In nature, plants are constantly challenged by disease-causing pathogens such as viruses, bacteria, and fungi. Pathogen infection can severely reduce the survival and reproduction of native plants. Plant disease resistance traits are those that reduce host contact with the pathogen and those that reduce the growth rate of the pathogen after infection has occurred. Genetic interactions between host and pathogen populations result in abundant natural variation in host disease resistance-related genes. Most studies leading to the identification and cloning of disease resistance genes have focused on major genes for disease-resistance. However quantitative disease resistance is often determined by many genes with relatively small effects. Relative to major genetic resistance, quantitative resistance is generally considered more persistent but is also more difficult to study because the effects of individual genes are small, and phenotyping experiments must be performed with high precision. Currently, little is known about the genes and mechanisms underlying quantitative disease resistance, in part because individual genes have a small impact on the resistance phenotype.

Fig. 1. Phenotypic evaluation of powdery mildew disease resistance in 188 F5 population along with the parental lines of pepper. (Zeng et al., 2022)

Our disease resistance traits analysis service

CD Genomics is committed to agrigenomics research and provides comprehensive plant and animal disease resistance traits analysis services to help researchers and breeders elucidate the genetic basis of crop disease resistance and accelerate crop breeding and improvement programs. We offer next-generation sequencing (NGS) based genotyping by sequencing (GBS) to generate a large number of molecular markers in a wide range of species that can be used to construct genetic maps. These markers, or single nucleotide polymorphisms (SNPs), detect base pair differences and help breeders identify which individuals carry the best alleles for disease resistance traits.

We have successfully conducted genome-wide association studies (GWAS) using restriction site associated DNA (RAD) sequencing for disease resistance traits in a variety of crops including sugarcane, maize, barley, and potato. The main advantage of genomic selection over traditional selection for disease resistance traits is that once detailed evaluations of individual training populations have been conducted, candidates in major breeding programs can be screened without exposure to disease, thus enabling breeders to use them later as breeding stock. By utilizing high-throughput sequencing platforms and advanced data analysis, we provide a comprehensive understanding of the gene pool for plant resistance to pathogens.

• Genotyping and SNP analysis. By genotyping populations, we can identify genetic variants associated with disease resistance traits. SNPs are the most common type of genetic variation and are valuable markers for studying the genetic basis of complex traits. Using state-of-the-art genotyping techniques, we accurately capture and analyze SNPs in plant genomes, allowing us to identify candidate genes associated with disease resistance.
• Transcriptome analysis. By sequencing and analyzing transcriptomes, we gain insight into the expression profiles of genes associated with disease resistance. Differential gene expression analysis allows us to identify genes that are up or down-regulated in response to pathogen attack. This information helps decipher the molecular mechanisms of disease resistance.
• GWAS. Utilizing the power of GWAS, our disease resistance trait analysis service can identify genetic variation associated with disease resistance traits in different plant populations. By analyzing the genetic diversity present in a population, we can identify genomic regions containing genes responsible for disease resistance. This knowledge helps in the development of marker-assisted breeding strategies to enhance crop resistance.

Our services can be applied to the following research areas

• Crop improvement and breeding
• Precision disease agriculture management
• Conservation and ecosystem health

Service workflow

Fig. 2. CD Genomics' disease resistance traits analysis service process.

Our advantages and features

• Cutting-edge technology. We utilize state-of-the-art sequencing platforms and advanced bioinformatics tools to ensure accurate and high-quality data generation and analysis.
• Interdisciplinary expertise. Our team of experts consists of experienced researchers, bioinformaticians, and geneticists with extensive knowledge of plant biology and disease resistance.
• Customized solutions. Whether it's a large-scale population analysis or a gene-specific targeted study, we offer flexible and tailored approaches to meet your research goals.
• Fast turnaround times. our streamlined workflows and efficient processes allow us to deliver results within the required timeframe.

CD Genomics provides RAD sequencing for association mapping of crop and animal disease resistance traits. By leveraging our expertise and advanced technologies, researchers and breeders can unravel the genetic basis of disease resistance traits and accelerate crop improvement programs. If you are interested, please feel free to contact us.

Reference

1. Manivannan, Abinaya, et al. Genotyping by sequencing-based discovery of SNP markers and construction of linkage map from F 5 population of pepper with contrasting powdery mildew resistance trait. BioMed Research International. 2021 (2021).