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

<p>Abstract</p> <p>Background</p> <p>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 (<it>Triticum aestivum</it>, genomes AABBDD) and wild tetraploid wheat (<it>Triticum turgidum </it>ssp. <it>dicoccoides</it>, 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.</p> <p>Results</p> <p>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, <it>T. urartu</it>, <it>Aegilops speltoides</it>, and <it>Ae. tauschii</it>, 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 <it>Ae. tauschii </it>genetic map, and the map was superimposed on wheat deletion-bin maps. The agreement between the maps was assessed.</p> <p>Conclusions</p> <p>In a young polyploid, exemplified by <it>T. aestivum</it>, 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 <it>T. aestivum </it>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.</p

ESTs, cytogenetic stocks, and other tools for oat genomics

The development of tools for structural and functional genomics is essential for the application of these technologies to oat genetics and germplasm improvement. To supplement the fewer than six hundred DNA expressed sequence tags (ESTs) present to date in public data bases for oat, we have sequenced and are annotating for submission to GenBank an additional ~7,700 oat EST sequences. These 5' single pass sequences are derived from random clones isolated from cDNA libraries developed from polyA RNA isolated from 3-week-old green leaf (~2,500 clones), 6-day-old etiolated leaf (~2,600 clones), and 6-day-old root tissue (~2,500 clones) of 'Ogle-C', a reselection of cv. Ogle. About 85% of the oat sequences match Triticeae sequences present in the data base. We have been developing and characterizing cytogenetic stocks to use for relating previously identified oat genetic linkage groups to physical chromosome. Detection of molecular marker deficiencies in monosomic and nullisomic lines, where the missing chromosome or chromosome pair has been identified by C-banding analysis, has allowed assignment of most of the major oat linkage groups to chromosome for the monosomic stocks available. New monosomic stocks are being produced and characterized in an attempt to obtain a complete monosomic series in a single genetic background, cv. Sun II. These are recovered as products of abnormal meiosis in haploid oat plants derived from crosses of oat x maize. The described materials together with genomic tools reported from other labs including a barley DNA gene chip showing about 27% cross detection with oat expressed RNAs (Close et al. 2004), a DNA large fragment library for diploid oat (Bakht et al. 2003), and additional ESTs (e.g. Bräutigm et al., Molnar, this conference) provide opportunities for not only improved understanding of oat genome structure and function but also applications to oat genetic improvement. Close, T.J. et al. 2004. Plant Physiology 134:960-968; Bakht, S. et al. 2003. http://www.intl-pag.org/11/abstracts/P2a_P82_XI.html.vokMyynti MTT tietopalvelu