Glenn B. Gregorio, g.gregorio@cgiar.org, IRRI

Rice plant. Photo by IITA

Improving crop varieties used to be a matter of trial and error. Matching and crossing of parents to identify a lucky combination that possesses the desirable traits for a crop variety could be a gamble. With dwindling funding for research, the luxury of using this trial-and-error approach has to end. What we need now is precision breeding.

Precision breeding is designing a crop, using the best choice of parents, to predict a more exact product that will address the needs of the farmers, such as for instance, robust rice varieties for Africa. A rice breeder must be a scientific matchmaker who possesses in-depth knowledge about the germplasm so as to choose the best parents as the source of desirable traits. Knowledge of how potential parents are related will empower breeders to be good matchmakers. However, this empowerment requires some technical knowledge as a basis to support the choice of parent germplasm in breeding strategies. Molecular marker technology is a powerful tool for measuring the relationships and relatedness of a pool of germplasm.

Why do relationships matter? When the parent cultivars are closely related, less variation can be expected in the offsprings. They are likely to be weaker than those with more distantly related parents. Thus in rice, crossing closely related germplasm will be likely to produce poor combinations and weaker progenies. However, relatedness is not the only consideration. The ability of germplasm to defy environmental stresses, such as drought, salinity, and other problems in soils cannot be ignored at all!

Hybrid rice field, AfricaRice-IITA, Ibadan

In developing a robust rice variety for Africa, the formula for success lies in identifying parent germplasm that harbor beneficial traits, especially tolerance for environmental stresses, and in knowing the degree of relatedness.

West African (WSA) lines, along with some Asian rice germplasm, were analyzed for genetic variation or relatedness, using molecular marker technology. Our aim was to determine the genetic diversity of the germplasm as a basis for choosing suitable parents for the WSA rice breeding programs.

From the IRRI germplasm collection, 114 rice accessions—102 from WSA countries and 12 from Asian countries—were characterized using 65 molecular markers or DNA fingerprints at IITA’s Central Biotech laboratory and at IRRI’s Gene Array and Molecular Marker Applications (GAMMA) laboratory. These DNA fingerprints can show the genetic relationships among genotypes. These rice accessions underwent rigorous tests for tolerance to specific soil stresses including salinity, Fe toxicity, Zn deficiency, and rice blast disease. Tolerance to these stresses is vital for future rice varieties that will be grown in Africa.

Clustering these rice accessions according to their genetic relationships based on DNA fingerprints showed three major grouping with additional subclustering within groups. The first grouping was composed of 12 WSA and 3 Asian rice accessions. The second grouping had 9 WSA and 9 Asian rice accessions, and the third had 100% WSA rice accessions (Fig. 1A).

(A) The genetic relationship among 114 rice accessions based on 65 molecular markers. (B) Phylogram based on the source country (WA countries in red mark).

Cluster analysis revealed a narrow genetic diversity among WSA germplasm compared with Asian rices (Fig. 1B). This could be due to the involvement of similar or related parents especially for the development of the WAS (WARDA Senegal) lines. The rice cultivars in WSA especially in the lowland ecosystem, are more related to one another, making them more vulnerable with their narrow diversity once these newly bred types are released as varieties. No clear grouping was evident on soil stresses and rice blast disease, except for Fe toxicity. The clustering in terms of Fe toxicity of moderately tolerant to tolerant Senegal rice accessions demonstrated that population groups identified based on molecular marker analysis may also have distinct phenotypic characteristics.

Molecular markers or DNA fingerprinting can be a powerful tool in assessing the genetic variability and understanding the relationships among rice germplasm.

How then can we breeders apply these results? The information about the genetic diversity of WSA rice germplasm will be useful for the proper identification and selection of appropriate parents for use in the rice breeding program. WSA rice germplasm can also be exploited in Asia to increase the genetic diversity of future rice varieties.

Rice breeders can equip themselves with such information and be more creative in designing rice for Africa.