An explanation of nomenclature and methods used by the Cytogenetic Map of Maize project
By: Amarillo, F., Koumbaris, G., & Bass, H.W. (2005)
Probe Nomenclature for Maize Core Bin Marker Loci
spb-CBM9.02_S65 (bz1) as an example
-CBM = cross-hybridizing at high stringency to the
is the core bin marker for locus 9.2 (as used in the
UMC 1998 linkage map
G. Davis et al.)
_S65 = the
Short arm cytogenetic locus,
65% of the distance from the centromere (at 0%) to telomere (at 100%); synonyms for this cytological locus include
9S.65 and map position -.65
(bz1) = the maize DNA sequence,
; used for biochemical or electronic queries of the sorghum genome to select a corresponding sorghum BAC clone (the
Therefore, the probe named spb-CBM9.02_S65 (bz1) refers to a
Sorghum propinquum BAC FISH probe identified as having a high degree of sequence similarity to the maize core bin marker
9.2 and producing cytogenetic FISH signals at 9S.65 on pachytene-stage chromosome spreads.
Probe Nomenclature for Other Maize Markers
spb-9.03_L04 (rgpr3235a) as an example
-9.03 = a designation for the maize genetic bin. The FISH probe was selected using a maize marker sequence known to map
within the genetic linkage bin 9.03, somewhere between CBM9.03 and CBM9.04. The bins are from
Davis et al., 1999.
_L04 = the
Long arm cytogenetic locus,
4% of the distance from the centromere (at 0%) to the telomere (at 100%); synonyms for this cytological locus include
9L.04 and map position .04
(rgpr3235a) = the maize DNA sequence,
rpgr3235a; used for biochemical or electronic queries of the sorghum genome to select a corresponding sorghum BAC clone
Therefore, the probe named spb-9.03_L04 (rgpr3235a) refers to a
Sorghum propinquum BAC FISH probe identified as having a high degree of sequence similarity to the maize marker probe
rgpr3235. The name also indicates that the maize marker is located within the linkage bin 9.03, and that the FISH signals were
detected at 9L.04 on pachytene-stage chromosome spreads.
Methods (as described by
Koumbaris & Bass 2003 and updated by
Ferdie Amarillo and
Sorghum BAC FISH
probe selection methods:
Maize marker-selected sorghum BAC FISH probes have been identified in several different ways, depending on (
method of detection, and (
probe/query type. Any combination of detection and probe type can be used, as tabulated below.
1) DNA from the sorghum BAC was labeled in situ with digoxigenin or directly with a fluorescent dCTP
(Alexa-fluor 546-OBEA-dCTP) by random-primed labeling.
2) Labeled DNA was used as FISH probes on pachytene chromosome spreads from maize chromosome addition lines of oat.
3) FISH was carried out with three-color probe mix containing:
(a) maize total DNA direct-labeled with Alexa488-dUTP to paint the entire maize chromosome.
4) Images were collected with a digital camera and de-blurred by iterative
MCCY, a Cy-5 oligonucleotide probe homologous to the maize CentC repeat sequence,
marking the centromere.
(c) Sorghum digoxigenin-labeled BAC hybridization was detected by indirect immmunofluorescence with commercial
detection kits in which the FITC reagents were substitued with rhodamine reagents. The Alexa546-labeled probes were detected
directly without secondary staining.
5) Chromosomes were straightened and measured computationally.
6) Mean locations are reported as the fractional (relative) distance along a chromosomal arm. Each arm has a length
of 1.0 with the centromere being set to 0 for each arm. The length of each arm is divided into 100
centiMcClintocks with, for instance, a cytogenetic position of 9S.33 indicating detection of
discrete FISH signals at a point 33% of the distance along the short arm of chromosome 9 from the centromere.
7) Identification of sorghum BACs for use as FISH probes were selected by online searching using the following
http://www.maizegdb.org (for finding an overgo probe used for each marker or locus)
finding the BAC address)
(for finding the contig for each BAC)
Koumbaris G & Bass HW (2003) A new single-locus cytogenetic mapping system
for maize (
Zea mays L.): overcoming FISH detection limits with marker-selected sorghum (
S. propinquum L.) BAC clones.
Additional Information and Links:
Koumbaris G & Bass HW (2002) Pachytene arm ratios for maize
chromosome 9 in OMAd9.2, a maize chromosome addition line of oat.
Maize Genetics Cooperation - Newsletter
Project Web Site: