Is a non-synonymous SNP in the HvAACT1 coding region associated with acidic soil tolerance in barley?

Jéssica Rosset Ferreira,Euclydes Minella,Bruna Franciele Faria,Moacyr Comar Junior,Carla Andréa Delatorre,Jorge Fernando Pereira

doi:10.1590/1678-4685-gmb-2016-0225

Abstract

The barley HvAACT1 gene codes for a citrate transporter associated with tolerance to acidic soil. In this report, we describe a single nucleotide polymorphism (SNP) in the HvAACT1 coding region that was detected as T-1,198 (in genotypes with lower root growth on acidic soil) or G-1,198 (greater root growth) and resulted in a single amino acid change (L/V-172). Molecular dynamic analysis predicted that HvAACT1 proteins with L or V-172 were stable, although the substitution led to structural changes within the protein. To evaluate the effect of the SNP on tolerance to acidic soil, barley accessions were separated into haplotypes based on the presence of a 1 kb insertion in the HvAACT1 promoter and a 21 bp insertion/deletion. These markers and the SNP-1,198 allowed the identification of five haplotypes. Short-term soil experiments showed no difference in root growth for most of the accessions containing the 21 bp insertion and T or G-1,198. In contrast, genotypes showing both the 21 bp deletion and G-1,198, with one of them having the 1 kb insertion, showed greater root growth. These results indicate that the SNP was not advantageous or deleterious when genotypes from the same haplotype were compared. The occurrence of the SNP was highly correlated with the 21 bp insertion/deletion that, together with the 1 kb insertion, explained most of the barley tolerance to acidic soil.

Highlights

The toxic trivalent aluminium cation (Al3+) occurs at higher concentration in acidic soils (Kinraide, 1991)
When a 1 kb insertion is detected upstream of the HvAACT1 coding region, is the expression enhanced but it switches to the root apex, thereby altering the primary function of this gene, which is the release of citrate to the xylem to facilitate iron translocation (Fujii et al, 2012)
This change occurred in exon 3 when a thymidine (T-1,198), present in genotypes MN 6021 and Paraí-I that showed lower root growth on acidic soil, was replaced by a guanine (G-1,198) in cultivars Antarctica 01 and FM 404 that showed greater root growth. This mutation resulted in leucine (L-172) present in the HvAACT1 protein from MN 6021 and Paraí-I being changed to valine (V-172) in Antarctica 01 and FM 404

Summary

Introduction

The toxic trivalent aluminium cation (Al3+) occurs at higher concentration in acidic soils (pH < 5.0) (Kinraide, 1991). The higher expression of the HvAACT1 gene in the root apex is correlated with the amount of citrate released by the barley root tip which is, correlated with the Al3+ tolerance (Zhao et al, 2003; Wang et al, 2007; Fujii et al, 2012) Another important variation, not found in the HvAACT1 coding region, is a 21 bp insertion/deletion detected by the marker HvMATE-21indel (Bian et al, 2013). Both the 1 kb insertion at the HvAACT1 promoter and the HvMATE-21indel marker can be detected by PCR, allowing the characterization of barley accessions

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Results

Conclusion