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WHAT ARE MAP COORDINATES?

Coordinate Definition:
The numeric value that positions a locus on the map.

Why are some coordinates displayed in bold type?
Coordinates shown in bold are the well-ordered loci on a given map. These are called 'on frame' by MapMaker. Other loci are placed approximately by MapMaker or other tools.


For Genetic Maps the unit of the coordinate system is the genetic map unit or centiMorgan (cM), which is based upon recombination frequency between loci.

Because unlinked loci are 50 cM apart, locus coordinates along the map are calculated using the coordinates of nearby loci. If loci are close together, double crossovers are negligible, but for longer intervals the presence of double crossovers is accounted by calculating expected coincidental events in the interval (Haldane 1919 J Genet 8:299-309, Kosambi 1944 Ann Eugenics 12:172-175). The locus on the short arm of any chromosome that is most distal to the centromere lies at coordinate 0 by definition, and the other coordinates are calculated based upon this locus' position. For instance, looking at the IBM 9 map you will find that umc1957 is the most distal locus on this map for the short arm. That makes its coordinate 0 by definition. The locus umc109 is at coordinate 5 (it is 5 cM from umc1957), and bz1 is at coordinate 88.1. The bz1 coordinate (which is greater than 50 cM from umc109), could be designated if (within the context of this particular map) it is known that lim343 is 41.2 cM from umc109, and bz1 is 46.9 cM from lim343 with umc1957 and bz1 occuring as unlinked loci.

Related information contributed by Ed Coe:
Genetic Maps are developed by combining frequencies of recombination between genetic markers. In testcross progenies the frequencies are directly calculated as gametic frequencies, while in F2 or other progenies they are defined by simple formulas based on the compounded gametic frequencies. In principle, recombination frequencies are compared two points at a time and three points at a time, and order of loci is determined by maximizing the statistical likelihood among all possible orders (which typically minimizes the length of the resulting map). Computation is aided by robust algorithms such as MapMaker of Lander and Botstein (PNAS USA 83:7353-7357). MapMaker is applied to coherent data from sets of individuals derived from the same segregating population or combined sets. These sets can be testcross or F2 families, or recombinant inbreds produced by selfing F2 individuals through single-seed descent to homozygosity. At the simplest level, however, a map can be assembled from different data sources, using common markers between them and intercalating to construct an approximated map; this has been the practice in deriving the classical "Genetic Maps" of combined gene-to-gene data.

For Physical Maps the unit of the coordinate system is the base pair (bp). Coordinates on IBM2 FPC are based on the nearest upstream IBM2 coordinate in an anchored contig, followed by a decimal and a 4-digit value after the decimal that specifies the position within the contig, namely the CB (consensus band) units assigned by agarose FPC for the locus or BAC in a given contig. A CB is about 4000 bp for the agarose maize FPC.

For Cytogenetic Maps the unit of the coordinate system is the centiMcClintock.


What is a centiMorgan? One centiMorgan is defined as one genetic map unit, which equals the distance between loci for which one product of meiosis out of 100 is recombinant. CentiMorgans are so named in honor of Thomas Hunt Morgan.

The term 'centiMorgan' is defined classically by Haldane 1919 J Genet 8:299-309. When the distance between two loci is listed as 1 cM, there will be one cross over per 100 meioses (which is to say that, for example, on an ear with 100 kernels, the crossover genotype is present in only one kernel). This is in contrast to high-resolution genetic maps, (such as the various IBM maps) that represent enhanced meioses with inflated cM values. See also Liu et al. 1996 Genetics 142:247-258; Lee et al. 2002 Plant Mol Biol 48:453-461; Sharopova et al. 2003 Plant Mol Biol 48:463-481; and Winkler et al. 2003 Genetics 164:741-745.

What is a centiMcClintock? For example (using chromosome 9), the centromere is at 9SL.00 (or 0), the tip of the short arm is at 9S1.00 (or -1.00) and tip of long arm is at 9L1.00 (or 1.00). Each chromosome arm constitutes one "McClintock" which equals 100 centiMcClintocks (cMC). Therefore, each chromosome has 200 cMC total. The distance from 9L.95 to 9L.90 is 5 cMC. CentiMcClintocks are so named in honor of Barbara McClintock.


Information Specific to Certain Maps:

Bins maps
Coordinates are named by the chromosome number, followed by a decimal, and a numeric identifier. 1.00 is the most distal (left or top-most) bin on the short arm of the chromosome. Bin boundaries are defined by a set of Core Markers. All mapped loci are assigned a bin.

IBM neighbors
These are merged genetic maps with IBM as framework and were initially developed to anchor BAC contigs to a chromosomal position. Only IBM on-frame loci are considered on-frame loci in this computation. The IBM neighbors frame maps include all the IBM loci and well-ordered loci on other maps. The most current maps are displayed on locus pages.

IBM FPC
These maps provide a way to refine the IBM neighbors maps with data from BAC contigs (http://www.genome.arizona.edu/fpc/maize). Coordinates are named by the average IBM coordinate for an anchored BAC contig, followed by a decimal, and the BAC coordinate for that locus. For example, loci AY110401 and smt2 are on the same BAC contig at positions 45 and 421. The contig's anchors on the genetic map have an average IBM value of 83 (Feb 2004). Coordinates on the IBM FPC are 83.0045 and 83.0421, respectively.

FPC Fingerprinted Contigs
Coordinates within a BAC contig are expressed as CB units or consensus bands, which are also known as restriction fragment units. The length of a contig is equal to the approximate number of consensus bands. The average size of a band in maize is about 4,900 nucleotides.

In IBM2 maps, what are IcM coordinates?
The IBM2 maps were derived with an intermated (syn 4) recombinant inbred population from intermated B73/Mo17, in which meioses had accumulated to the equivalent of 4-fold over those in a typical recombination experiment (Lee et al., 2002, Plant Mol Biol 48:453; http://www.ncbi.nlm.nih.gov/pubmed/11999829). The MapMaker results have not been adjusted to typical centiMorgans but have been retained as the original products, i.e., as IBM centimorgans or IcM. The "Neighbors" maps are based on the IBM2 framework with intercalations from other maps. In short intervals (i.e., 10 IcM or less, as in a dense map such as IBM2), the multiplier is 3.63 or greater, approaching 4.00 at 0.00 IcM (per equation 9 of Winkler et al., 2003, Genetics 164: 741; http://www.ncbi.nlm.nih.gov/pubmed/12807793; personal communication from Jim Holland). Adjustments to typical centimorgans were applied in deriving the ISU IBM maps (Fu et al., 2006, Genetics 174:1671; http://www.ncbi.nlm.nih.gov/pubmed/16951074) and the IBM GNP maps (Falque et al., 2005, Genetics 170:1957; http://www.ncbi.nlm.nih.gov/pubmed/15937132). A converter is available at http://bioinformatics.oxfordjournals.org/content/21/16/3441.long.




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Last updated 1:49 pm, Dec 03, 2014.

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