Alteration of aluminum tolerance mediated by insertion of same transposable element at different sites in the upstream region of <i>HvAACT1</i> in Japanese barley accessions

Aluminum (Al) toxicity is a major limiting factor for crop production in acid soils. Barley is highly sensitive to Al, so the genetic improvement of its Al tolerance is required. However, useful breeding materials and genetic factors for improving its tolerance are remain largely unclear. Here, we compared the Al tolerance of ‘Minorimugi’ and ‘Fibersnow,’ both six-rowed hulled barley cultivars grown mainly in northern Japan, using relative root length (RRL) as an index, and found that Minorimugi had higher tolerance. Quantitative trait locus (QTL) analysis using recombinant inbred lines (RILs) derived from the two cultivars detected a major QTL at the <i>HvAACT1</i> (<i>Al-ACTIVATED CITRATE TRANSPORTER 1</i>) locus that explained approximately 36% of the variance. The PCR amplification analysis revealed a 1-kb transposable element (TE) insertion at −1.9 kb in the upstream region of <i>HvAACT1</i> in Minorimugi that enhances <i>HvAACT1</i> expression. The TE has the same nucleotide sequence as one previously found at −4.8 kb in the upstream region of <i>HvAACT1</i> in ‘Murasakimochi,’ which is an Al tolerant cultivar. In the Japanese barley population, the Murasakimochi-type <i>HvAACT1</i> upstream allele is shared mainly among barley accessions developed in the Shikoku area, while the Minorimugi-type allele is shared mainly among accessions developed in the Hokuriku and Nagano area. This geographic difference indicates that both alleles are shared among different subpopulations in Japanese barley, which may be advantageous for growth in acid soils. Our results provide information about a new allele of the <i>HvAACT1</i> upstream region and potential breeding materials for improving the Al tolerance of barley.