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

Abstract

BackgroundA 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.ResultsNucleotide 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.ConclusionsIn 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.

The wheat pangenome: assembly and analysis

“…(Lorenc et al, 2012, Lai et al, 2015b. genetic diversity (Akhunov et al, 2010). Another study by showed that the number of SNP markers in a framework genetic map of hexaploid wheat were in asymmetrical proportions of 30:50:17 for the A, B and D genomes respectively (Allen et al, 2011) which is also supported by our observation of a greater SNP density in the B genome compared to the A and D genomes ( Figure 4-1).…”

“…2005, Haudry et al, 2007, Akhunov et al, 2010 so it is more likely that a weaker purifying selection affected the majority of genes and that greater positive selection only affected genes directly linked with specific traits. Variable genes, which appear to be enriched with functions associated with responses to biotic and abiotic stress (Figure 3.5) are usually more diverse than other functional categories (Tatarinova et al, 2016) and this diversity may have been kept in the wheat germplasm because it conferred important traits like disease resistance and climate adaptability.…”

“…tauschii followed by induction of genome duplication of the amphiploids and are usually used to increase the diversity of the D genome in wheat breeding programs (Warburton et al, 2006). It has been shown that synthetic wheat cultivars are genetically distant from most elite wheat cultivars and contain a higher nucleotide diversity (Akhunov et al, 2010) which is why these are being increasingly used in breeding programs for introgression of genes from wild germplasm into elite cultivars , Warburton et al, 2006, del Blanco et al, 2001.…”

“…In the late 1990's and early 2000's microsatellites and AFLPs were the preferred tools to study the phylogenetic and evolutionary relationships between wild and domesticated wheat as well as between elite cultivars developed during the green revolution and landraces (Plaschke et al, 1995, Ishii et al, 2001, Akbari et al, 2006, Akhunov et al, 2010.…”

Gene Therapy of Some Genetic Diseases by Transferring Normal Human Genomic DNA into Somatic Cells and Stem Cells from Patients

“…tauschii) has 14 (2x), tetraploid wheat (Triticum turgidum ssp. dicoccoides) has 28 (4x), and hexaploid wheat (Triticum aestivum) has 42 (6x) chromosomes respectively; diploid wheat is the ancestor of the tetraploid and hexaploid wheat (Akhunov et al, , 2010Dvorak & Akhunov, 2005;S. Huang et al, 2002 More than 99% of the genomic DNA sequences of a Japanese male were same to the reference human genome, but there were still 3,132,608 single nucleotide variations (SNVs) compared to other six reported human genomes (Fujimoto et al, 2010).…”