Breeding Rice In Latin America Gets A Boost From Genomics

What does your rice taste like? Does it taste sticky or fluffy? Is it brown or white? Among the many characteristics that determine rice sales and consumption around the world are grain length, width, appearance, and other characteristics. Region also makes a difference. Compared to West Africa, Japan, India, and other places, Latin American rice preferences are very different.

The fact that rice breeders spend little time improving and refining eating quality and regional preference is somewhat surprising in light of how important these traits are. Unfortunately, testing and selecting lines based on the sticky grain after cooking or cooking time is costly and time-consuming. In addition to yield and disease resistance, breeders have to pay attention to other important traits.

Latin American rice breeders can select eating-quality traits from the start of a breeding program by collaborating with researchers from the University of Illinois and the Latin American Fund for Irrigated Rice (FLAR). This is expected to alleviate time, effort, and cost associated with breeding programs.

Traditionally, an eating quality selection was carried out at the end of the breeding program. This could result in a variety that yields well and is disease-resistant, but whose grain quality is poor. In this case, the variety is discarded. In this way, you can focus on other traits once you have a more targeted approach,” says Juan Arbelaez, assistant professor in the Department of Crop Sciences and co-author of the new study in The Plant Genome.

Breeding Rice In genomics

In a sample of 284 rice lines that span 20 years of breeding in Latin America and the Caribbean, Arbelaez and his collaborators identified genetic markers linked to 10 grain-quality traits.

The markers were known to be associated with traits previously, but no previous studies have identified them in Latin American germplasm. We confirmed our findings in a separate sample of 2,000 rice lines, so we are confident they work,” Arbelaez says. FLAR’s partners across Latin America can now routinely use these markers through a service provider in Sweden.”

In addition to predicting amylose content (a determinant of sticky properties), gelatinization temperature (cooking time), and setback viscosity (texture), the markers also predicted milling quality and appearance.

It has been possible to use genome-wide prediction strategies to predict more complex grain quality traits, such as milling quality. That’s a new, exciting field of research with more complex predictions that incorporate genomics and high-throughput phenotyping,” Arbelaez says.

A lot of rice breeding will be done more efficiently in Latin America because of the advancement.

Historically, Arbelaez has described the breeder’s process as a funnel. In the large-scale production of rice, many thousands of lines are grown and analyzed for obvious red flags, e.g., disease susceptibility or stunted growth. The genotype of a plant is determined by its appearance. The genotypes of a plant are harvested with the aim of starting the next generation. The process continues, culling low-performing plants, advancing promising varieties, collecting seeds, until a hearty, desirable variety remains at the end of the funnel.

In order to test some features, such as setback viscosity, seed and specialized machines are needed. Such testing is expensive. It is for this reason that breeders often wait until the end of the funnel to test these traits.

When marker-assisted selection is used, the selection cycle is shortened. In a greenhouse, thousands of seedlings can be planted as seeds at the wide end of the funnel. An inspection of its leaves and a visit to the lab are all that is required to determine whether a seedling deserves to grow to maturity and carry on with the process.

It is Arbelaez’s expectation that Latin American rice will have a long and bright future, especially in niche markets like Peru, where Japanese immigrants have shifted people’s preference for sticky rice. His vision also includes applying the markers beyond Latin America.

In different breeding programs around the world, he says, the potential for these markers to be validated by their germplasm identification or characterization is great. In this way, you can see if these markers can be used to target early stages and help selection.”

Source: Maribel Cruz et al. Genetic and phenotypic characterization of rice grain quality traits to define research strategies for improving rice milling, appearance, and cooking qualities in Latin America and the Caribbean. The Plant Genome, 2021; DOI: 10.1002/tpg2.20134

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