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Cucurbit Genetics Cooperative Report 19:7-9 (article 3) 1996

Lost Information

J.E. Staub

Vegetable Crops Research, USDA/ARS, Department of Horticulture, University of Wisconsin-Madison, WI 53706 U.S.A.

The proceedings of the international symposium entitled "Cucurbitaceae '94: Evaluation and enhancement of cucurbit germplasm" was published in 1995. Information was omitted from a report of the proceedings entitled "Problems associated with map construction and the use of molecular markers in plant improvement" (1). The information omitted was present in tables which described the results of a survey of vegetable breeders asked to comment on their use of molecular markers for map construction. Because I believe that this survey was a relatively accurate description of the feelings of vegetable breeders at that time, it forms a historical record that should be preserved. Thus, I repeat the text of the article below dealing with this survey and present herein the tables that were omitted from the symposium report.

A survey was conducted in which a group of 25 plant breeders and geneticists (U.S. and Europe) who employ molecular markers for map construction were asked to identify the marker types they use, the level of polymorphism they observe and the intended use of these markers (Table 1). Researchers in this sampling were not currently using AFLPs, SCARs, microsatellites or CAPs for map construction and/or board-based genetic analysis. It was clear from their responses that no one marker type currently under study (i.e., isozyme,. RAPD, or RFLP) was preferred, and that the level of polymorphism depended on the species and the marker type utilized. While the level of polymorphisms in apple, Brassica spp., maize, pea, potato, radish and soybean are relatively high (20 - ~ 100% bands polymorphic) depending on marker type, polymorphisms in chickpea, cucumber, lentil, onion, pepper and tomato are considerably lower (0-20%). Researchers intend to use the variation observed at the protein and DNA level to select for economically important qualitative (e.g., disease and insect resistance) and quantitative (e.g., yield and quality components) traits. Several problems such as the low levels of polymorphism (all marker types) observed in some crops species, the reproducibility and repeatability of RAPDs (e.g., Brassica spp., pepper, melon), complex banding patterns (e.g. RFLPs in onions), the genetics of the organism (e.g., carrot, garlic), and procedural and technical constraints (e.g., automation for large scale screening purposes) may not impede the implementation of marker technologies (Table 2).

Table 1. Relative abundance of molecular marker polymorphisms in an array of crop species.

 
Polymorphism (%)z
Mapped marker (no.)
 
Crop Isozyme RAPD RFLP Isozyme RAPD RFLP Intended use for marker assisted selection
Alfalfa
-60
60-75
80
60
Forage yield & quality, disease resistance
Alfalfa
59-75
100
Winter survival, yield
Apple
30-60
-100
30-50
-30
>400
10
Fungal resistance, cold tolerance
Barley
5-20
10-30
30-50
-30
>400
10
Disease resistance, cold tolerance
Bean
10-30
25-40
10-30
-10
-200
2
Phyotoperiod response, fungal resistance, yield, biomass
Bean
10-50
30-50
40-80
11
20
>700
Disease resistance, quality factors, drought resistance
Carrot
20-40
10-30
30-40
Disease resistance
Cauliflower
60-70
15
250
Cytoplasmic male sterility
Chickpea
0-2
2-10
0-2
10
20
10
Aschochyta blight resistance, drought resistance
Cucumber
0-30
5-10
5-10
21
-100
-70
Disease resistance, plant habit, yield components
B. oleracea
46-88
150
Maturity time, yield
B. rapas
62-87
150
Maturity time, yield
B. napas
46-61
150
Maturity time, yield
Garlic
0-30
Clove quality, disease resistance, fertility restoration
Lentil
5-10
10-20
5-10
20
30
30
Aschochyta blight resistance, winter hardiness
Maize
25-50
40-80
40-80
>40
>1000
Grain yield
Melon
0-5
20
 
Onion
5-10
10-20
10
Fertility restoration, bulb color & quality
Pea
20-40
50-75
20-50
-30
>600
-30
Virus & fungal resistance, nitrogen fixation
Pea
10-15
10-20
10-20
25
45
35
Virus resistance, drought resistance
Pepper
-10
40
900
 
Pepper
0-15
0-40
30
 
Potato
>80
>80
50-60
15
>60
>100
Dry matter, dormancy, sugar levels, yield components
Radish
40
73
2
63
Yellow's & mosaic resistance, bolting
Soybean
-15
-10
20-50
10
12
500
Disease resistance, iron chlorosis, protein & oil content, photoperiod
Tomato
-10
40
1000
Increased shelflife
Tomato
0-5
0-5
10-30
1000
White fly resistance
Tomato
0-25
0-10
100
 

RFLP = restriction fragment length polymorphisms, RAPD = random amplified polymorphic DNA.

Table 2. Common problems encountered in molecular marker development in several crop species.

Crop
Marker Classz
Problem
Potential solution
Alfalfa
RFLP
Probes with complex patterns
Screen more probes, low copy sequences
Apple
RFLP
Low level of polymorphism
Alternative marker systems
Bean
RFLP
Low level of polymorphism
Screen different libraries
Bean
RAPD
Clustering of mapped markers
Alternative marker systems
Brassica
RFLP
Duplicate loci
Microsatelites
Brassica
RAPD
Rapeatability
Alternative marker systems, SCARs
Carrot
Morph
Lack of true breeding lines
Inbreed
Garlic
Morph
Lack of true breeding lines
Development of a true seed system
Celery
RFLP
Low level of polymorphism
Microsatellites
Chickpea
RAPD
Low level of polymorphism
Use wild/unadapted accessions
Cucumber
RFLP
Low level of polymorphism
Alternative marker systems
Cucumber
RAPD
Low level of polymorphism
Alternative marker systems, SCARs
Onion
RFLP
Probes with complex patterns
Screen more probes
Onion
RAPD
Heterozygous popularions
Pea
RFLP
Low level of polymorphim
Alternative marker systems
Pepper
RAPD
Repeatabiltiy
Alternative marker systems, SCARs
Melon
RAPD
Repeatability
Alternative marker systems, SCARs
Pepper
RAPD
Low level of polymorphism
Screen more primers
Soybean
RFLP
Low level of polymorphism
Alternative marker systems
Tomato
RFLP
DNA isolation/purification
System automation, robotization
Tomato
RAPD
Low level of polymorphism
Screen more primers

z RFLP = restriction fragment length polymorphism, RAPD = random amplified polymorphic DNA, morph - morphological marker.

Literature Cited

  1. Staub, J. 1995. Problems associated with map construction and the use of molecular markers in plant improvement In: Lester, G.E. and J.R. Dunlap, eds. Proceedings Cucurbitaceae ';94: Evaluation and enhancement of cucurbit germplasm. p. 86-91.
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Page citation: Wehner, T.C., Cucurbit Genetics Cooperative;
Created by T.C. Wehner and T. Ng, 1 June 2005; design by C.T. Glenn;
send questions to T.C. Wehner; last revised on 15 December, 2009