Showing papers by "Eduard Akhunov published in 2012"

Comparative Analysis of Syntenic Genes in Grass Genomes Reveals Accelerated Rates of Gene Structure and Coding Sequence Evolution in Polyploid Wheat

Abstract: Cycles of whole-genome duplication (WGD) and diploidization are hallmarks of eukaryotic genome evolution and speciation. Polyploid wheat (Triticum aestivum) has had a massive increase in genome size largely due to recent WGDs. How these processes may impact the dynamics of gene evolution was studied by comparing the patterns of gene structure changes, alternative splicing (AS), and codon substitution rates among wheat and model grass genomes. In orthologous gene sets, significantly more acquired and lost exonic sequences were detected in wheat than in model grasses. In wheat, 35% of these gene structure rearrangements resulted in frame-shift mutations and premature termination codons. An increased codon mutation rate in the wheat lineage compared with Brachypodium distachyon was found for 17% of orthologs. The discovery of premature termination codons in 38% of expressed genes was consistent with ongoing pseudogenization of the wheat genome. The rates of AS within the individual wheat subgenomes (21%–25%) were similar to diploid plants. However, we uncovered a high level of AS pattern divergence between the duplicated homeologous copies of genes. Our results are consistent with the accelerated accumulation of AS isoforms, nonsynonymous mutations, and gene structure rearrangements in the wheat lineage, likely due to genetic redundancy created by WGDs. Whereas these processes mostly contribute to the degeneration of a duplicated genome and its diploidization, they have the potential to facilitate the origin of new functional variations, which, upon selection in the evolutionary lineage, may play an important role in the origin of novel traits.

Whole Genome Profiling provides a robust framework for physical mapping and sequencing in the highly complex and repetitive wheat genome

Abstract: Sequencing projects using a clone-by-clone approach require the availability of a robust physical map. The SNaPshot technology, based on pair-wise comparisons of restriction fragments sizes, has been used recently to build the first physical map of a wheat chromosome and to complete the maize physical map. However, restriction fragments sizes shared randomly between two non-overlapping BACs often lead to chimerical contigs and mis-assembled BACs in such large and repetitive genomes. Whole Genome Profiling (WGP™) was developed recently as a new sequence-based physical mapping technology and has the potential to limit this problem. A subset of the wheat 3B chromosome BAC library covering 230 Mb was used to establish a WGP physical map and to compare it to a map obtained with the SNaPshot technology. We first adapted the WGP-based assembly methodology to cope with the complexity of the wheat genome. Then, the results showed that the WGP map covers the same length than the SNaPshot map but with 30% less contigs and, more importantly with 3.5 times less mis-assembled BACs. Finally, we evaluated the benefit of integrating WGP tags in different sequence assemblies obtained after Roche/454 sequencing of BAC pools. We showed that while WGP tag integration improves assemblies performed with unpaired reads and with paired-end reads at low coverage, it does not significantly improve sequence assemblies performed at high coverage (25x) with paired-end reads. Our results demonstrate that, with a suitable assembly methodology, WGP builds more robust physical maps than the SNaPshot technology in wheat and that WGP can be adapted to any genome. Moreover, WGP tag integration in sequence assemblies improves low quality assembly. However, to achieve a high quality draft sequence assembly, a sequencing depth of 25x paired-end reads is required, at which point WGP tag integration does not provide additional scaffolding value. Finally, we suggest that WGP tags can support the efficient sequencing of BAC pools by enabling reliable assignment of sequence scaffolds to their BAC of origin, a feature that is of great interest when using BAC pooling strategies to reduce the cost of sequencing large genomes.

High-throughput approaches to genome-wide analysis of genetic variation in polyploid wheat

