identified in this investigation provide a foundation for dissecting genetic and molecular regulation of salt tolerance in maize and related grasses.


Salinity Zea mays Maize Salt tolerance Gene expression GWA 



Authors would also like to thank two anonymous reviewers for their valuable suggestions to improve the manuscript.

Funding information

Dr. Rohit Kumar is supported by United States Department of Agriculture (USDA) Hatch project SC-1700520. Additional support came from the USDA - Agricultural Research Services, National Program 301: Plant Genetic Resources, Genomics and Genetic Improvement (project number 2036-13210-012-00-D).

Compliance with ethical standards


Mention of trade names or commercial products in this publication is solely for providing specific information on equipment and materials and does not imply recommendation or endorsement by the U.S. Department of Agriculture.

Supplementary material

10142_2019_707_MOESM1_ESM.pptx (14.9 mb)
Figure S1 Visual details of the experiment (PPTX 15256 kb)
10142_2019_707_MOESM2_ESM.pptx (94 mb)
Figure S2 Quantile-quantile plots for the genome wide association (GWA) analysis of three phenotypic traits (PPTX 96236 kb)
10142_2019_707_MOESM3_ESM.xlsx (29 kb)
Table S1 Salt tolerance index for four plant traits for maize inbred lines used in the study (XLSX 29 kb)
10142_2019_707_MOESM4_ESM.xlsx (116 kb)
Table S2 Mean quantification cycle (Cq) values for two maize lines in the control and the salt treatments for the genes used for validation (XLSX 116 kb)
10142_2019_707_MOESM5_ESM.xlsx (67 kb)
Table S3 QTLs associated with six traits studied in this investigation and list of genes within 200-kb window around the most significant genome wide association SNP (XLSX 67 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.US Salinity Lab (USDA-ARS)RiversideUSA
  2. 2.Department of Genetics and BiochemistryClemson UniversityClemsonUSA
  3. 3.College of Natural and Agricultural SciencesUniversity of California RiversideRiversideUSA
  4. 4.Department of Mathematical SciencesClemson UniversityClemsonUSA

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