Nucleotide diversity maps reveal variation in diversity among wheat genomes and chromosomes

Abstract

Background: A genome-wide assessment of nucleotide diversity in a polyploid species must minimize the inclusion of homoeologous sequences into diversity estimates and reliably allocate individual haplotypes into their respective genomes. The same requirements complicate the development and deployment of single nucleotide polymorphism (SNP) markers in polyploid species. We report here a strategy that satisfies these requirements and deploy it in the sequencing of genes in cultivated hexaploid wheat (Triticum aestivum, genomes AABBDD) and wild tetraploid wheat (Triticum turgidum ssp. dicoccoides, genomes AABB) from the putative site of wheat domestication in Turkey. Data are used to assess the distribution of diversity among and within wheat genomes and to develop a panel of SNP markers for polyploid wheat.

Results: Nucleotide diversity was estimated in 2114 wheat genes and was similar between the A and B genomes and reduced in the D genome. Within a genome, diversity was diminished on some chromosomes. Low diversity was always accompanied by an excess of rare alleles. A total of 5,471 SNPs was discovered in 1791 wheat genes. Totals of 1,271, 1,218, and 2,203 SNPs were discovered in 488, 463, and 641 genes of wheat putative diploid ancestors, T. urartu, Aegilops speltoides, and Ae. tauschii, respectively. A public database containing genome-specific primers, SNPs, and other information was constructed. A total of 987 genes with nucleotide diversity estimated in one or more of the wheat genomes was placed on an Ae. tauschii genetic map, and the map was superimposed on wheat deletion-bin maps. The agreement between the maps was assessed.

Conclusions: In a young polyploid, exemplified by T. aestivum, ancestral species are the primary source of genetic diversity. Low effective recombination due to self-pollination and a genetic mechanism precluding homoeologous chromosome pairing during polyploid meiosis can lead to the loss of diversity from large chromosomal regions. The net effect of these factors in T. aestivum is large variation in diversity among genomes and chromosomes, which impacts the development of SNP markers and their practical utility. Accumulation of new mutations in older polyploid species, such as wild emmer, results in increased diversity and its more uniform distribution across the genome.

Figure 1

Project flow chart.

Figure 2

Nucleotide diversity θ_π of individual A-genome genes. Gene diversity along the A-genome chromosomes in T. aestivum and wild emmer (T. dicoccoides) in the Diyarbakir region in Turkey. Chromosome 4A is excluded because the order of genes does not conform to the Ae. tauschii genetic map. Monomorphic loci are depicted with zero diversity. The gene order along the diversity maps in Additional file 2 Table S1 is used on the X-axis, and the maps are oriented with the most distal gene in the short arm to the left. Centromere is indicated by a triangle. Genetic distances between genes are not depicted.

Figure 3

Nucleotide diversity θ_π of individual B-genome genes. Gene diversity along the B-genome chromosomes in T. aestivum and wild emmer (T. dicoccoides) in the Diyarbakir region in Turkey. See Figure 2 for details.

Figure 4

Nucleotide diversity θ_π of individual D-genome genes. Gene diversity along the D-genome chromosomes in T. aestivum. See Figure 2 for details.

Figure 5

The folded site frequency spectra. Folded site frequency spectra of minor SNP alleles at silent and replacement positions in the A and B genomes, Td (A) and Td (B) respectively, in a sample of 10 homozygous accessions of wild emmer (T. dicoccoides). Each homozygous accession is equivalent to one chromosome. The plot depicts numbers of SNPs with the minor allele being observed in an indicated number of sampled chromosomes. (B) The folded site frequency spectrum of minor SNP alleles at the silent and replacement positions in the A, B, and D genomes, Ta (A), Ta (B), and Ta (D), respectively, in a sample of 13 homozygous accessions of T. aestivum. Each homozygous accession is equivalent to one chromosome. The plot depicts numbers of SNPs with the minor allele being observed in an indicated number of sampled chromosomes.