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United States Department of Agriculture

Agricultural Research Service

Title: Simple Sequence Repeat Markers Developed from Maize Sequences Found in the Genbank Database: Map Construction

Authors
item Senior, Mary
item Chin, E - NORTH CAROLINA STATE UNIV
item Lee, M - NORTH CAROLINA STATE UNIV
item Stuber, Charles
item Smith, J - NORTH CAROLINA STATE UNIV

Submitted to: Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: June 10, 1996
Publication Date: N/A

Interpretive Summary: The genetic makeup of all plants and animals resides within each cell of the organism in structures known as chromosomes. The main component of the chromosome is DNA, which is comprised of four nucleotide bases arranged in many different patterns, known as sequences. These sequences make each DNA molecule unique and provide the instructions for the synthesis of proteins. DNA-based molecular markers rely on the fact that DNA sequences can differ slightly from one organism to another. When methods are found that can detect these differences, they can be used to study plant and animal species on the DNA level. Simple sequence repeats (SSRs) are regions of the DNA sequence where a pattern of 2-6 nucleotides is repeated from 5, to 30 or more times. The length of these repeats can vary even among closely related organisms. Using a procedure called the Polymerase Chain Reaction, we can replicate these regions many times. If the length of the repeated nucleotides varies among the organisms being studied, the differences can be detected using a size separation technique known as electrophoresis. We have identified many of these repeated regions in maize. To make them more useful, however, we must determine where they are located on the 10 chromosomes of maize. Using a population of plants known as recombinant inbreds, we have been able to determine the location of 45 such regions.

Technical Abstract: Simple sequence repeats (SSRs) are rapidly becoming an important class of DNA markers that are being widely used to map both plant and animal genomes. SSRs have the advantage of providing a codominant marker system based on a polymerase chain reaction (PCR) methodology. Although the presence of microsatellites is now well documented in the plant kingdom, the availability of a well-mapped set of primer sequences in maize (Zea mays L.) is still limited. Polymorphic primer pairs developed from maize sequences found in Genbank were mapped to 42 distinct loci in maize using either a B73xMo17, M017 x H99 or B73xG35 recombinant inbred population. All SSR loci were found to be linked to one or more adjacent restriction fragment length polymorphism (RFLP) and/or isozyme loci. Segregation followed a pattern of Mendelian inheritance with one SSR locus deviating from expected ratios at an alpha=.01 level of significance. The SSRs were distributed evenly throughout the maize genome with no evidence of clustering. A single set of segregating bands was produced for each primer pair. Because F3 bulks of F2 plants are sometimes used in mapping studies, a simulation involving amplification of SSR loci in the heterozygous condition was conducted. In a bulk of 10 plants, a 4:16 or greater ratio of genome A :genome B or greater was needed to accurately score the presence of the A genome. Ratios lower than 4:16 occur with a probability low enough that this should not be seen as a deterrant for SSR mapping in these populations.

Last Modified: 7/24/2014
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