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

item AKHUNOV, EDUARD - Kansas State University
item AKHUNOVA, ALINA - Kansas State University
item Anderson, Olin
item ANDERSON, JAMES - University Of Minnesota
item BLAKE, NANCY - Montana State University
item CLEGG, MICHAEL - University Of California
item COLEMAN-DERR, DEVIN - University Of California
item CONLEY, EMILY - University Of Minnesota
item CROSSMAN, CURT - University Of California
item DEAL, KARIN - University Of California
item DUBCOVSKY, JORGE - University Of California
item GILL, BIKRAM - Kansas State University
item Gu, Yong
item HADAM, JAKUB - Kansas State University
item HEO, HWAYOUNG - Montana State University
item HUO, NAXIN - University Of California
item Lazo, Gerard
item LUO, MING-CHENG - University Of California
item MA, YAQIN - University Of California
item Matthews, David
item MCGUIRE, PATRICK - University Of California
item MORRELL, PETER - University Of Minnesota
item QUALSET, CALVIN - University Of California
item RENFRO, JAMES - University Of California
item TABANAO, DINDO - University Of Minnesota
item TALBERT, LUTHER - Montana State University
item TIAN, CHAO - University Of California
item TOLENO, DONNA - University Of California
item WARBURTON, MARILYN - International Maize & Wheat Improvement Center (CIMMYT)
item YOU, FRANK - University Of California
item ZHANG, WENJUN - University Of California
item DVORAK, JAN - University Of California

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/7/2010
Publication Date: 12/14/2010
Citation: Akhunov, E.D., Akhunova, A., Anderson, O.D., Anderson, J., Blake, N., Clegg, M., Coleman-Derr, D., Conley, E., Crossman, C., Deal, K., Dubcovsky, J., Gill, B., Gu, Y.Q., Hadam, J., Heo, H., Huo, N., Lazo, G.R., Luo, M., Ma, Y., Matthews, D.E., Mcguire, P., Morrell, P., Qualset, C., Renfro, J., Tabanao, D., Talbert, L., Tian, C., Toleno, D., Warburton, M., You, F., Zhang, W., Dvorak, J. 2010. Nucleotide diversity maps reveal variation in diversity among wheat genomes and chromosomes. Biomed Central (BMC) Genomics. 11:702-710.

Interpretive Summary: Interpretive Summary: 20-75 CHARACTER LINES Wheat is one of the most important food crops in the world. However, its polyploid nature represents a great challenge in several aspects of research including developing molecular markers for genotyping and marker-assisted breeding. Therefore, understanding the nucleotide diversity in a polyploid wheat species will facilitate discovery and application of single nucleotide polymorphism markers for crop improvement. In this manuscript, a genome-wide assessment of nucleotide diversity was performed in the polyploid wheat species by sequencing genes in cultivated hexaploid wheat and wild tetraploid wheat. The data obtained are used to assess the distribution of diversity among and within wheat genomes and develop a panel of SNP markers for polyploid wheat.

Technical Abstract: Technical Abstract: 20-75 CHARACTER LINES A strategy for 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 respective genomes. In this study, nucleotide diversity was estimated in 2114 wheat genes and found to be similar between the A and B genomes but greatly reduced in the D genome. Within a genome, diversity was diminished in some chromosomes, where loss of diversity took place along entire chromosomes or large portions of them. Low diversity was always accompanied by excess of rare alleles. A total of 5,471 SNPs were discovered in 1791 wheat genes and 41,271, 1,218, and 2,203 SNPs were discovered respectively in the 488, 463, and 641 genes of wheat putative diploid ancestors, T. urartu, Aegilops speltoides, and Ae. tauschii. 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 were placed on an Ae. tauschii genetic map, and the map was superimposed on wheat deletion-bin maps. The agreement between the maps was assessed. In a young polyploid, such as T. aestivum, gene flow from the ancestors plays an overwhelmingly important role in the acquisition of gene diversity. The low effective recombination due to self-pollination and the activity of a genetic mechanism precluding homoeologous chromosome pairing during polyploid meiosis shape diversity and can lead to the loss of diversity from large chromosome regions. Thus in T. aestivum today, the net effect of these factors is great variation in diversity among genomes and chromosomes, which impacts the development of SNP markers and their practical utility. As time passes, new mutations accumulate, and diversity increases and becomes more uniformly distributed across the genome, as seen in wild emmer today, a polyploid species much older than T. aestivum. -