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Marked for speed

Molecular markers give breeders the edge in the race against crop loss due to pests and disease. A marker is a segment of DNA that is both easy to detect and located close to an allele (version of a gene) that controls an important trait - close enough that the allele and marker are effectively inseparable. Tracking the inheritance of markers thus allows breeders to track key alleles more accurately and quickly than they can by growing the plants to maturity and observing their traits.

Farming paddy rice in Laos (IRRI)
Farming paddy rice in Laos

As genetic mapping improves, molecular marker-aided selection promises to help tackle the highly complex problem of producing crop varieties able to tolerate submergence, problem soils and drought. Each improved draft of the 12 rice chromosomes has added to the catalogue of molecular markers, and the sequencing in 2003 of the entire rice genome was a milestone in the development of this technology.

Breeders transfer a target allele from a donor variety to a popular cultivar by a repetitive process called backcrossing - which, unfortunately, is slow and uncertain. Breeding a plant that has the desired donor allele but otherwise looks just like the popular cultivar usually takes four years or longer. Worse, the augmented variety may look just like the popular cultivar, but it inevitably retains stray chromosome segments from the donor. Consequently, to a greater or lesser extent, it will fail to perform exactly like the popular cultivar, thus limiting its appeal to farmers.

Marker-assisted breeding tackles both problems by allowing breeders to identify young plants with the desired trait and by facilitating the removal of stray donor genes from intermediate backcrosses. The result, in about two years, is an improved variety exactly like the popular cultivar except that it possesses the transferred advantageous gene.

Time saved

In principle, this technique can be applied to the breeding of any crop or farm animal. So far, however, breeders of trees and rice have dominated the field. Because markers allow breeders to select immature plants, the time saved in breeding slow-growing trees is immense. In the case of rice, the crop's relatively advanced state of genetic mapping has facilitated the application of molecular marker techniques.

Over the past decade, scientists have pinned down the chromosome locations of hundreds of advantageous genes, many of which confer resistance to diseases and pests. Against some diseases, notably bacterial blight in rice, breeders have used marker-assisted selection to "pyramid" into rice cultivars resistance conferred by several separate genes. Pyramided genes - which pile up various modes of resistance effective against different strains of the pathogen - promise broader and more durable resistance than a single gene.

Breeders have enjoyed success in transferring genes that single-handedly offer black-or-white, or qualitative, resistance to a particular disease or pest, thereby reducing farmers' need to spray their crops. A recent example is a new pearl millet hybrid resistant to downy mildew, the first example of marker-assisted breeding of this crop for release in India*. However, most of the traits that breeders are striving to improve today - including grain yield and tolerance of such complex abiotic stresses as problem soils, submergence and drought - are quantitative. This means they depend on more than one gene, with each individual gene controlling a relatively small effect.

Submergence tolerance

Four rice varieties after undergoing submersion stress (IRRI)
Four rice varieties after undergoing submersion stress

Illustrating the promise of using molecular markers to breed for tolerance of abiotic stresses is work being carried out at the International Rice Research Institute (IRRI) to develop submergence-tolerant rice varieties for low-lying rainfed areas of South and Southeast Asia. Five days of complete submergence will destroy most rice crops, but some rice plants can survive under water for two weeks - plants whose low yields and poor grain quality make them unsuitable as cultivars. The submergence tolerance displayed by one such plant, an Indian variety called FR13A, results mostly from a single gene or quantitative trait locus (QTL).

Careful molecular marking precisely mapped the location of the gene to a small segment of chromosome 9 now designated Sub1 (short for "submergence"). The German government funding agency BMZ is supporting an IRRI project to transfer Sub1 into at least six widely grown rice cultivars in Asia, including the South Asian favorite Swarna and the popular IRRI variety IR64. Swarna-Sub1 seeds have been sent to India for field testing.

Success with Sub1 encourages the application of this strategy to other QTLs that have a relatively large effect. Fortunately, such potent QTLs exist for phosphorus uptake and tolerance of salt and aluminum toxicity, among other traits. The goal is to breed cultivars with defences against the array of stresses that routinely depress yield, and occasionally wipe out entire crops, in unfavorable rice-growing environments. Among these is the most widespread and damaging stress of all - drought.

*The pearl millet hybrid resistant to downy mildew HHB 67-2 was bred by the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) and Haryana Agricultural University.

Adapted from an article by Dr. David Mackill, head of IRRI's Plant Breeding, Genetics and Biotechnology Division, in Rice Today magazine.

Date published: March 2005


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