Molecular Biology and Sugarcane Breeding in Louisiana

Linda Benedict, Hoy, Jeffrey W., Parco, Arnold, Pontif, Michael J., Kimbeng, Collins A., Khan, Nisar, Gravois, Kenneth, Baisakh, Niranjan  |  9/4/2014 10:54:33 PM

Niranjan Baisakh, Mavir Carolina Avellaneda, Andres Gutierrez, Arnold Parco, Nisar Khan, Jeff Hoy, Michael Pontif, Collins Kimbeng and Kenneth Gravois

Sugarcane is one of the most highly valued row crop in Louisiana, contributing $2.79 billion to the state’s economy when considering value-added components. In 2013, the crop was harvested from 439,256 acres with a yield of 34.3 tons of cane per acre, which translated to 1.46 million tons of raw sugar. This achievement has resulted from the combination of improved varieties, cultural practices and a growth-conducive cropping period.

New varieties are the life blood of Louisiana’s sugar industry. Genetically improved varieties have sustained the productivity and profitability of the industry for more than 200 years. To date, sugarcane breeding has relied on intercrossing elite varieties, which are essentially derived from early hybrids of only a few clones within Saccharum officinarum and S. spontaneum. This has resulted in a narrowing down of the genetic base of the sugarcane gene pool, which can have negative repercussions, including low genetic gain for agronomic traits, which can lead to yield stagnation, and vulnerability to diseases and insect pests. Therefore, selection of the right parents with maximum genetic diversity is crucial in the primary crossing stage to realize maximum genetic gain in the next generation of new varieties.

Biotic stresses, such as brown rust and leaf scald diseases, and abiotic stresses, such as cold temperatures, cause considerable economic losses to the Louisiana sugar industry. Disease-resistant and stress-tolerant varieties are the most economical and environmentally friendly in an integrated crop management program. Growers suffer no direct costs. However, sugarcane breeding is time-consuming, and variety development takes 13 years. In Louisiana, variety development has been primarily reliant on traditional selection based on observable characteristics. This is unpredictable because most traits in sugarcane are quantitatively inherited with low to moderate heritability, and their expression is highly influenced by environmental conditions. For example, rating for disease resistance based on the severity of symptoms can be misleading because disease development depends on weather conditions. Also, the durability of resistance can be limited by changes in the pathogen population that cause a resistant variety to become susceptible. Environmental variation masks the true genetic potential of plants, which makes identification and selection of the best progeny difficult.

Molecular markers, on the other hand, are unique DNA sequences linked with a particular trait of interest that are faithfully inherited over generations without being affected by the environment. Molecular markers are like landmarks on chromosomes that can direct us to select for a particular trait. Testing for the presence of a marker directly selects for a trait of interest. Selection based on molecular markers (marker-assisted selection MAS) can be cost-effective. A large number of plants can be monitored for the presence of a gene or desirable trait by a marker in the lab instead of erratic testing in the field.

Sugarcane, unlike rice, is not an easy crop for genetic studies because it has a highly complex genetic makeup.
Identification of molecular markers for a particular trait is time-consuming. However, scientists at the LSU AgCenter are now developing molecular genetics tools to complement conventional breeding for development of improved varieties. Their approach is two-fold: 1) use modern molecular biology and genomics (genetics of the total gene pool of the crop) tools, such as gene expression, genetic mapping, etc., to identify molecular markers linked to a particular trait, and 2) use the molecular markers from the development pipeline in marker-assisted selection to enhance the efficiency of traditional breeding.

LSU AgCenter researchers are focusing on these objectives:

Maximizing genetic gain through desirable gene combination. Using molecular markers, the genetic diversity of Louisiana sugarcane commercial germplasm has been characterized. In this way, useful genes from ancestral wild species are being tracked. This study provides an opportunity for informed selection of parents for crossing that will maximize hybrid vigor of the progeny.

Identification of molecular markers for disease resistance. Molecular markers have identified the frequency and distribution of a brown rust resistance gene, known as Bru1, in the entire germplasm of sugarcane and related species in Louisiana. This effort led to identification of Louisiana sugarcane varieties that possess novel brown rust resistance genes. The aim is to identify multiple genes contributing to disease resistance and markers linked to the genes. This will allow stacking of genes (gene pyramiding) through MAS that can provide a high level of durable resistance. Markers for resistance to leaf scald also are being developed.

• Identification of molecular markers for cold tolerance. AgCenter researchers have identified cold-responsive genes in a cold-tolerant energy cane (sugarcane bred exclusively for biomass). These genes are being mapped on the sugarcane chromosomes to identify molecular markers linked to cold tolerance genes. Identified genes and linked markers will be applied two ways: 1) selecting sugarcane with cold tolerance genes to extend the cropping season by protecting against occasional freezing temperatures and sugar loss due to subsequent bacterial invasion and 2) screening for cold tolerance genes in early generation hybrids to allow expansion of their cultivation as a second generation bioenergy crop outside of the traditional Sugar Belt.

Molecular marker technology has been successfully employed in other crops. Technology and a research team are now in place to enable integration of molecular marker technology with traditional sugarcane breeding. This will reap far-reaching benefits to the Louisiana sugar industry.

Niranjan Baisakh is an assistant professor in the School of Plant, Environmental and Soil Sciences. Co-authors are Mavir Carolina Avellaneda, Ph.D. student in the Department of Plant Pathology and Crop Physiology; Andres Gutierrez, Ph.D. student, and Arnold Parco and Nisar Khan, both postdoctoral research associates, all in the School of Plant, Environmental and Soil Sciences; Jeff Hoy, professor, Department of Plant Pathology and Crop Physiology; and Michael Pontif, assistant professor, and Collins Kimbeng and Kenneth Gravois, both professors, all at the Sugar Research Station.

This article was published in the summer 2014 issue of Louisiana Agriculture Magazine.

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