Potato (Solanum tuberosum L.) is the most important vegetable crop in the world and the third largest food crop in the world. It is a unique biological system belonging to the Solanaceae family. It is an autotetraploid crop with complex genetics, severe inbreeding depression, and highly heterozygous nature. Despite the potato's worldwide importance as an important food crop, the genetics of its many traits are poorly understood and complicated by its polyploid genome. Many important qualitative and quantitative agronomic traits are unknown, the genes affecting these traits remain largely undiscovered, and QTL mapping is often imprecise. Sequencing the potato genome will provide a major boost to a better understanding of potato trait biology and will provide the basis for future breeding efforts.

CD Genomics is a leading service provider for agricultural genomics research, offering reliable potato genome sequencing services to support research and breeding efforts in the field of potato genomics for clients worldwide. Our services help develop potato varieties targeted to pest, disease, and climatic extremes, as well as nutritionally enhanced.

Our potato genome sequencing service

CD Genomics offers comprehensive and customizable potato genome sequencing services using cutting-edge technology and expertise to characterize the potato genome at the cytogenetic, genetic, and molecular levels. Our services cover all stages of the sequencing process, from library preparation to data analysis, ensuring high-quality and accurate results.

With our advanced next-generation sequencing and long-read sequencing technology platforms, as well as bioinformatics tools, we can accurately sequence the 840 Mb genome of potato's 12 chromosomes to understand the structure and function of its genes. Our provision of complete genome sequences contributes to a better understanding of potato biology, supporting evolutionary processes, genetics, breeding, and molecular efforts to improve a variety of important traits involved in potato growth and development.

Our sequencing strategies for potato

CD Genomics offers whole-genome shotgun sequencing strategies for potatoes. We use large-insert bacterial artificial chromosome (BAC), phage (P1), and transformation-competent artificial chromosome (TAC) libraries as the primary substrates for sequencing. The multimodal approach allowed us to capture the full complexity of the potato genome, including repetitive regions, structural variation, and gene regulatory elements.

• Produce a high-quality draft of the potato genome, containing at least 95% of the genes.
• Sequencing-based potato clone development comprehensive genetic and physical map with different types of sequencing markers.
• Potato genome assembly.
• Gene prediction methods for annotating protein-coding genes.
• Construct consensus gene set by merging all genetic resources and prediction methods.
• Validated by deep transcriptome analysis and RNA-seq analysis.

Applications of potato genome sequencing

The potato genome sequencing contributes to numerous applications in basic potato genetic research, breeding, and agriculture.

• Crop improvement and breeding

The availability of the potato genome sequence can provide breeders with a wealth of information for developing improved potato varieties. By identifying genes associated with desired traits, breeders can selectively breed potatoes with enhanced characteristics, such as disease resistance, yield, nutrient content, and tolerance to environmental stress. The genome sequence also facilitates marker-assisted selection, where specific genetic markers associated with desired traits can be used to speed up the breeding process.

• Understanding disease resistance mechanisms

Potato is susceptible to a wide range of pathogens and pests, leading to severe yield losses. The potato genome sequence provides insights into the genetic basis of disease resistance, enabling researchers to identify resistance genes and understand underlying mechanisms.

• Functional genomics and gene discovery

The potato genome sequence provides a rich resource for functional genomics research, enabling researchers to study gene function and regulatory networks. By integrating transcriptomic data with other genomic approaches, such as proteomics and metabolomics, researchers can gain a comprehensive understanding of potato's complex biological processes.

Our Advantages

• Radical effects on efficiency of potato breeding.
• Overcome many negative aspects of potato as a genetic system.
• Enhance our ability to identify the desirable allelic variants of genes underlying important quantitative traits in potato.
• Facilitate gene isolation and allow molecular geneticists to use candidate gene approaches for trait gene discovery.
• Shorten the time taken to breed new varieties as well as reducing the cost.

Case study of potato genome sequencing

The potato genome is usually homotetraploid, consisting of four copies of each chromosome. However, local varieties of cultivated potato exhibit a wide range of ploidy levels, from diploid to pentaploid, while wild potato varieties include hexaploids. Polyploid genomes are characterized by high heterozygosity, which is mainly due to the self-incompatibility of diploid potato species. The heterozygosity and complexity of polyploid genomes make their assembly a difficult task. The researchers aim to assemble six polyploid potato genomes using a combination of NGS and long-read sequencing technologies.

• Heterozygosity analysis: To understand the complexity of the genomes, the researchers calculated genome-wide heterozygosity for each genome using k-mer frequencies derived from sequencing reads.
• Genome assembly strategies: Researchers used different assembly methods depending on the available genome and sequencing data. For the ADG1 genome, which was sequenced using long-read sequencing data, a hybrid read approach combining long and linked reads was used to improve assembly.
• Assessment of genome assembly: The quality of the assembled genome is assessed based on several parameters, including read coverage and heterozygosity. Illumina reads provide read coverage ranging from approximately 36X to 44.4X, while the average read coverage of ADG1 genomes assembled using long-read sequencing data is 50X.

Fig. 1. Bar chart with summary assessments for the proportion of genes present in six assembled polyploid potato (Solanum sp.) genomes. (Kyriakidou et al., 2020)

CD Genomics offers cutting-edge potato genome sequencing services to provide comprehensive genomic information to researchers and breeders for their studies. We aim to provide data to support basic research on the genetics of important potato traits and to promote potato improvement. If you are interested, please feel free to contact us.

Reference

1. Kyriakidou, Maria, et al. Genome assembly of six polyploid potato genomes. Scientific data. 7.1 (2020): 88.