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

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