OUC’s research team led by Professor Gao Qinfeng from Fisheries College, in collaboration with Shandong Marine Group Co., Ltd., and Higentec Co., Ltd., has developed China's first SNP breeding chip for rainbow trout by utilizing cGPS-targeted sequencing genotyping technology. The newly developed chip was named Hongxin No.1 (Figure 1). This achievement represents the only industry-specific chip in China's rainbow trout breeding sector with independent intellectual property rights. It marks a significant breakthrough in the independent research and development of domestic rainbow trout breeding chips, providing a powerful new tool for precision breeding and high-quality development of the rainbow trout industry.
Breeding chips are crucial tools in modern molecular breeding, enabling rapid and accurate genotyping of a vast number of SNP loci in germplasm resources at a relatively low cost per test. The world's first rainbow trout breeding chip was developed by the USDA (United States Department of Agriculture) in 2014, containing 57,501 SNP loci. However, due to technological limitations at the time, approximately 20,000 SNP loci on the chip were redundant, impacting its genotyping efficiency. In 2021, INRAE (National Research Institute for Agriculture, Food and Environment) in France released the world's second rainbow trout SNP breeding chip (667K), with genetic information for the loci sourced from public databases of the USDA and INRAE, as well as from breeding and wild populations of rainbow trout in Russia and Canada. Due to its excessively high locus density and a narrow target on European and North American wild and breeding populations of rainbow trout, this chip has shown limited applicability to Asian rainbow trout breeding populations, restricting its use in scientific research on rainbow trout in China.
The Hongxin No.1 liquid-phase breeding chip incorporates genetic information of rainbow trout breeding and wild populations from home and abroad. It contains 51,508 high-quality SNP loci, with over 67% of these loci originating from domestic rainbow trout populations. The Hongxin No.1 liquid-phase chip offers a wide range of applications, which will address the research needs for germplasm resource identification, genetic diversity assessment, genome-wide selection breeding, genome-wide association studies (GWAS), and genetic map construction. This will facilitate the elucidation of the genetic basis of important economic traits and the discovery of superior genetic resources.
The primary advantages of Hongxin No.1 are as follows: The liquid-phase chip can capture more mSNP (multiple nucleotide polymorphism) markers, embodying the distinct strengths of evenly distributed imputed loci, rich diversity information, and accurate genotyping. Compared to traditional resequencing methods, Hongxin No.1 is easy to operate, requiring no complex data analysis procedures. SNP genotyping can be completed rapidly within a week, and the cost is approximately one-quarter that of resequencing, significantly improving detection efficiency and reducing expenses. Furthermore, the Hongxin No.1 liquid-phase chip is highly flexible and adaptable, allowing for the addition of new SNP loci to the existing chip at any time as needed, without requiring complete re-customization.
