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United States Department of Agriculture

Agricultural Research Service


item Vroh, Bi Irie
item Mcmullen, Michael
item Sanchez-villeda, Hector
item Schroeder, Steve
item Gardiner, Jack
item Schaeffer, Mary
item Soderlund, Cari
item Wing, Rod
item Fang, Zhiwei
item Coe Jr, Edward

Submitted to: Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/3/2005
Publication Date: 1/1/2006
Citation: Vroh, B., Mcmullen, M.D., Sanchez-Villeda, H., Schroeder, S., Gardiner, J., Soderlund, C., Wing, R., Fang, Z., Coe Jr, E.H. 2006. Single nucleotide polymorphisms and insertion-deletions for genetic markers and anchoring the maize fingerprint contig physical map. Crop Science. 46:12-21.

Interpretive Summary: Many genes that control agronomic traits are known only from their genetic location. An integrated genetic and physical map is required to isolate these genes. A physical map consists of large, ordered fragments of DNA known as contigs. Currently, there is no comprehensive, integrated genetic and physical map for corn. To develop such a map large numbers of genes that identify contigs must be genetically mapped at high resolution. In this manuscript we demonstrate the utility of using sequence variation in genes, either single changes in DNA nucleotides known as single nucleotide polymorphisms, or insertions of DNA nucleotides known as InDels (insertions/deletions) as genetic markers to create links between the genetic and physical maps of corn. The integrated genetic and physical map for corn will aid scientists in isolating genes that affect corn productivity thus enabling crop improvement. In addition, the integrated genetic and physical map serves as the foundation of genome sequencing in corn.

Technical Abstract: Single nucleotide polymorphisms (SNPs) and Insertion-Deletion (InDels) are becoming important genetic markers for major crop species. In this study we demonstrate their utility for locating fingerprint contigs (FPC) to the genetic map. To derive SNP and InDel markers we amplified genomic regions corresponding to 3,000 unigenes across 12 maize lines of which, 194 unigenes (6.4%) showed size polymorphism InDels between B73 and Mo17 on agarose gels. The analysis of these InDels in 83 diverse inbred lines showed that InDels are often multiallelic markers in maize. Single nucleotide polymorphism discovery conducted on 592 unigenes revealed that 44% of the unigenes contained B73/Mo17 SNP(s), while 8% showed no sequence variation among the 12 inbred lines. On average, SNPs and InDels occurred every 73 bp and 309 bp, respectively. Multiple SNPs within unigenes led to a SNP haplotype genetic diversity of 0.61 among inbreds. The unigenes were previously assigned to maize FPC contigs by overgo hybridization. From this set of unigenes, 311 (133 SNP and 178 InDel loci) were mapped on the high-resolution mapping population (IBM). These markers provided unambiguous anchoring of 129 FPC contigs and orientation for 30 contigs. The FPC anchored map of maize will be useful for map-based cloning, for genome sequencing efforts in maize, and for comparative genomics in grasses. The amplification primers for all mapped InDel and SNP loci, the diversity information for SNPs and InDels, and the corresponding overgoes to anchor BAC contigs are provided as genetic resources.

Last Modified: 05/25/2017
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