Abstract: Can. J. Plant Sci. Downloaded from pubs.aic.ca by Calif Dig Lib - Davis on 06/26/13 For personal use only. 596 CANADIAN JOURNAL OF PLANT SCIENCE specialized multitrophic pest complexes whose members interact in both positive and negative ways. In this context, management recommendations based on the traditional single-species pest control paradigm may lead to undesirable outcomes. Our goal was to evaluate a modeling framework to make multi-pest management decisions that take into account the existence of direct and indirect interactions among pests belonging to different trophic levels. We adopted a Bayesian decision theory approach in combination with path analysis to evaluate interactions between Bromus tectorum (cheat- grass), Fusarium crown rot, and Cephus cinctus (wheat stem sawfly). We assessed the joint response of these pests to seeding rates, cultivar competitiveness, and cultivar wheat stem sawfly tolerance. Results indicate that yield differences can be more readily explained as a result of the effects of management on pests and multi- pest interactions, rather than just by the direct effect of any particular management scheme on yield. For example, wheat stem sawfly tolerant varieties should be planted at a low seeding rate under high insect pressure. However, this variety should be replaced by a compe- titive and drought tolerant cultivar at high seeding rates as B. tectorum levels increase, despite the persisting wheat stem sawfly infestation. Also, the incidence of Fusarium can be explained by the abundance of B. tectorum, an alternative host for this disease. Our research suggests a framework for establishing a balance between model simplicity and the complexity of the process being modeled. High-throughput approaches to genome-wide analysis of genetic variation in polyploid wheat. E. Akhunov 1 *, S. Chao 2 , C. Saintenac 2 , S. Kiani 2 , D. See 3 , G. Brown- Guedira 4 , M. Sorrells 5 , A. Akhunova 6 , J. Dubcovsky 7 , C. Cavanagh 8 , and M. Hayden 9 . 1 Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA; 2 USDA-ARS Biosciences Research Laboratory, Fargo, ND, USA; 3 USDA Western Regio- nal Small Grains Genotyping Lab, Johnson Hall, WSU, Pullman, WA, USA; 4 USDA-ARS Eastern Regional Small Grains Genotyping Lab., 4114 Williams Hall, NCSU, Raleigh, NC, USA; 5 Plant Breeding & Genetics, Cornell University, NY, USA; 6 Integrated Genomics Facility, Kansas State University, Manhattan, KS, USA; 7 Department of Plant Sciences, University of California, Davis, CA, USA; 8 CSIRO, Food Futures National Research Flagship, Canberra, ACT 2601, Australia; and 9 Department of Primary Industries Victoria, Victorian AgriBiosciences Center, 1 Park Drive, Bundoora, VIC 3083, Australia. Genome-wide analysis of genetic variation is a powerful tool for detecting marker-trait associations in diversity panels and mapping populations. Genome scale geno- typing data can be generated using high-throughput assays capable of detecting allelic variation in a pre- defined set of SNP loci or by direct sequencing. The combined effort of several research groups in collaboration with the International Wheat SNP Work- ing Group developed high-throughput SNP genotyping assays based on the Illumina iSelect platform. The assay was used to genotype 12 000 wheat lines including cultivars, landraces, wild relatives and the progeny of several mapping populations. Out 9000 SNP assays 95% produced high-quality genotype calls with up to 70% being polymorphic in a diverse sample of wheat cultivars with a minor allele frequency 0.05. Two high-density genetic maps based on SynOp and 4- way MAGIC populations were developed. An alterna- tive approach to SNP detection relies on next-generation sequencing technologies for direct sequencing of complexity reduced genomic libraries prepared either by restriction digestion or by selective capture of genomic regions of interest. These sequence-based genotyping approaches demonstrated high efficiency for detecting allelic variation in the wheat genome. The applicability of iSelect assay and genotyping-by- sequencing approaches for the analysis of genetic variation and genotype-phenotype relationships in wheat will be presented. Overview and progress of the CTAG project. C. McCartney 1 , C. Pozniak 2 , A. Sharpe 3 , R. MacLachlan 3 , P. Hucl 3 , M. Jordan 3 , R. Knox 4 , H. Randhawa 5 , D. Spaner 6 , F. Bekkaoui 6 , V. Galushko 7 , and R. Gray 8 . 1 AAFC-Cereal Research Centre, 195 Dafoe Road, Winnipeg, Manitoba, Canada; 2 Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK; 3 Plant Biotechnology Institute, National Research Council of Canada, Saska- toon, Saskatchewan, Canada; 4 AAFC-Semiarid Prairie Agricultural Research Centre, Box 1030, Swift Current, Saskatchewan, Canada; 5 AAFC-Lethbridge Research Centre, 5403 1st Ave South, Lethbridge, Alberta, Canada; 6 Department of Agricultural, Food and Nutritional Science, University of Alberta, 4-16D Agri- culture/Forestry Ctr, Edmonton, Alberta, Canada; Department of Economics, University of Regina, 3737 Wascana Parkway, Regina, Saskatchewan, Canada; and Department of Bioresource Policy, Business & Econom- ics, University of Saskatchewan, 51 Campus Drive, Saskatoon, Saskatchewan, Canada. The Canadian Triticum Advancement through Geno- mics (CTAG) project aims to provide genetic informa- tion and tools for the improvement of molecular breeding in wheat. The project has four major activities: (1) generating the first complete sequence of chromo- some 6D, (2) capturing and sequencing genomic coding sequences from Canadian wheat varieties, (3) identify- ing, validating, and mapping SNP markers in Canadian wheat germplasm, and (4) examination of the role of public-private partnerships in wheat genomics and breeding (GE3LS research). Sequencing of chromosome 6D will be done on a BAC by BAC basis, as agreed