A Chromosome Bin Map of 16,000 Expressed Sequence Tag Loci and Distribution of Genes Among the Three Genomes of Polyploid Wheat

Qi, Lili; Echalier, Benjamin; Chao, Shiaoman; Lazo, Gerard R.; Butler, Gregory J.; Anderson, Olin D.; Akhunov, Eduard; Dvořák, Jan; Linkiewicz, Anna; Ratnasiri, A.; Dubcovsky, Jorge; Bermudez-Kandianis, C. E.; Greene, Robert A.; Kantety, Ramesh V.; Rota, C. M. La; Munkvold, Jesse; Sorrells, S. F.; Sorrells, Mark E.; Dilbirliği, Muharrem; Sidhu, Deepak; Erayman, Mustafa; Randhawa, H. S.; Sandhu, Devinder; Bondareva, S. N.; Gill, Kulvinder S.; Mahmoud, Ahmed A.; Ma, Xuefeng; Miftahudin, Miftahudin; Gustafson, J. P.; Conley, E. J.; Nduati, Vivienne; Gonzalez-Hernandez, Jose L.; Anderson, James A.; Peng, Junhua; Lapitan, Nora L. V.; Hossain, Khwaja; Kalavacharla, Venu; Kianian, Shahryar F.; Pathan, M. S.; Zhang, D. S.; Nguyen, Henry T.; Choi, Dong-Woog; Fenton, Raymond D.; Close, Timothy J.; McGuire, Patrick E.; Qualset, C. O.; Gill, Bikram S.

doi:10.1534/genetics.104.034868

Cited by 370 publications

(278 citation statements)

References 79 publications

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“…However, NSH sequences were overall significantly less GC-rich (47.6% vs. 52.3%; P Ͻ Ͻ 0.0001) than other mapped ESTs. The proportion of NSH TCs and singleton ESTs matching loci in two or three homoeologous groups was Ϸ20%, similar to the 17% reported (27) for all physically mapped ESTs. Rapidly evolving low-copy retroelements would not be expected to retain homoeologous relationships after genome divergence.…”

Section: Sources Of Error In Evolutionary Speculation Based On Nonhomsupporting

confidence: 78%

“…The deletion bin between 0.68 and 0.70 characterized by 4BL7-0.70, with only two ESTs (BG313203 and a transposed duplicated EST BG263385), was removed from the analysis. The presence-absence pattern of DNA hybridization signals among the stocks allows assignment of EST loci to one or more specific deletion bins (27).…”

Section: Methodsmentioning

confidence: 99%

“…For the rice Southern blots, 500 ng of genomic DNA from two varieties (Milyang 23, a Japonica͞Indica hybrid, and Gihobyeo, a Japonica variety) was digested with EcoRI. All restriction fragment length polymorphism conditions were the same as used for wheat (27).…”

Section: Methodsmentioning

confidence: 99%

“…More recently, high-density deletionbin maps of the 21 chromosomes of wheat have been produced by restriction fragment hybridization of 5,762 ESTs to a panel of 101 wheat deletion stocks, each missing a different terminal portion of a chromosome arm (http:͞͞wheat.pw.usda.gov͞NSF͞data.html) (27). These maps have been aligned to the sequenced genome of rice.…”

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confidence: 99%

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Gene evolution at the ends of wheat chromosomes

See

Brooks

Nelson

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

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Wheat ESTs mapped to deletion bins in the distal 42% of the long arm of chromosome 4B (4BL) were ordered in silico based on blastn homology against rice pseudochromosome 3. The ESTs spanned 29 cM on the short arm of rice chromosome 3, which is known to be syntenic to long arms of group-4 chromosomes of wheat. Fine-scale deletion-bin and genetic mapping revealed that 83% of ESTs were syntenic between wheat and rice, a far higher level of synteny than previously reported, and 6% were nonsyntenic (not located on rice chromosome 3). One inversion spanning a 5-cM region in rice and three deletion bins in wheat was identified. The remaining 11% of wheat ESTs showed no sequence homology in rice and mapped to the terminal 5% of the wheat chromosome 4BL. In this region, 27% of ESTs were duplicated, and it accounted for 70% of the recombination in the 4BL arm. Globally in wheat, no sequence homology ESTs mapped to the terminal bins, and ESTs rarely mapped to interstitial chromosomal regions known to be recombination hot spots. The wheat–rice comparative genomics analysis indicated that gene evolution occurs preferentially at the ends of chromosomes, driven by duplication and divergence associated with high rates of recombination.

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Section: Sources Of Error In Evolutionary Speculation Based On Nonhomsupporting

confidence: 78%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

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Gene evolution at the ends of wheat chromosomes

See

Brooks

Nelson

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

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“…In addition, we have aligned sequence-based genetic markers from maize (4,906 markers) available from the IBM2 Neighbors map at Maize GDB (http://www.maizegdb. org/) and wheat (Qi et al, 2004;5,996 bin-mapped markers) available from the GrainGenes Database (http://wheat.pw.usda.gov/cgi-bin/westsql/map_ locus.cgi) with the rice BAC/PAC clones to provide syntenic maps between rice and these cereal species. Displays, as well as downloadable tab-delimited files, of the alignments between the maize and wheat genetic markers with the rice genome are available from the project Web pages.…”

Section: Functional Annotation Data Typesmentioning

confidence: 99%

The Institute for Genomic Research Osa1 Rice Genome Annotation Database

Yuan¹,

Ouyang²,

Wang³

et al. 2005

Plant Physiology

193

192

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We have developed a rice (Oryza sativa) genome annotation database (Osa1) that provides structural and functional annotation for this emerging model species. Using the sequence of O. sativa subsp. japonica cv Nipponbare from the International Rice Genome Sequencing Project, pseudomolecules, or virtual contigs, of the 12 rice chromosomes were constructed. Our most recent release, version 3, represents our third build of the pseudomolecules and is composed of 98% finished sequence. Genes were identified using a series of computational methods developed for Arabidopsis (Arabidopsis thaliana) that were modified for use with the rice genome. In release 3 of our annotation, we identified 57,915 genes, of which 14,196 are related to transposable elements. Of these 43,719 nontransposable element-related genes, 18,545 (42.4%) were annotated with a putative function, 5,777 (13.2%) were annotated as encoding an expressed protein with no known function, and the remaining 19,397 (44.4%) were annotated as encoding a hypothetical protein. Multiple splice forms (5,873) were detected for 2,538 genes, resulting in a total of 61,250 gene models in the rice genome. We incorporated experimental evidence into 18,252 gene models to improve the quality of the structural annotation. A series of functional data types has been annotated for the rice genome that includes alignment with genetic markers, assignment of gene ontologies, identification of flanking sequence tags, alignment with homologs from related species, and syntenic mapping with other cereal species. All structural and functional annotation data are available through interactive search and display windows as well as through download of flat files. To integrate the data with other genome projects, the annotation data are available through a Distributed Annotation System and a Genome Browser. All data can be obtained through the project Web pages at http://rice.tigr.org.

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