Sequencing of 15 622 Gene-bearing BACs Clarifies the Gene-dense Regions of the Barley Genome

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

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

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.Keywords: Aegilops tauschii, Barley, centromere BACs, HarvEST:Barley, gene distribution, synteny, recombination frequency, Hordeum vulgare L., BAC sequencingThis is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by John Wiley & Sons Ltd. on behalf of the Society for Experimental Biology. The published article can be found at: http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291365-313X. Supporting information is available online at: http://onlinelibrary.wiley.com/doi/10.1111/tpj.12959/abstrac

Wild Relatives of Maize, Rice, Cotton, and Soybean: Treasure Troves for Tolerance to Biotic and Abiotic Stresses

Global food demand is expected to nearly double by 2050 due to an increase in the world's population. The Green Revolution has played a key role in the past century by increasing agricultural productivity worldwide, however, limited availability and continued depletion of natural resources such as arable land and water will continue to pose a serious challenge for global food security in the coming decades. High yielding varieties with proven tolerance to biotic and abiotic stresses, superior nutritional profiles, and the ability to adapt to the changing environment are needed for continued agricultural sustainability. The narrow genetic base of modern cultivars is becoming a major bottleneck for crop improvement efforts and, therefore, the use of crop wild relatives (CWRs) is a promising approach to enhance genetic diversity of cultivated crops. This article provides a review of the efforts to date on the exploration of CWRs as a source of tolerance to multiple biotic and abiotic stresses in four global crops of importance; maize, rice, cotton, and soybean. In addition to the overview of the repertoire and geographical spread of CWRs in each of the respective crops, we have provided a comprehensive discussion on the morphological and/or genetic basis of the traits along with some examples, when available, of the research in the transfer of traits from CWRs to cultivated varieties. The emergence of modern molecular and genomic technologies has not only accelerated the pace of dissecting the genetics underlying the traits found in CWRs, but also enabled rapid and efficient trait transfer and genome manipulation. The potential and promise of these technologies has also been highlighted in this review

Molecular Characterization of Transgenic Events Using Next Generation Sequencing Approach.

Demand for the commercial use of genetically modified (GM) crops has been increasing in light of the projected growth of world population to nine billion by 2050. A prerequisite of paramount importance for regulatory submissions is the rigorous safety assessment of GM crops. One of the components of safety assessment is molecular characterization at DNA level which helps to determine the copy number, integrity and stability of a transgene; characterize the integration site within a host genome; and confirm the absence of vector DNA. Historically, molecular characterization has been carried out using Southern blot analysis coupled with Sanger sequencing. While this is a robust approach to characterize the transgenic crops, it is both time- and resource-consuming. The emergence of next-generation sequencing (NGS) technologies has provided highly sensitive and cost- and labor-effective alternative for molecular characterization compared to traditional Southern blot analysis. Herein, we have demonstrated the successful application of both whole genome sequencing and target capture sequencing approaches for the characterization of single and stacked transgenic events and compared the results and inferences with traditional method with respect to key criteria required for regulatory submissions

L'Écho : grand quotidien d'information du Centre Ouest

14 janvier 19311931/01/14 (A60).Appartient à l’ensemble documentaire : PoitouCh

L'Écho : grand quotidien d'information du Centre Ouest

29 avril 19251925/04/29 (A54).Appartient à l’ensemble documentaire : PoitouCh

Molecular characterization of transgenic events by traditional and advanced approaches.

<p>Molecular characterization of transgenic events by traditional and advanced approaches.</p

Molecular characterization of transgenic soybean Transgenic Event 1 (TE1) and Transgenic Event 2 (TE2) using whole genome sequencing.

<p>Genomic DNA of TE1 and TE2 was randomly sheared and sequenced using Illumina's HiSeq2000 instrument. The genome coverage was ~ 10X, i.e. 10 copies of soybean haploid genome. Short HiSeq2000 reads (A) spanning entire T-DNA within TE1 and TE2 (B) were mapped back to transformation plasmid that contained intended T-DNA (C1) and backbone (C2). Uninterrupted blue bars aligned to the intended T-DNA (C1) of the transformation plasmid confirms the integrity of T-DNA within events. No blue bars over plasmid backbone (C2) confirms the absence of those sequences within the genome of TE1 and TE2 events. Twenty chromosomes (<i>Gm</i>1-20) of soybean reference genome (Williams 82 version X) are represented in circular fashion (D). Reads spanning junction regions were mapped back to soybean reference genome, which showed single insertion site on chromosome 6 (E) in TE1 and chromosome 2 (E) in TE2.</p

Molecular characterization of soybean breeding stack Transgenic Event 1 x Transgenic Event 2 (TE1 x TE2) using whole genome sequencing.

<p>Genomic DNA of TE1 x TE2 was randomly sheared and sequenced using Illumina's HiSeq2000 instrument. The genome coverage was ~ 14X, i.e. 14 copies of soybean haploid genome. Short HiSeq2000 reads (A) spanning entire T-DNA within TE1 and TE2 (B) were mapped back to transformation plasmid that contained intended T-DNA (C1) and backbone (C2). Uninterrupted blue bars aligned to the intended T-DNA (C1) of the transformation plasmid confirms the integrity of T-DNA within TE1 and TE2. No blue bars over plasmid backbone (C2) confirms the absence of those sequences within the genome of TE1 and TE2. Twenty chromosomes (<i>Gm</i>1-20) of soybean reference genome (Williams 82 version X) are represented in circular fashion (D). Reads spanning junction regions were mapped back to soybean reference genome, which showed single insertion site on chromosome 6 (E) in TE1 and on chromosome 2 (E) in TE2. T-DNA insert in both TE1 and TE2 share the same fragment at the 3'border region (F).</p