Fast detection of disease and pest-resistant native corn through molecular characterization

There are now more than 100 million Filipinos and still growing. The Department of Agriculture (DA), together with its bureaus and attached agencies are, therefore, hard pressed to meet the demands of this population. Even marginal lands are being marshalled to be more productive and be a source of employment. Under these challenging conditions, the usefulness of biotechnology comes to the fore.


Corn is one of the most phenotypically diverse of cultivated crops as it can grow over a wide range of environments. Breeders emphasize selection for a desired mix of traits that are controlled by multigenes. Known as quantitative traits, these include important agronomic characteristics such as yield and yield components, and resistance to pests and diseases. In looking for these, the application of biotechnology is vital.


The effectiveness of selection for different quantitative traits lies in the effectiveness of screens used in determining the traits. Variations among corn lines can be determined using phenotypic markers but their performance is strongly affected by environmental factors. Molecular markers for detecting total genetic variation of corn lines are preferred when environmental influences are not desired.


The use of molecular markers, or microsatellites, can facilitate the breeding process. The time needed to reach breeding objectives is much reduced as it entails less field assays. For many crops, molecular markers have been determined. With the use of molecular markers, genetic variation and the genome dynamics of many plants including corn are now better understood, leading to improved breeding efficiency.


With the biotechnology tools available at their disposal, a team of researchers at the Institute of Plant Breeding of the University of the Philippines Los Baños led by Ms. Alma Canama, set out to assess the genetic diversity among the country’s native corn populations using SSR DNA markers. Guided by the institute’s aim for its corn breeding program which is to develop corn varieties for biotic and abiotic stress resistance and nutritional properties, a proposal titled, “Molecular Characterization of Philippine Native Maize Populations (Year 2)”, was submitted to the Bureau of Agricultural Research and was approved for funding in 2016.


No study on molecular genetic diversity analysis of native corn populations had previously been done. Knowledge about diversity and relationships among the Philippine native corn populations is important for the corn breeding program of UPLB-IPB and will benefit the corn program of DA. The new study built up on the assessment done under the project’s Year 1 for genetic diversity among native corn populations on resistance to corn borer infestation and downy mildew infection with the use of SSR DNA markers and dendrogram (a tree diagram used to represent data where each group or “node” links to two or more successor groups based on similarity of traits).


Among the molecular markers, simple sequence repeats (SSR) microsatellites are commonly used for genetic diversity analyses due to their high level of polymorphism, repeatability and low cost. SSRs are abundant and their chromosomal assignments have been established, thus, the corn genome can be uniformly sampled and analyzed.


Polymorphic SSR markers can distinguish the allelic profiles of resistant lines over susceptible lines to particular pests and diseases. With knowledge about the allelic profiles of resistant/tolerant corn, molecular screening criteria can be used to sort out various crop lines as to resistance. It can be expected that high heterosis in yield and its components could be obtained from crosses among those lines belonging to different heterotic groups.


In the Project Year 2’s Activity 1, a total of 20 SSR markers were used to screen the inter-population diversity among 26 native corn populations. These populations were chosen based on a Project Year 1 constructed dendrogram (a tree diagram used to represent data where each group or “node” links to two or more successor groups based on similarity of traits eventually creating a viewable clustering) that assessed the genetic diversity among native corn populations using SSR DNA markers.


A new dendrogram was created using 20 representative populations with five (5) samples each utilizing 12 SSR markers. The dendrogram showed high diversity within a population. From this, the researchers infer that the samples within a population are very diverse owing to corn’s open pollinated nature.


For Activity 2, allelic diversity between susceptible and resistant populations on downy mildew infection and corn borer infestation were studied. Unique alleles were found to be associated with either downy mildew-resistant or susceptible populations with the use of an SSR marker.


As for corn borer resistance and susceptibility, populations that exhibited high susceptibility showed a more complex banding pattern and a monomorphic pattern. Also, more alleles were observed compared to the populations that are highly resistant to the pest. The populations that exhibit high resistance to corn borer infestation tended to exhibit a more polymorphic pattern.  


The researchers conclude that the results indicate the reliability of the information provided by the dendrogram from Project Year 1 and can be the basis for breeders to devise better breeding programs and choose populations which are distant from one another to create better breeds or varieties. The SSRs used were also found to be informative markers that revealed genetic variation among the inbred lines studied and that SSR markers tightly linked and associated with pest and disease resistance can be utilized to screen populations at the DNA level.


The knowledge generated about diversity and relationships among Philippine native corn populations, through the use of SSRs in the search for resistance to corn borer infestation and downy mildew infection, will lessen the time and cost it will take to conduct breeding efforts for native corn. ### [VictorianoB. Guiam]




For more information:

Ms. Alma O. Canama

University Researcher and Project Leader

Institute of Plant Breeding

University of the Philippines Los Baños

Tel: (49) 557-3568