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.
Highlights
It is estimated that more than 800 million hectares of land worldwide and approximately 20% of irrigated farmland are negatively impacted by salinity (FAO, 2009)
A phylogenetic analysis of the corresponding predicted amino acid sequences of the encoded proteins revealed that B. rapa is likely to express five intracellular class one (IC-I) genes, two intracellular class two (IC-II) genes and two plasma membrane (PM) clade members (Figure 2A)
The proteins encoded by the two class II-intracellular localized (IC) NHX genes identified in B. rapa are clearly differentiated from other members of the A. thaliana NHX family (Figure 2A) and are likely to be the true orthologs of AtNHX5 and AtNHX6
Summary
It is estimated that more than 800 million hectares of land worldwide and approximately 20% of irrigated farmland are negatively impacted by salinity (FAO, 2009). Members of the monovalent cation/proton antiporter (CPA1) gene family exchange a sodium, potassium or lithium ion for a hydrogen ion across a cellular membrane. They can be classified into two distinct sub families, the plasma membrane (PM) localized NHAP family and the intracellular localized (IC) NHX family (Brett et al, 2005a; Chanroj et al, 2012). Members of the PM (AtNHX7/SOS1) and IC-I (AtNHX1) clades have been shown to be upregulated in response to NaCl, and to confer salt tolerance upon over-expression in A. thaliana (Apse et al, 1999; Shi et al, 2002, 2003; Shi and Zhu, 2002). Recent work has shown that AtNHX5 and AtNHX6 are functionally redundant, www.frontiersin.org
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