Improving sugarcane using molecular genetics

Linda Benedict  |  7/7/2008 11:27:17 PM

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Collins A. Kimbeng, Kenneth A. Gravois and Keith B. Bischoff  

Sugarcane breeding, leading to the release of genetically improved varieties, has played a vital role in sustaining Louisiana’s sugar industry. Past sugarcane breeding efforts have relied solely on traditional breeding approaches. In traditional breeding, two plants (parents) are crossed, and the breeder selects from among the progeny those plants that have inherited the desired set of characteristics from both parents. Selection of parents and progeny is based upon phenotypic data – their appearance or performance in field trials for the desired set of characteristics.

Traditional breeding is time-consuming, and breeding a new sugarcane variety can take up to 13 years. Even then, the release of a genetically improved variety is not guaranteed. In addition, unavoidable environmental variation may mask the actual genetic potential of plants, making it difficult to identify accurately the best progeny. In recent years, LSU AgCenter researchers have investigated using molecular markers (or DNA markers) to improve the efficiency of traditional breeding.

Molecular markers can be viewed as constant landmarks on a genome, which is the complete set of genes possessed by an organism. In the same way that road signs guide motorists, molecular markers can help guide scientists by showing them the presence and location of genes associated with desirable characteristics. Molecular markers are identifiable DNA sequences found at specific locations on the plant’s genome. They can be used to tag the position of a particular gene responsible for the inheritance of a particular characteristic, such as disease resistance. This happens when differences on the DNA sequence among multiple plants can be associated with differential performance for specific characteristics among the plants.

Molecular markers are transmitted from one generation to the next in the same way as phenotypic characteristics. But unlike phenotypic characteristics, the presence or absence of molecular markers in a plant is independent of variation due to environmental conditions. This feature makes molecular markers a potentially powerful tool for improving the selection process. For example, in a genetic cross, the characteristics of interest stay linked with the molecular markers. Individual plants carrying the molecular markers linked to the particular characteristic can be identified in the laboratory and then quickly and accurately selected. Thus, it is feasible, especially for characteristics controlled by a few genes, to select desirable plants early at the initial seedling stage before resources are spent evaluating them in field trials.

LSU AgCenter researchers have initiated research in three areas to help facilitate the integration of molecular marker technology into the traditional sugarcane breeding program.

Mapping and tagging the sugarcane genome
LSU AgCenter researchers have developed genetic linkage maps of sugarcane using molecular markers. The concept of linkage mapping is based on the tendency of two or more factors – in this case molecular markers – to be inherited together. The locations of markers on a map are estimated by studying how often multiple pairs of markers are inherited together in multiple progenies from a particular cross. The map represents the linear order of genes on a sugarcane genome. The map is used to tag the locations of several genes associated with favorable characteristics, including sugar content, plant height and disease resistance.

Unlocking the door to novel genetic variation in wild relatives of sugarcane
Current sugarcane varieties are hybrids derived from crosses between two different sugarcane species. The previously cultivated type provided the genes for high sugar content while genes from a wild type provided an ability to increase the number of annual crops a planting can produce, to tolerate several diseases and insects, and to adapt to a wide range of environments.

Louisiana lies at the northern limit of the sugarcane cultivation range, and freezing temperatures present added challenges not faced in tropical environments. The very existence of a thriving sugar industry in Louisiana can be attributed to genes inherited from this wild relative of cultivated sugarcane.

A large inventory of many closely related species of sugarcane from diverse regions of the world is being conserved by the U.S. Department of Agriculture in Coral Gables, Fla., with a smaller collection at Houma, La. Studies using molecular markers have helped in understanding the distribution of genetic diversity among the individual plants and species in these collections and the extent to which the available diversity can be used to improve cultivated sugarcane.

LSU AgCenter research has identified several plants displaying unique diversity patterns not found in cultivated sugarcane. Genetic mapping studies have allowed for the identification of novel genes associated with specific characteristics, such as high sugar accumulation, which can be inherited from these grassy-looking, low-sugar, wild-type relatives of sugarcane.

The challenge is to incorporate these genes into new sugarcane varieties while avoiding the undesirable, hitchhiking genes often associated with the negative characteristics of these weedy species. To accomplish this, molecular markers are being used to tag the presence and location of both useful and undesirable genes affecting sugar accumulation from these weedy species. Selecting these genomic regions in tandem will help sugarcane breeders speed up the development of new sugarcane varieties with increased sugar content.

Predicting progeny performance
Each year, LSU AgCenter sugarcane breeders begin a new selection cycle by planting about 100,000 seedlings in the field. Each seedling is a unique individual with an equal chance of becoming a variety at the end of the breeding cycle. These seedlings are derived from true seed obtained from two-parent crosses designed to produce progeny with new genetic combinations. This is the only stage in the 13 years of the breeding cycle where plants are established from true seed.

Stalks to plant in the next stage of the selection cycle are then cut from seedlings with desirable characteristics. The buds along the planted stalks germinate and grow to produce new plants, a process known as vegetative or clonal propagation.

The cycle of selecting plants and cutting and planting those stalks continues until only a handful of top-performing potential varieties are planted in many fields across the state. Success in identifying a superior sugarcane variety is first contingent upon producing superior genetic combinations during crossing.

LSU AgCenter researchers have investigated the utility of molecular markers for making early predictions of progeny performance. Heterosis, or hybrid vigor – the performance of hybrid progenies relative to their parents – is being evaluated in two-parent crosses.

Heterosis is a desirable characteristic in sugarcane because highly heterotic progenies perform better than either one or both of their parents. Heterosis increases as the genetic differences between the two parents increases. Using this type of information, scientists can plan crosses between parents from the most divergent backgrounds to maximize heterosis while increasing the genetic diversity among the varieties grown in Louisiana.

Molecular markers represent a new tool available to sugarcane breeders. The goals are to use molecular markers to identify existing and new genes that will allow improvements in desired characteristics and to then efficiently select new, superior sugarcane varieties for the Louisiana sugarcane industry.

Collins A. Kimbeng, Associate Professor, School of Plant, Environmental & Soil Sciences, LSU AgCenter, Baton Rouge, La.; Kenneth A. Gravois Graugnard Brothers Professor and Resident Coordinator, and Keith P. Bischoff, Andrew P. Gay Professor, Sugar Research Station, St. Gabriel, La.

(This article was published in the spring 2008 issue of Louisiana Agriculture.)
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