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Title: Utilization of deletion bins to anchor and order sequences along the wheat 7B chromosome

item BELOVA, TATIANA - Norwegian University Of Life Sciences
item GRONVOLD, LARS - Norwegian University Of Life Sciences
item KUMAR, AJAY - North Dakota State University
item Kianian, Shahryar
item HE, XINYAO - International Maize & Wheat Improvement Center (CIMMYT)
item LILLEMO, MORTEN - Norwegian University Of Life Sciences
item SPRINGER, NATHAN - University Of Minnesota
item LIEN, SIGBJORN - Norwegian University Of Life Sciences
item OLSON, ODD-ARNE - Norwegian University Of Life Sciences
item SANDVE, SIMEN - Norwegian University Of Life Sciences

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/13/2014
Publication Date: 8/19/2014
Citation: Belova, T., Gronvold, L., Kumar, A., Kianian, S., He, X., Lillemo, M., Springer, N.M., Lien, S., Olson, O., Sandve, S.R. 2014. Utilization of deletion bins to anchor and order sequences along the wheat 7B chromosome. Theoretical and Applied Genetics. 127:2029-2024.

Interpretive Summary: In order to improve cultivated wheat, genes and traits of agricultural importance need to be positioned accurately on chromosomes and closely linked markers identified to allow rapid selection in breeding programs. In this study a method of accurately placing thousands of markers onto chromosome intervals was evaluated. A total of 3,671 sequence contigs and scaffolds were mapped to deletion bins on wheat chromosome 7B providing a foundation for developing high-resolution integrated physical map for this chromosome. This is a pre-requistied to complete sequencing of this chromosomes and identifying the important genes that can be used to improve modern wheat cultivars.

Technical Abstract: Bread wheat (Triticum aestivum L.) has a large, complex and highly repetitive genome which is challenging to assemble into high quality pseudo-chromosomes. As part of the international effort to sequence the hexaploid bread wheat genome by the international wheat genome sequencing consortium (IWGSC) we are focused on assembling a reference sequence for chromosome 7B. The successful completion of the reference chromosome sequence is highly dependent on the integration of genetic and physical maps. To aid the integration of these two types of maps, we have constructed a high-density deletion bin map of chromosome 7B. Using the 270 K Nimblegen comparative genomic hybridization (CGH) array on a set of cv. Chinese spring deletion lines, a total of 3,671 sequence contigs and scaffolds (~7.8 % of chromosome 7B physical length) were mapped into nine deletion bins. Our method of genotyping deletions on chromosome 7B relied on a model-based clustering algorithm (Mclust) to accurately predict the presence or absence of a given genomic sequence in a deletion line. The bin mapping results were validated using three different approaches, viz. (a) PCR-based amplification of randomly selected bin mapped sequences (b) comparison with previously mapped ESTs and (c) comparison with a 7B genetic map developed in the present study. Validation of the bin mapping results suggested a high accuracy of the assignment of 7B sequence contigs and scaffolds to the 7B deletion bins.