Identification and characterization of orthologs of AtNHX5 and AtNHX6 in Brassica napus

Abstract

Improving crop species by breeding for salt tolerance or introducing salt tolerant traits is one method of increasing crop yields in saline affected areas. Extensive studies of the model plant species Arabidopsis thaliana has led to the availability of substantial information regarding the function and importance of many genes involved in salt tolerance. However, the identification and characterization of A. thaliana orthologs in species such as Brassica napus (oilseed rape) can prove difficult due to the significant genomic changes that have occurred since their divergence approximately 20 million years ago (MYA). The recently released Brassica rapa genome provides an excellent resource for comparative studies of A. thaliana and the cultivated Brassica species, and facilitates the identification of Brassica species orthologs which may be of agronomic importance. Sodium hydrogen antiporter (NHX) proteins transport a sodium or potassium ion in exchange for a hydrogen ion in the other direction across a membrane. In A. thaliana there are eight members of the NHX family, designated AtNHX1-8, that can be sub-divided into three clades, based on their subcellular localization: plasma membrane (PM), intracellular class I (IC-I) and intracellular class II (IC-II). In plants, many NHX proteins are primary determinants of salt tolerance and act by transporting Na+ out of the cytosol where it would otherwise accumulate to toxic levels. Significant work has been done to determine the role of both PM and IC-I clade members in salt tolerance in a variety of plant species, but relatively little analysis has been described for the IC-II clade. Here we describe the identification of B. napus orthologs of AtNHX5 and AtNHX6, using the B. rapa genome sequence, macro- and micro-synteny analysis, comparative expression and promoter motif analysis, and highlight the value of these multiple approaches for identifying true orthologs in closely related species with multiple paralogs.

The Reference Genome of the Halophytic Plant Eutrema salsugineum

“…Gene copies arising from whole-genome duplication event may be either lost or develop new biological functions, which can be inferred from their differential expression patterns (Fang et al, 2012; Ford et al, 2012). We therefore compared gene copy number in families of transcription factors (TFs) and the families of SOS-like genes in E. salsugineum and A. thaliana .…”

Species- and genome-wide dissection of the shoot ionome in Brassica napus and its relationship to seedling development

“…The gene SOS1 that was found in the proximity (about 540 kb) to the association hotspot is known to be an Na + /H + antiporter that controls the uptake and efflux of Na, a mechanism which is crucial for plants under Na-rich conditions (Fraile-Escanciano et al, 2010 ). SOS1 was first identified in A. thaliana (Wu et al, 1996 ), and its orthologs in Brassica species are also known (Chakraborty et al, 2012 ; Ford et al, 2012 ). Our identification of a closely situated gene that plays a key role in Na tolerance underlines the importance of the hotspot, which includes the genetic region Na-A9, in B. napus .…”

Engineering Multiple Abiotic Stress Tolerance in Canola, Brassica napus

“…The genome-wide identification of other transporter gene families such as NHX, HKT, and TMTs is further required in B. napus to understand their role in response to various abiotic stresses. However, Ford et al (2012) identified orthologs of AtNHX5 and AtNHX6 using the B. rapa genome as the sequence of B. napus was not available at that time. They reported differential expression of BnNHX6.1 (ortholog of AtNHX5) in response to salt stress.…”