Nucleotide diversity and linkage disequilibrium in antioxidant genes of Brachypodium distachyon

Brachypodium distachyon (Brachypodium) is a powerful model system for studying cereal, bioenergy, forage, and turf grasses. Nucleotide diversity (pi) and linkage disequilibrium (LD) in candidate genes involved in the antioxidative pathways in this species are not known. The average pi for CAT encoding catalase, GPX encoding glutathione peroxidase, DHAR encoding dehydroascorbate reductase, MDHAR encoding monodehydroascorbate reductase, and APX ecoding ascorbate peroxidase was 0.0027 among 19 accessions contrasting for drought tolerance. The highest value of pi was found in APX (0.0046) and the lowest pi was in MDHAR (0.0006). The average single nucleotide polymorphism (SNP) frequency across these five genes was one SNP per 131 bp between two randomly sampled sequences for the five genes in the sequence length ranging from 1447 bp to 1701 bp. The LD decay was slow and extended to a distance of more than 1.2 kb for all genes. The neighbor-joining tree analyses of DHAR, MDHAR, and CAT generally separated accessions differing in drought tolerance. The results indicate a putative role of these candidate genes in increasing general fitness of Brachypodium. (C) 2012 Elsevier Ireland Ltd. All rights reserved.