Nucleotide diversity and molecular evolution of the WAG-2 gene in common wheat (Triticum aestivum L) and its relatives

Abstract

In this work, we examined the genetic diversity and evolution of the WAG-2 gene based on new WAG-2 alleles isolated from wheat and its relatives. Only single nucleotide polymorphisms (SNP) and no insertions and deletions (indels) were found in exon sequences of WAG-2 from different species. More SNPs and indels occurred in introns than in exons. For exons, exons+introns and introns, the nucleotide polymorphism π decreased from diploid and tetraploid genotypes to hexaploid genotypes. This finding indicated that the diversity of WAG-2 in diploids was greater than in hexaploids because of the strong selection pressure on the latter. All dn/ds ratios were < 1.0, indicating that WAG-2 belongs to a conserved gene affected by negative selection. Thirty-nine of the 57 particular SNPs and eight of the 10 indels were detected in diploid species. The degree of divergence in intron length among WAG-2 clones and phylogenetic tree topology suggested the existence of three homoeologs in the A, B or D genome of common wheat. Wheat AG-like genes were divided into WAG-1 and WAG-2 clades. The latter clade contained WAG-2, OsMADS3 and ZMM2 genes, indicating functional homoeology among them.

Molecular cloning, characterization and expression analysis of WAG-1 in the pistillody line of common wheat

“…AG-like group C-class genes from monocots contain two clades, WAG-1 and WAG-2 clade, WAG-1 (WAG-1-1AS, WAG-1-1BS, WAG-1-1DS) formed the WAG-1 clade together with wheat TaAG-1, barely HvAG2, maize ZAG1, and rice OsMADS58, whereas WAG-2 grouped into the WAG-2 clade with wheat AGL39, WM29A, and WM29B, and barley HvAG1, maize ZMM2 and rice OsMADS3 (Figure 4). Using the deduced amino acid sequences, phylogenetic analyses showed that WAG-1 and WAG-2 are orthologs of the rice AG-type genes, Os-MADS58 and OsMADS3, respectively (Hirabayashi and Murai, 2009;Wei et al, 2011). WAG-1 and WAG-2 have also been referred to as TaAG-2 and TaAGL39, respectively (Zhao et al, 2006;Paolacci et al, 2007).…”

Genetic variation of six desaturase genes in flax and their impact on fatty acid composition

“…Most of these point mutations were synonymous substitutions that did not alter the underlying amino acid sequences. SNPs are the most abundant type of DNA variation of plant genomes (Brookes 1999; Wei et al 2011). However, their frequency varies among the different plant species (Wei et al 2011).…”

“…SNPs are the most abundant type of DNA variation of plant genomes (Brookes 1999; Wei et al 2011). However, their frequency varies among the different plant species (Wei et al 2011). Inbred rice and Arabidopsis display one SNP in every 300 bp (Schmid et al 2003), while outbreeding maize has one SNP/60 bp (Ching et al 2002).…”

“…Both SNPs and indels were present in introns, whereas exons contained only SNPs (Table 2). Exons are under stronger selection pressure resulting in a slower mutation rate caused by the elimination of deleterious mutations from the gene pool (Wei et al 2011; Gaut 1998). …”

SNP Discovery through Next-Generation Sequencing and Its Applications

“…Seed shattering (or loss thereof) has been associated with an SNP through a GWAS aimed at unraveling the evolution of rice that led to its domestication [141]. SNPs have also been used to study the evolution of genes such as WAG-2 in wheat [142]. Algorithms such as neighbor-joining and maximum likelihood implemented in the PHYLIP [143] and MEGA [144] software are commonly used to generate phylogenetic trees.…”