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Sequencing of 15 622 gene-bearing BACs clarifies the gene-dense regions of the barley genome

  • Author(s): Muñoz-Amatriaín, M
  • Lonardi, S
  • Luo, M
  • Madishetty, K
  • Svensson, JT
  • Moscou, MJ
  • Wanamaker, S
  • Jiang, T
  • Kleinhofs, A
  • Muehlbauer, GJ
  • Wise, RP
  • Stein, N
  • Ma, Y
  • Rodriguez, E
  • Kudrna, D
  • Bhat, PR
  • Chao, S
  • Condamine, P
  • Heinen, S
  • Resnik, J
  • Wing, R
  • Witt, HN
  • Alpert, M
  • Beccuti, M
  • Bozdag, S
  • Cordero, F
  • Mirebrahim, H
  • Ounit, R
  • Wu, Y
  • You, F
  • Zheng, J
  • Simková, H
  • Dolezel, J
  • Grimwood, J
  • Schmutz, J
  • Duma, D
  • Altschmied, L
  • Blake, T
  • Bregitzer, P
  • Cooper, L
  • Dilbirligi, M
  • Falk, A
  • Feiz, L
  • Graner, A
  • Gustafson, P
  • Hayes, PM
  • Lemaux, P
  • Mammadov, J
  • Close, TJ
  • et al.

Published Web Location

https://doi.org/10.1111/tpj.12959
Abstract

© 2015 The Authors The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd. Barley (Hordeum vulgare L.) possesses a large and highly repetitive genome of 5.1 Gb that has hindered the development of a complete sequence. In 2012, the International Barley Sequencing Consortium released a resource integrating whole-genome shotgun sequences with a physical and genetic framework. However, because only 6278 bacterial artificial chromosome (BACs) in the physical map were sequenced, fine structure was limited. To gain access to the gene-containing portion of the barley genome at high resolution, we identified and sequenced 15 622 BACs representing the minimal tiling path of 72 052 physical-mapped gene-bearing BACs. This generated ~1.7 Gb of genomic sequence containing an estimated 2/3 of all Morex barley genes. Exploration of these sequenced BACs revealed that although distal ends of chromosomes contain most of the gene-enriched BACs and are characterized by high recombination rates, there are also gene-dense regions with suppressed recombination. We made use of published map-anchored sequence data from Aegilops tauschii to develop a synteny viewer between barley and the ancestor of the wheat D-genome. Except for some notable inversions, there is a high level of collinearity between the two species. The software HarvEST:Barley provides facile access to BAC sequences and their annotations, along with the barley-Ae. tauschii synteny viewer. These BAC sequences constitute a resource to improve the efficiency of marker development, map-based cloning, and comparative genomics in barley and related crops. Additional knowledge about regions of the barley genome that are gene-dense but low recombination is particularly relevant.

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