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ARS Home » Plains Area » Fargo, North Dakota » Edward T. Schafer Agricultural Research Center » Cereal Crops Research » Research » Publications at this Location » Publication #217120

Title: Progress towards the construction of a sequence-ready physical map of the 3AS chromosome arm of hexaploid wheat

item Gill, Bikram
item Li, Wanlong
item Sehgal, Sunish
item Faris, Justin
item Reddy, Leela
item Devos, Katrien
item Buell, Robin
item Gornicki, Piotr
item Rabinowicz, Pablo
item Dolezel, Jaroslav
item Simkova, Hana
item Safar, Jan
item Ma, Yaqin
item Chen, Frances
item Lucretti, Sergio
item You, Frank
item Luo, Ming-cheng

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 11/1/2007
Publication Date: 1/10/2008
Citation: Gill, B., Li, W., Sehgal, S.K., Faris, J.D., Reddy, L., Devos, K.M., Buell, R., Gornicki, P., Rabinowicz, P.D., Dolezel, J., Simkova, H., Safar, J., Ma, Y., Chen, F., Lucretti, S., You, F.M., Luo, M. 2008. Progress towards the construction of a sequence-ready physical map of the 3AS chromosome arm of hexaploid wheat. Plant and Animal Genome Conference XVI abstracts pg. 9

Interpretive Summary:

Technical Abstract: The large genome size (~17 Gb), polyploid nature, and repetitive sequence content (>90%) of hexaploid wheat (Triticum aestivum) present a challenge for constructing physical maps, which are fundamental resources to aid genomic sequencing and annotation, and gene cloning. One approach to reduce the complexity of the analysis is to establish physical maps and sequences of isolated chromosomes or chromosome arms. Progress on a pilot project on chromosome arm 3AS is reported here. A bacterial artificial chromosome (BAC) library for 3AS (Chinese Spring) was constructed from flow-sorted chromosomes with 12' chromosome equivalent. A total of 55,584 BAC clones were fingerprinted and assembled into 1,677 contigs (provide 10-fold 3AS arm coverage) and 11,939 singletons. Ten thousand random BACs were end sequenced and 16,795 high-quality BAC-end sequences (BESs) showing an average read-length of 500 bp with a total of 8.3 Mb of genomic sequences. Microsatellite primers were successfully developed from 598 SSRs found in BES and on the average 20 and 11 % of markers were polymorphic in T. monococcum and T. turgidum species, respectively. Another 504 genic sequences were identified from the BES and were used to screen the 3AS BAC fingerprint database. Primers were developed from 279 genic sequences that were present in BAC contigs and will be used for anchoring those contigs to the genetic map. EST-STS markers were developed from bin-mapped ESTs and rice. All markers are PCR-based and are being used to physically anchor the BAC contigs using 190 six-dimensional BAC pools. Progress is being made on the construction of 20 Mb BAC-contig for comparative sequencing of the Fhb1/Rph7 region. This project was supported by the USDA-CSREES in the US, and by the Ministry of Education, Youth and Sports of the Czech Republic (LC06004), Czech Science Foundation (521/06/723 and 521/07/1573) and the Italian Ministry of Agriculture and Forest Policy (FRUMISIS 418/7303/03).