Long Read Sequencing for Crop and Livestock Breeding

Genomics-assisted breeding, which harnesses the potential of modern genomic resources to characterize allelic variation for germplasm enhancement and breed development, is now being effectively incorporated into crop and livestock programs. CD Genomics, a leading company with extensive experience in genomics research, has been at the forefront of driving advances in crop and livestock breeding using long read sequencing solutions. Our experts specialize in agrigenomics for crop and livestock breeding.

Introduction to Crop and Livestock Breeding

Agriculture plays an important role in the global economy. The need to produce more food for a rapidly growing population puts pressure on crop and animal production. The goal of crop and livestock breeding is not only to increase yields, but also for various other applications, such as improved eating quality, high functional content, and processing adaptability. Genome sequencing is important for discovering key genes in animals and crops and for improving the efficiency of genome breeding. Over the past few years, scientists have used genotyping and next-sequencing (NGS) technologies to study agricultural species and better understand the genetic variation that affects phenotypes. However, short-read sequencing has made it difficult to fully locate highly repetitive sequences, which are often found in the large genomic DNA of crops with overlapping genomic DNA, such as soybeans. Even with targeted sequencing, which sequences only regions of genes, it is difficult to simultaneously analyze genes with similar sequences. To address this problem, long-read, long-sequencing technology has recently been developed, which produces sequenced DNA that is more than 100 times longer than that obtained using conventional short-read sequencing technology, and can accelerate a wide variety of crop and livestock breeding studies.

Fig. 1. An Overview of Genomics-Assisted Breeding v 2.0 (GAB 2.0) to Deliver Future Crops. (Varshney et al., 2021)

Solutions Offering at CD Genomics

CD Genomics offers customized long read sequencing solutions for genome breeding. Whether it's to enhance marker development, promote the production of more nutritious foods, protect livestock health, or improve crop yields, we provide comprehensive long-read sequencing data to help you gain biological insights.

Our long read sequencing provides breeders with a data-driven approach to marker-assisted selection by identifying desired traits in plants and animals, and unlocking entirely new capabilities for your plant or livestock breeding program by rapidly assembling stage-specific reference-quality genomes to estimate the most desirable complex traits.

• Our long read sequencing solutions attribute desired traits to single nucleotide polymorphisms (SNPs), structural variants, and complex genotypes.
• By capturing genomic variation in distant lines, inbred lines, and populations on a genome-wide scale, breeders can gain a more comprehensive understanding of the genetic diversity within their target species.
• We also focus on constructing reference-quality, haplotype-resolved whole genomes that can serve as valuable resources for marker development, trait discovery, and germplasm characterization.

Applications of Our Long Read Sequencing Solutions for Crop and Livestock Breeding

• Unraveling Complex Genomes

Crops, such as corn, rose, and soybean, often have complex genomes characterized by large size, high heterozygosity levels, and polyploidy. Our long read sequencing can identify these complex genomic regions and link them to important traits. We aim to provide reliable and comprehensive genomic information for crop breeding programs and the development of quality varieties.

• Apple Breeding

We also provide whole genome sequencing and assembly for haplotype resolution of apples by long read sequencing. By evaluating the genomes of apple trees that flower and mature at different times during the growing season, breeders can identify genetic variation that contributes to climate resilience. We aim to help you develop apple varieties that can adapt to unpredictable weather events, cope with the impacts of climate change, and improve overall apple resilience.

• Potato Breeding

As a major food crop, potato faces challenges such as clonal propagation, disease susceptibility, and limited genetic gain in breeding. We offer long read sequencing for potato breeding, working to transform the potato into a more productive crop with improved nutritional content and reduced environmental impact. A comprehensive understanding of the potato genome helps breeders to produce pure and fertile potato lines, overcoming barriers associated with mutation and hybridization.

• Livestock Breeding

CD Genomics, in collaboration with an international team of researchers, provides long read sequencing solutions to study large structural variations in repetitive or challenging regions of the livestock genome, such as single nucleotide polymorphisms (SNPs) and small insertion deletions. The ability of long read sequencing to analyze and interpret genetic variation at higher resolution enables more precise selection and breeding strategies to improve livestock productivity, disease resistance, and overall genetic enhancement.

Our long read sequencing is a powerful tool in the field of crop and livestock breeding, enabling breeders to gain a comprehensive understanding of complex genomes and make informed decisions about trait selection and genetic improvement. CD Genomics continues to drive innovation and contribute to sustainable agriculture, including increasing crop productivity, improving nutrient content, and increasing the resilience of animal populations under changing environmental conditions. If you have any questions, please feel free to contact us. We look forward to working with you on projects of interest.

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