A Study on Genetic Markers and Their Efficiency in the Cultivation of High-Quality Rice

For individual organisms, genetic markers, like simple sequence repeat (SSR), fragment length polymorphisms (RFLP), and single-nucleotide polymorphisms (SNPs), offer unique identifiers. This helps in the determination of important genetic variations in plants, enabling modern plant breeding to choose high-quality crop varieties.

Scientists from China have desinged a new single-nucleotide polymorphism chip that can help us identify genetic markers of desirable traits in rice, opening doors to superior rice varieties that can ensure food security and flavor diversification. Image Credit: Toshiyuki IMAI from flickr

Next-generation sequencing (NGS) has improved backcross breeding or marker-assisted selection of crops, which is the transmission of a preferred trait like that into the preferred genetic background of another.

Nevertheless, owing to its affluent nature and wide-ranging data processing needs, NGS is not practical for screening large populations of crop plants, particularly among medium and small breeders. A further affordable and proficient solution to test preferred genetic traits in these populations is SNP arrays.

DNA probes have been embedded by such chips. Those probes communicate with a genetic sample, facilitating the detection of hundreds of thousands of alterations among multiple plant samples.

Tapping the capacity of this method, Associate Professor Wensheng Wang from the Chinese Academy of Agricultural Sciences and his study group have formed an SNP array that comprises more than 56,606 genetic markers for rice.

Globally, more than 2.6 billion people rely on rice as a staple in their diet. The gene chip developed in our study can be an effective tool for breeders in selecting superior, new, high-quality rice varieties that are more flavorful, better tasting, salt tolerant, and resistant to diseases and insects. Moreover, the gene chip can be used for various genetic studies.”

Associate Professor Wensheng Wang, Chinese Academy of Agricultural Sciences

The scientists built the custom SNP array by sequencing and collecting genetic samples that belong to 3,024 rice samples from across the world. Among 18.9 million top-quality SNPs from this sample, around 2.5 million polymorphic SNPs were found and retained in the array design. Then, such SNPs were printed on a genotyping chip platform (Affymetrix) with four designs.

The efficiency of the array was assessed with the use of a representative set of 192 rice varieties, and the findings were striking. On average, it correctly found 99.6 % of the relevant genome, while also establishing high density and even coverage with a mean distance of 6.7-kb between two adjacent SNPs. Moreover, the data achieved from this platform provided more genetic variability data than other earlier-developed arrays.

The results were reported The Crop Journal in KeAi.

Rice3K56 can help small and medium-sized companies select for superior rice varieties in a manner that is less subjective and low-effort. Our work makes genotyping more mechanized and streamlined, resulting in higher efficiency and accuracy. In the long run, this can ensure not only food security but also a diversification of rice flavors.”

Associate Professor Wensheng Wang, Chinese Academy of Agricultural Sciences