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

Authors: Sandhu, Devinder; Pudussery, Manju; KUMAR, ROHIT - Clemson University; PALLETE, ANDREW - University Of California; MARKLEY, PAUL - University Of California; BRIDGES, WILLIAM - Clemson University; SEKHON, RAJANDEEP - Clemson University

Submitted to: Functional and Integrative Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/8/2019
Publication Date: 9/14/2019
Citation: Sandhu, D., Pudussery, M.V., Kumar, R., Pallete, A., Markley, P., Bridges, W.C., Sekhon, R.S. 2020. Characterization of natural genetic variation identifies multiple genes involved in salt tolerance in maize. Functional and Integrative Genomics. 20:261-275. https://doi.org/10.1007/s10142-019-00707-x.
DOI: https://doi.org/10.1007/s10142-019-00707-x

Interpretive Summary: Maize (Zea mays), the third major cereal crop grown worldwide after wheat and rice, is a staple food for humans and a primary source of nutrients for animal feed. Maize growth, development, and production potential are severely affected by salinity. Maize is moderately sensitive to salinity, therefore, soils or irrigation water with high salt concentrations pose serious threat to global maize production particularly in arid and semi-arid regions. Due to the complex nature of the trait, the most efficient approach for improving salt tolerance in modern cultivars is through exploitation of the available naturally diverse germplasm. Here we used 399 maize lines to study genome wide associations between salt tolerance and early vigor traits including shoot length, shoot weight, root length and root weight. This analysis resulted in detection of 57 markers associated with early vigor under salinity stress and allowed us to identify candidate genes. Characterization of these genes will provide novel sources for salt tolerance in maize. In addition, this study sheds light on the understanding of the genetic mechanisms regulating salt tolerance in maize and other related crops. These finding will be useful to breeders and geneticists in developing new salt-tolerant commercial cultivars that are suitable for marginal lands high in salinity.

Technical Abstract: 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.