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Functional features of a single chromosome arm in wheat (1AL) determined from its structure

Lucas, Stuart J. and Simkova, Hana and Safar, Jan and Jurman, Irena and Cattonaro, Federica and Vautrin, Sonia and Bellec, Arnaud and Berges, Helene and Dolezel, Jaroslav and Budak, Hikmet (2012) Functional features of a single chromosome arm in wheat (1AL) determined from its structure. Functional and Integrative Genomics, 12 (1). pp. 173-182. ISSN 1438-793X (Print) 1438-7948 (Online)

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Official URL: http://dx.doi.org/10.1007/s10142-011-0250-3

Abstract

Bread wheat (Triticum aestivum L.) is one of the most important crops globally and a high priority for genetic improvement, but its large and complex genome has been seen as intractable to whole genome sequencing. Isolation of individual wheat chromosome arms has facilitated large-scale sequence analyses. However, so far there is no such survey of sequences from the A genome of wheat. Greater understanding of an A chromosome could facilitate wheat improvement and future sequencing of the entire genome. We have constructed BAC library from the long arm of T. aestivum chromosome 1A (1AL) and obtained BAC-end sequences from 7470 clones encompassing the arm. We obtained 13,445 (89.99%) useful sequences with a cumulative length of 7.57 Mb, representing 1.43% of 1AL and about 0.14% of the entire A genome. The GC content of the sequences was 44.7%, and 90% of the chromosome was estimated to comprise repeat sequences, while just over 1% encoded expressed genes. From the sequence data we identified a large number of sites suitable for development of molecular markers (362 SSR and 6948 ISBP) which will have utility for mapping this chromosome and for marker assisted breeding. From 44 putative ISBP markers tested 23 (52.3%) were found to be useful. The BAC-end sequence data also enabled the identification of genes and syntenic blocks specific to chromosome 1AL, suggesting regions of particular functional interest and targets for future research.

Item Type:Article
Uncontrolled Keywords:Wheat – A genome – BAC end sequencing – Comparative genomics – Marker design
Subjects:Q Science > QH Natural history > QH506 Molecular biology
Q Science > QK Botany
Q Science > QH Natural history > QH426 Genetics
ID Code:17521
Deposited By:Stuart J. Lucas
Deposited On:28 Nov 2011 11:59
Last Modified:20 Apr 2012 10:39

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