Improve sugarcane with genomic research


Increased research into genomics is needed to improve the variety and yield of Philippine sugarcane, particularly by increasing its resistance to common diseases, the Philippine Sugar Research Institute (PhilSURIN) said.

The sugarcane industry is considered the Philippines second-most important crop after rice, according to the Department of Science and Technology (DOST), contributing to industries such as bioethanol fuel production as well as food needs.

According to data from the Bureau of Local Employment at the beginning of the year, sugar-related jobs were at one point the second-most in demand employment in the Philippines, with an estimated 12,400 vacancies for sugarcane farmers and 100 job openings for millers.

In an interview at the time, then-Department of Labor and Employment Secretary Rosalinda Baldoz claimed that this could be attributed to stable sugar prices in the global market.

To sustain the industry’s growth, new and superior varieties of sugarcane should be developed, Dr. Liwayway M. Engle of the Philippine Sugar Research Institute (PhilSURIN) told attendees at the recent S&T Agri Biotech Forum held at the Bureau of Soils and Water Management Convention Hall.

The problem is, sugarcane breeding which includes marker assisted selection of promising varieties, is a long and tedious process—taking as many as 8 to 9 years—thus requiring a lot of human and financial resources. The process is long due to sugarcane’s long life cycle and complex genetic nature, which requires huge breeding populations of 100,000 to 400,000 genotypes, Engle explained.

To solve this problem, Engle said that genetic improvement of sugarcane must be continuously undertaken. Engle stressed that sugar genomics is good for the increased productivity, profitability, sustainability, and global competitiveness of the Philippine sugar industry.

Organized by the Department of Science and Technology (DOST)-Philippine Council for Agriculture and Aquatic Resources Research and Development, the forum was part of the activities for the 12th National Biotechnology Week held last month.

Engle and her team, which includes a pathologist, agronomist, and breeders, started a project in 2012 that sought to apply genomics in sugarcane variety development. For this, PhilSURIN partnered with the Philippine Genome Center, whose state-of-the-art DNA sequencing facilities were funded by DOST.

The objective was to reduce the time it takes to develop a new variety by two to three years, thus shortening the process from 8 to 9 years to 5 to 6 years, “so we can bring new varieties to sugarcane planters a lot quicker,” Engle said.

In particular, the group wants to produce high-yielding varieties while eliminating their susceptibility to two major diseases affecting sugarcane, downy mildew and smut. The research is guided through a process called DNA marker assisted selection (MAS).

MAS is a process in which scientists search for biomarkers associated with a particular trait. When a marker is found to be consistently associated with a specific trait, scientists can screen for the marker in other varieties. Biomarkers therefore help speed up the development of new sugarcane varieties.

Under the conventional 8- to 9-year breeding program, there are two stages where selection against diseases is done.

For screening of downy mildew, the team would select the best in terms of morphological traits among the 100,000 varieties they produce. These selected ones would then be subjected to a further screening procedure involving direct exposure to the downy mildew pathogens to see which of them are resistant against the disease.

For screening of smut, the planting materials are soaked in the inoculum containing the smut pathogens after which incubation is done. Then the planting materials are planted in the field and the team awaits the growth of the seedlings. The team then rates the plants on whether they are susceptible or resistant to smut.

In identifying the markers for these diseases, they collect samples of sugarcane at an age of three to six months. The samples were ground to isolate the genomic DNA, which was then multiplied and subjected to electrophoresis, a technique for separating the components of a mixture of charged molecules in an electric field.

Through electrophoresis, different band patterns, commonly referred to as “DNA fingerprints,” consisting of different segments of DNA may be seen, which allows differentiation and matching of sugarcane parent varieties, and reveals unique patterns that identify genetic markers.

These DNA fingerprints are also used in variety integrity tests to check the authenticity of the sugarcane variety, after which a certification is issued. This will ensure that farmers are planting the right variety in their fields.

This is an advance because previously, a variety may only be identified via its morphological and agronomic characteristics, after it has produced enough stalk and it exhibits the physical traits unique to its variety.

So far, Engle and her team have already identified a number of promising sugarcane varieties based on field trials in Victorias City and La Carlota in Negros Occidental, and in Bukidnon. They hope to eventually produce five promising varieties.

Other partners for the project are the Sugar Regulatory Administration and the National Institute of Molecular Biology and Biotechnology of the University of the Philippines.


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