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United States Department of Agriculture

Agricultural Research Service

Title: Sequencing a 1.3 Mb Contig Spanning the Rf1 Fertility Restorer Locus As a Prototype to Assess Complex-Genome Coverage Strategies

item Kronmiller, Brent - IOWA STATE UNIVERSITY
item Gobelman Werner, Karin
item Wise, Roger

Submitted to: Maize Genetics Conference Abstracts
Publication Type: Proceedings
Publication Acceptance Date: January 10, 2005
Publication Date: March 10, 2005
Citation: Kronmiller, B., Gobelman Werner, K.S., Wise, R.P. 2005. Sequencing a 1.3 Mb contig spanning the rf1 fertility restorer locus as a prototype to assess complex-genome coverage strategies. 47th Annual Maize Genetics Conference Abstracts. P184.

Technical Abstract: In T-cytoplasm maize, Cytoplasmic male sterility (CMS) is attributed to the presence of the unique mitochondrial gene, T-urf13. Full suppression of T-urf13-mediated CMS is directed by the combined action of dominant alleles of the nuclear (fertility restorer) genes, rf1 and rf2a. To facilitate a candidate approach towards identification of the rf1 gene, three B73 BAC libraries were used to create a physical map of 794 clones from the centromeric region of chromosome 3 anchored to the rf1 locus. A minimum-tiling path of 14 contiguous BACs covering 1.3 megabases were shotgun sequenced, assembled, and finished to completion for annotation and display in the GBrowse viewer. Eighty-seven percent of the sequence has been identified as repetitive, with most transposable elements found in large nested clusters spanning up to 300 kb with insertion chronologies of –0.19 to –8.50 million years. GeneSeqer, Fgenesh, and GeneMark.hmm were used to predict consensus locations and structures for 53 genes. Thirty-seven of these are positioned in gene clusters with as many as 8 members. Two hundred fifty-four GSS assemblies (including MAGIs, TIGR’s AZM and PlantGDB’s GSS) aligned to the 1.3 Mb contig, 36 of which aligned to predicted genes. Two hundred eighteen GSS assemblies aligned to regions not predicted as genes, revealing that only 15% of GSS contigs align to genes in this region. Seventeen predicted genes did not correspond to any GSS assembly, indicating that at least in the centromeric region of chromosome 3, finished sequence can provide a significant number of previously undescribed gene predictions.

Last Modified: 4/18/2015
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