| Summary: | <i>Brassica</i> species show varying levels of resistance to salt stress. To understand the genetics underlying these differential stress tolerance patterns in Brassicas, we exposed two widely cultivated amphidiploid <i>Brassica</i> species having different genomes, <i>Brassica juncea</i> (AABB, <i>n</i> = 18) and <i>Brassica napus</i> (AACC, <i>n</i> = 19), to elevated levels of NaCl concentration (300 mM, half the salinity of seawater). <i>B. juncea</i> produced more biomass, an increased chlorophyll content, and fewer accumulated sodium (Na<sup>+</sup>) and chloride (Cl<sup>−</sup>) ions in its photosynthesizing tissues. Chlorophyll fluorescence assays revealed that the reaction centers of PSII of <i>B. juncea</i> were more photoprotected and hence more active than those of <i>B. napus</i> under NaCl stress, which, in turn, resulted in a better PSII quantum efficiency, better utilization of photochemical energy with significantly reduced energy loss, and higher electron transport rates, even under stressful conditions. The expression of key genes responsible for salt tolerance (<i>NHX1</i> and <i>AVP1</i>, which are nuclear-encoded) and photosynthesis (<i>psbA</i>, <i>psaA</i>, <i>petB</i>, and <i>rbcL</i>, which are chloroplast-encoded) were monitored for their genetic differences underlying stress tolerance. Under NaCl stress, the expression of <i>NHX1</i>, <i>D1</i>, and <i>Rubisco</i> increased several folds in <i>B. juncea</i> plants compared to <i>B. napus</i>, highlighting differences in genetics between these two Brassicas. The higher photosynthetic potential under stress suggests that <i>B. juncea</i> is a promising candidate for genetic modifications and its cultivation on marginal lands.
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