“Paleogenomics: Connecting the dots of crop evolution from Modern and Ancient DNA”

 

  Paleogenomics is a specialized field of study dedicated to unraveling the genetic information of ancient organisms. Unlike traditional genomics that focuses on living organisms, paleogenomics examines the genomes of species that lived in the past. Recent advancements in ancient DNA (aDNA) research, fuelled by improved methods for recovering and sequencing DNA from ancient samples, have propelled paleogenomics into a new era. These advancements include enhanced understanding of DNA degradation patterns, identification of variation in DNA yield from different fossils and the development of specialized techniques for aDNA extraction and library construction. Consequently, whole-genome sequencing of numerous ancient individuals and extinct species has become feasible, leading to a surge in ancient DNA studies and sequence data. However, the degraded nature of ancient DNA presents challenges for bioinformatic analysis, necessitating caution in the application of tools and the development of standardized analytical pipelines tailored for aDNA data4.

Paleogenomics in plant breeding utilizes aDNA from fossils to uncover genetic diversity, evolutionary history, population dynamics over millennia. Knowledge of mechanisms and rates of evolution of land plants can be directly achieved through experiments with both modern and ancient samples2. This information obtained can be applied in modern agriculture and various fields of research. By analyzing ancient plant genomes, researchers can uncover structural variations, that have shaped plant evolution. This genetic information provides breeders with a deeper understanding of the genetic basis of traits related to environmental adaptation, disease resistance and yield potential. These ancient traits can be recovered by using the latest genetic engineering techniques1. Ancient genomics can provide insights into plant-pathogen interactions, revealing details about the coevolution of crops and pathogens, with implications for modern crop breeding and management. For example, DNA analysis of historical herbarium specimens showed that the strain of Phytophthora infestans involved in the nineteenth century Irish potato famine differs from all examined modern strains3.

Despite challenges like high costs and assembly errors, the future of paleogenomics in plant breeding holds great promise as a powerful tool for reconstructing the genetic history of ancient life forms and ecosystems. Through the analysis of ancient DNA, researchers can unravel the mysteries of the past and gain valuable insights into the processes that have shaped life on Earth. Advances in sequencing technologies and bioinformatics tools are expected to streamline Paleogenome construction and visualization in future for integration of paleogenomic data into breeding programs.

References: 

1. DONATO, A., FILIPPONE, E., ERCOLANO, M. R. AND FRUSCIANTE, L., 2018, Genome sequencing of ancient plant remains: findings, uses and potential applications for the study and improvement of modern crops. Front. Plant Sci., 9: 441.

 2. KISTLER, L., MAEZUMI, S. Y., GREGORIO DE SOUZA, J., PRZELOMSKA, N. A., MALAQUIAS COSTA, F., SMITH, O., LOISELLE, H., RAMOS-MADRIGAL, J., WALES, N., RIBEIRO, E. R. AND MORRISON, R. R., 2018, Multiproxy evidence highlights a complex evolutionary legacy of maize in South America. Science, 362(6420): 1309-1313. 

3. MARTIN, M. D., CAPPELLINI, E., SAMANIEGO, J. A., ZEPEDA, M. L., CAMPOS, P. F., SEGUIN-ORLANDO, A., WALES, N., ORLANDO, L., HO, S. Y., DIETRICH, F. S. AND MIECZKOWSKI, P. A., 2013, Reconstructing genome evolution in historic samples of the Irish potato famine pathogen. Nat. Commun., 4(1): 2172.

 4. PONT, C., WAGNER, S., KREMER, A., ORLANDO, L., PLOMION, C. AND SALSE, J., 2019, Paleogenomics: reconstruction of plant evolutionary trajectories from modern and ancient DNA. Genome Biol., 20(1): 1-17.