Untangling Nucleotide Diversity and Evolution of the H Genome in Polyploid Hordeum and Elymus Species Based on the Single Copy of Nuclear Gene DMC1

Abstract

Numerous hybrid and polypoid species are found within the Triticeae. It has been suggested that the H subgenome of allopolyploid Elymus (wheatgrass) species originated from diploid Hordeum (barley) species, but the role of hybridization between polyploid Elymus and Hordeum has not been studied. It is not clear whether gene flow across polyploid Hordeum and Elymus species has occurred following polyploid speciation. Answering these questions will provide new insights into the formation of these polyploid species, and the potential role of gene flow among polyploid species during polyploid evolution. In order to address these questions, disrupted meiotic cDNA1 (DMC1) data from the allopolyploid StH Elymus are analyzed together with diploid and polyploid Hordeum species. Phylogenetic analysis revealed that the H copies of DMC1 sequence in some Elymus are very close to the H copies of DMC1 sequence in some polyploid Hordeum species, indicating either that the H genome in theses Elymus and polyploid Hordeum species originated from same diploid donor or that gene flow has occurred among them. Our analysis also suggested that the H genomes in Elymus species originated from limited gene pool, while H genomes in Hordeum polyploids have originated from broad gene pools. Nucleotide diversity (π) of the DMC1 sequences on H genome from polyploid species (π = 0.02083 in Elymus, π = 0.01680 in polyploid Hordeum) is higher than that in diploid Hordeum (π = 0.01488). The estimates of Tajima's D were significantly departure from the equilibrium neutral model at this locus in diploid Hordeum species (P<0.05), suggesting an excess of rare variants in diploid species which may not contribute to the origination of polyploids. Nucleotide diversity (π) of the DMC1 sequences in Elymus polyploid species (π = 0.02083) is higher than that in polyploid Hordeum (π = 0.01680), suggesting that the degree of relationships between two parents of a polyploid might be a factor affecting nucleotide diversity in allopolyploids.

EST-SSR marker development based on RNA-sequencing of E. sibiricus and its application for phylogenetic relationships analysis of seventeen Elymus species

“…Genetic diversity analysis in different genomic combinations will facilitate the understanding of the evolution process and genetic differentiation among different species. The phylogenetic relationships of the StH , StY and StHY genome Elymus species have been reported by using molecular sequences [9, 10, 12, 17–19]. In this study, we used newly developed EST-SSR markers to analyze the phylogenetic relationships of 17 StH , StY and StHY genome Elymus species collected from diverse geographical regions.…”

“…Information on molecular phylogeny and genetic structure among different Elymus species is limited, but necessary for germplasm collection, conservation and utilization. The phylogenetic relationships and genetic components among different Elymus species are largely unknown because of the limited detection ability of specific or unique nuclear gene sequences [9, 10, 12, 17–19]. Genetic diversity analysis among phylogenetically related species is based on the development of transferable and orthologous molecular markers.…”

Phylogeny and molecular evolution of the DMC1 gene in the polyploid genus Leymus (Triticeae: Poaceae) and its diploid relatives

“…Molecular evolution of DMC1 in Leymus and its potential diploid genome donor species Analysis of the levels of diversity at homoeologous loci in polyploids compared to their diploid relatives may provide insight into how the evolutionary process differs between lineages and between homoeologous loci within lineages (Soltis et al, 2003;Fan et al, 2009Fan et al, , 2012Sun & Sun, 2012). Several studies suggested that genetic diversity in polyploids is often similar to or higher than their diploid progenitors (Otto & Whitton, 2000;Sun et al, 2007;Fan et al, 2009;Sun & Sun, 2012;Wang et al, 2012). However, comparisons of nucleotide diversity showed that the Gss locus on the D genome of hexaploid wheat is lower than that of diploid D genome donor Aegilops tauschii Coss.…”

“…Recent studies have shown that transposable element indels shaped the homoeologous loci, which was responsible for the patterns of diversity of duplicated genes (Sun et al, ; Fan et al, ). It was considered that the levels and patterns of genetic diversity in polyploid populations of independent origins varied depending on the amount of genetic variation initially contributed by the diploid progenitors (Fan et al, , ; Sun & Sun, ). Therefore, differences in the levels and patterns of nucleotide diversity of duplicate genes may reflect numerous influencing forces.…”

“…Polyploidization provides a reservoir of duplicate genes as substrates for potential evolutionary innovation (Hovav et al, ; Fan et al, ). Analysis of the levels of diversity and the patterns of genetic variation in duplicated gene not only traces the evolutionary history of polyploids (Soltis et al, ; Fan et al, ), but also provides insight into how the evolutionary process differs between lineages and between homoeologous loci within lineages (Sun & Sun, ; Fan et al, ). In the absence of diverged evolutionary pressures or genetic mechanisms, genetic diversity is expected to be equivalent among loci, both in comparisons of orthologous genes among species and paralogous genes within species (Wendel et al, ).…”