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      Rapid cloning of genes in hexaploid wheat using cultivar-specific long-range chromosome assembly

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          Abstract

          Rapid cloning of genes from any crop plant species (or cultivar) whose chromosomes can be flow sorted is enabled by a combination of short-read sequencing and proximity ligation.

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          Structural and functional partitioning of bread wheat chromosome 3B.

          Frédéric Choulet, Adriana Alberti, Sébastien Theil … (2014)
          We produced a reference sequence of the 1-gigabase chromosome 3B of hexaploid bread wheat. By sequencing 8452 bacterial artificial chromosomes in pools, we assembled a sequence of 774 megabases carrying 5326 protein-coding genes, 1938 pseudogenes, and 85% of transposable elements. The distribution of structural and functional features along the chromosome revealed partitioning correlated with meiotic recombination. Comparative analyses indicated high wheat-specific inter- and intrachromosomal gene duplication activities that are potential sources of variability for adaption. In addition to providing a better understanding of the organization, function, and evolution of a large and polyploid genome, the availability of a high-quality sequence anchored to genetic maps will accelerate the identification of genes underlying important agronomic traits. Copyright © 2014, American Association for the Advancement of Science.
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            Wheat Fhb1 encodes a chimeric lectin with agglutinin domains and a pore-forming toxin-like domain conferring resistance to Fusarium head blight

            Nidhi Rawat, Michael O Pumphrey, Sixin Liu … (2016)
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              A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor.

              Dan J. Stein, D. K. Sehgal, Yi Wang … (2013)
              The current limitations in genome sequencing technology require the construction of physical maps for high-quality draft sequences of large plant genomes, such as that of Aegilops tauschii, the wheat D-genome progenitor. To construct a physical map of the Ae. tauschii genome, we fingerprinted 461,706 bacterial artificial chromosome clones, assembled contigs, designed a 10K Ae. tauschii Infinium SNP array, constructed a 7,185-marker genetic map, and anchored on the map contigs totaling 4.03 Gb. Using whole genome shotgun reads, we extended the SNP marker sequences and found 17,093 genes and gene fragments. We showed that collinearity of the Ae. tauschii genes with Brachypodium distachyon, rice, and sorghum decreased with phylogenetic distance and that structural genome evolution rates have been high across all investigated lineages in subfamily Pooideae, including that of Brachypodieae. We obtained additional information about the evolution of the seven Triticeae chromosomes from 12 ancestral chromosomes and uncovered a pattern of centromere inactivation accompanying nested chromosome insertions in grasses. We showed that the density of noncollinear genes along the Ae. tauschii chromosomes positively correlates with recombination rates, suggested a cause, and showed that new genes, exemplified by disease resistance genes, are preferentially located in high-recombination chromosome regions.
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                Author and article information

                Journal
                Title: Nature Biotechnology
                Abbreviated Title: Nat Biotechnol
                Publisher: Springer Nature
                ISSN (Print): 1087-0156
                ISSN (Electronic): 1546-1696
                Publication date Created: May 15 2017
                Publication date (Print): May 15 2017
                Volume:
                Issue:
                Article
                DOI: 10.1038/nbt.3877
                PubMed ID: 28504667
                SO-VID: a446ef52-b447-4284-8992-67da621013b1
                Copyright © © 2017
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