Salt stress under the scalpel - dissecting the genetics of salt tolerance

Abstract

Salt stress limits the productivity of crops grown under saline conditions, leading to substantial losses of yield in saline soils and under brackish and saline irrigation. Salt tolerant crops could alleviate these losses while both increasing irrigation opportunities and reducing agricultural demands on dwindling freshwater resources. However, despite significant efforts, progress towards this goal has been limited, largely because of the genetic complexity of salt tolerance for agronomically important yield-related traits. Consequently, the focus is shifting to the study of traits that contribute to overall tolerance, thus breaking down salt tolerance into components that are more genetically tractable. Greater consideration of the plasticity of salt tolerance mechanisms throughout development and across environmental conditions furthers this dissection. The demand for more sophisticated and comprehensive methodologies is being met by parallel advances in high-throughput phenotyping and sequencing technologies that are enabling the multivariate characterisation of vast germplasm resources. Alongside steady improvements in statistical genetics models, forward genetics approaches for elucidating salt tolerance mechanisms are gaining momentum. Subsequent quantitative trait locus and gene validation has also become more accessible, most recently through advanced techniques in molecular biology and genomic analysis, facilitating the translation of findings to the field. Besides fuelling the improvement of established crop species, this progress also facilitates the domestication of naturally salt tolerant orphan crops. Taken together, these advances herald a promising era of discovery for research into the genetics of salt tolerance in plants.

Figure 1

A plant scientist's guide to dissecting salt tolerance. For application‐oriented research, salt tolerance should be assessed according to the final trait of interest, most commonly yield – these are typically highly complex. Overall salt tolerance can be hierarchically dissected to identify downstream traits that are more genetically tractable. Traits that are seen to correlate with overall salt tolerance point towards processes that contribute to overall salt tolerance, i.e. salt tolerance mechanisms. A non‐exhaustive list of salt tolerance‐related traits and mechanisms is presented with a broad sense of their hierarchical organisation. This top‐down approach can eventually lead to the identification of underlying genetic components. Importantly, salt tolerance can be calculated using various stress tolerance indices, each of which provides a different perspective and a distinct focus on different aspects of salt tolerance. Moreover, any measure of tolerance can be influenced by the conditions under which it is assessed (examples are illustrated in circles) and the causal mechanisms underlying each measure can be distinct. HI, harvest index; RMR, root‐mass‐ratio; RGR, relative growth rate; TUE, NUE, RUE, transpiration‐, nutrient‐ and radiation‐use efficiency, respectively; S/C, salt tolerance index (Munns, 2002); TOL, tolerance index (Fox and Rosielle, 1982; Fernandez, 1992); MP, mean productivity index (Rosielle and Hamblin, 1981); GMP, geometric mean productivity (Fernandez, 1992); SSI, susceptibility index (Fischer and Maurer, 1978); STI, stress tolerance index (Fernandez, 1992).

Figure 2

The phenotypic diversity of Chenopodium quinoa germplasm. The genetic diversity of quinoa germplasm can be clearly seen through the wide variety of panicle shapes, sizes and colours displayed in these field‐grown specimens (30 distinct accessions grown in the same season and field) (photo credits: Gabriele Fiene).