World Food Day, led by The Food and Agriculture Organization (FAO), is marked annually on 16 October. The theme of World Food Forum (WFF) 2023 is “Agrifood systems transformation accelerates climate action”.¹ Agriculture, food and climate change issues are more important than ever. How can we address the global food security challenges and meet the increasing demand of food production while ensuring the sustainable agricultural environment and adaptability?

Building comprehensive genome libraries for different species is proving to be a crucial step in unlocking the potential of genetic information for agricultural applications, such as protecting genetic diversity, maintaining and improving the adaptability of cultivars within a species, better understanding the biological pathways and functions that agricultural species execute, better understanding how species respond to selective pressures, and how disease resistance can be improved.

The pressing issues require innovative approaches that can unravel the complexities of agri-genomes and provide valuable insights into crop yield improvement and environmental resilience. Long-read sequencing technologies, such as PacBio and Oxford Nanopore, have been utilized to overcome the limitations of short-read sequencing. These technologies offer longer read lengths and can capture complex genomic structures, enabling more accurate identification of structural variations and facilitating the detection of mutations.

Novogene holds the mission: “Advancing Genomics, Improving Life” and endeavors to provide researchers with long-read sequencing services which help them better understand the crop genetics, pave the way for sustainable food production, and accelerate the progress towards a world with sustainable, resilient, inclusive and hunger-free future for all.

The Application of Long-Read Sequencing in Agri-Genomics

1. Exploring evolution and domestication of speciesLong-read sequencing has great value for accurate and comprehensive genome assembly, especially for species with large and complex genomes. By providing a more comprehensive view of genetic information, long-read sequencing and other sequencing technologies enables researchers to delve deeper into the intricate processes shaping the development and adaptation of organisms.

   Using a combination of short-read sequencing (Illumina HiSeq X Ten platform), long-read sequencing (Nanopore PromethION platform), and chromosome conformation capture (Hi-C) sequencing methods, Xia and colleagues assembled the first high-quality genome of a rare, wild diploid plant within the most commercialized kiwifruit species Actinidia chinensis var. deliciosa (Acd). 2 Although kiwifruit is an important global crop—annual global production is 4.34 million tons—building a high-quality genome for Acd has been challenging due to its high ploidy (allohexaploid) and large proportion of repetitive sequences. Xia and colleagues also compared their diploid Acd genome with other kiwifruit species, finding three whole genome duplication (WGD) events in Acd. This new, high-quality genome not only provides a strong foundation for future functional genomics studies in kiwifruit but also further elucidates the genome evolution of allohexaploid Acd. ²

2. Addressing environmental challengesClimate change and environmental pollution have led to constant changes in the growth environment of crops and livestock. Sequencing technologies, including long-read sequencing, can help identify genes that contribute to adaptability, thus facilitating the development of hardier plant and animal varieties.

   Soil quality decline and nutrient loss, as well as water deficit, have produced negative impact on agricultural production.³ Long-read sequencing can also be used for transcriptome (RNA) analysis, including identification and quantification of gene expression, alternative splicing, and post-transcriptional modifications. To better understand why certain maize cultivars have shown increased drought tolerance, Sen and colleagues worked with Novogene to apply PacBio Iso-Seq transcriptome generation strategies to create an annotated “SuperTranscriptome” of nodal root growth under varying water stress levels. ⁴ From these gene-length transcripts, they identified 128 “SuperTranscripts” that were potentially genotype-specific novel genes. GO annotation analysis showed that those transcripts were enriched for ion binding functions, microtubules, ATP binding activity, and membrane and integral membrane components—together suggesting roles in nutrient uptake and homeostasis.⁴ Those “SuperTranscripts” represent an important reference for analysis of the maize nodal root transcriptomic response to environmental perturbations, and also for future study and potential sources of crop improvement.

Summary From the examples discussed herein, we can summarize that long-read sequencing will be greatly important in advancing agri-genomics, especially when combined with well-established sequencing technologies such as next-generation sequencing. With these new insights into genome structure and composition come new opportunities for marker discovery and comparative studies. A deeper understanding of crop and animal responses to evolutionary and selective processes will yield new insights into the functions of existing gene and phenotype traits, as well as opportunities to enhance the fitness and resilience of crops and livestock.

Reference:

1. World Food Forum | 2023 Theme. (n.d.). WFF-Flagship-Event. https://flagship.world-food-forum.org/theme/en
2. Xia, H., Deng, H., Li, M., Xie, Y., Lin, L., Zhang, H., Luo, X., Lv, X., Wang, J., & Liang, D. (2023). Chromosome-scale genome assembly of a natural diploid kiwifruit (Actinidia chinensis var. deliciosa). Scientific data, 10(1), 92. https://doi.org/10.1038/s41597-023-02006-4
3. Kumar, S., & Nadda, A. K. (2023). Agri-food waste as environmental pollutant: Root causes, challenges and solution. Environmental pollution (Barking, Essex: 1987), 336, 122412. https://doi.org/10.1016/j.envpol.2023.122412
4. Sen, S., King, S. K., McCubbin, T., Greeley, L. A., Mertz, R. A., Becker, C., Niehues, N., Zeng, S., Stemmle, J. T., Peck, S. C., Oliver, M. J., Fritschi, F. B., Braun, D. M., Sharp, R. E., & Joshi, T. (2023). De novo transcriptome assembly from the nodal root growth zone of hydrated and water-deficit stressed maize inbred line FR697. Scientific reports, 13(1), 1960. https://doi.org/10.1038/s41598-023-29115-9