Correlations between restriction fragments and protein spots: integrating two-dimensional electrophoretic data with RFLP data

--J. W. Higginbotham

Restriction fragment length polymorphism (RFLP) data exist for 35 of 37 inbred lines used to construct a two-dimensional (2-D) electrophoresis dataset of seedling proteins. An introduction to the 2-D dataset appears above (Higginbotham, JJW et al., this Newsletter) and in Higginbotham et al. (Electrophoresis, in press).

Genes conditioning the expression of protein spots are being assigned to putative chromosome locations by correlating protein spots with restriction fragments. The probe library in use at Pioneer Hi-Bred was constructed from genomic DNA. A few probes are known to contain transcription regions, but the vast majority of them are anonymous pieces of DNA. By linking the 2-D protein profile data to the RFLP data, information on sites of active gene expression will be acquired. Furthermore, protein spots which appear to be associated with fragments known to be linked to quantitative trait loci (QTLs) may merit further scrutiny.

Table 1 lists seven putatively allelic pairs of proteins and three other proteins. The putative locations of the genes conditioning the expression of these proteins are shown along with the probes on that chromosome arm which were correlated with the proteins. Many of these probes are genetically linked to a number of QTLs which are given in Table 1.

Because this is a correlative study rather than a mapping project, the power of the analysis is limited. It is, however, a method of ascertaining probable sites of active gene expression in the absence of a cDNA linkage map. Proteins visualized on 2-D gels may, themselves, be used as markers especially when the segment is poorly marked. The short arm of chromosome 9 is such a segment.

Table 1.  Protein spots, RFLP probes, and quantitative traits which appear to be associated.  The chromosome arm locations of the RFLP probes are given.
 
Protein Spot # Chromosome Arm Probe ID Quantitative Trait
4204
4205
 
1S

 

PIO200689
PIO200603
UMC094
PIO200640
Heat units to pollen shed
Delay between shed and silk 
% moisture at harvest
8835
 
1L
 
UMC128
UMC033
PIO200668
8L
 
UMC089
UMC030
UMC007
Heat units to pollen shed
Heat units to silk
112
144
1L PIO200557
UMC084
318
401
 
2

 

UMC139
PIO200005
UMC034
BNL06.20
% moisture at harvest
Stay green
 
3806
4808
3L
 
PIO200509
PIO200576
PIO200558
311
312

 

4L
 

 

BNL07.65
PIO200071
BNL10.05
UMC019
UMC066
Ear height
 

 

5405
5406

 

5L
 

 

UMC040
PIO150018
PIO150024
PIO200589
PIO200715
Test weight
Cob diameter
Ear diameter
Row length
Row number
224
 
 

 

7L
 
 

 

PIO200593
BNL08.39
BNL08.32
PIO200684
PIO200708
PIO200746
Ear height
Stay green
% moisture at harvest

 

301
 
 

 

9S
 
 

 

UMC109
PIO100005
PIO200052
UMC081
 
Row number
Yield in bushels per acre
100 kernel weight
Plant height
Heat units to pollen shed
Heat units to silk
3804
3808
10L BNL10.13
UMC044A


Please Note: Notes submitted to the Maize Genetics Cooperation Newsletter may be cited only with consent of the authors

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