Bin Viewer

Maize Bin Viewer

Choose a region of the genome you're interested in from the image below, or read on to find out details about this genome display.




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For a set of 384 primer pairs that provide a marker approximately every 20 cM over the whole genetic map of maize go here.

What Are The Chromosome Splits Called 'Bin Boundaries' Based On?

The following explanation was submitted by Ed Coe.

The chromosome splittings above are based on the concept of bins. The genetic maps are divided into 100 segments, called bins, of approximately 20 centiMorgans between two fixed Core Markers (Gardiner et al. 1993 Genetics 134:917-930). The segments are designated with the chromosome number followed by a two-digit decimal ( e.g., 1.00, 1.01, 1.02, etc). A bin is the interval that includes all loci from the leftmost or top Core Marker to the next Core Marker. Placement of a locus to a bin is dependent on the precision of mapping data, and increases in certainty as markers increase in number or populations increase. Whenever the placement is statistically uncertain, 'Bin1' refers to the beginning of a range, and 'Bin2' refers to the end of the range.

A Core Marker is a Locus or Probe that defines a bin boundary (Gardiner et al. 1993 Genetics 134:917-930, Davis et al. 1999 Genetics 152(3):1137-1172).


Core Bin Marker (CBM) Assignment to V2-Curation Summary

The following explanation was provided by Jack Gardiner (April 2011).

90 CBMs were assigned to the V2 pseudomolecule assemblies. In most cases, their locations were not significantly different from those in V1 and the resulting changes can easily be reconciled to improvements in the pseudomolecules. The strategy taken for V2 was to assemble a FASTA file for each of the 10 maize chromosomes so that this process could be done quicker for future assemblies. These files also serve to document the EXACT sequence that was used to establish the CBM boundaries since in many cases there were several sequences available and they may or may not agree. In several cases (Bins 2.07/umc5a, 4.05/agrr37b, 6.02/umc59a, 10.04/umc64a) there were CBM's that were localized on V1 that were unable to be placed on V2 and it was unclear why they could be placed on V1 but not V2. In all cases these were RFLP probes that hit multiple loci that tend to give complex hybridization patterns. Further inspection indicates that some of these were placed on the assemblies using overgo hybridization to BAC data that gives approximate placement on the assemblies. Whatever the case may be, going forward, these CBMs were not good choices so it was best to pick alternative markers which were nearby and have reliable sequence. Lastly, one CBM (3.03. asg24(gts) ) was able to be placed on V2 even though it was unable to be placed on V1 and was replaced by mus2. In V2, and future assemblies, we will continue to use asg24(gts) since it has reliable sequence. The set of core markers are as follows:


Table for core bin markers

Notes for table below:
              The sequence for this core bin marker could not be placed on the B73 RefGen_v3 sequence.
              This Bin region used an alternative bin marker so it could be placed on the B73 RefGen_v3 sequence. Alternate markers were selected that have empirically confirmed positions on both genetic and physical map, and a sequence that aligns correctly on B73 RefGen_v3.

Chr1 Chr2 Chr3 Chr4 Chr5 Chr6 Chr7 Chr8 Chr9 Chr10
Bin Core Bin Marker Molecular
Marker/Probe
Type Insert Enzyme(s) Full Length
Insert Sequence
B73 RefGen_v3
Start Position
1.001
1.01 tub1 p-tub1 genomic158EcoRI/HindIII AY987961 2037772
1.02 umc157(chn) p-umc157 genomic1220PstI DQ123890 12397449
1.03 umc76 p-umc76 genomic760 PstI AY751079 29259990
1.04 asg45(ptk) p-asg45 genomic350PstI AY771210 52150220
1.05 csu3 p-csu3 cDNA1200 EcoRI/XhoI DQ123891 82584786
1.06 umc67a p-umc67 genomic650 PstI AY771211 175670048
1.07 asg62 p-asg62 genomic500PstI DQ001865 198887570
1.08 umc128 p-umc128 genomic740PstI DQ123892 228315518
1.09 cdj2 p-csu164 cDNA700EcoRI/XhoI DQ642431 250153976
1.10 umc107a(croc) p-umc107 genomic1090PstI DQ642432 267926978
1.11 umc161a p-umc161 genomic 700 PstI AY771212 283259156
1.12 bnl6.32 p-bnl6.32 genomic2250PstI G10770 298039872
 

Download all the core bin marker sequences for Chromosome 1