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