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ARS Home » Southeast Area » Stoneville, Mississippi » Crop Genetics Research » Research » Publications at this Location » Publication #417031
Research Project: Developing Strategies and Tools to Mitigate Biotic and Abiotic Stresses in Cotton and Managing the National Cotton Variety Testing Program

Location: Crop Genetics Research

Title: Technological development for analyzing and constructing plant pangenomes

Author
item SINGH, NAGENDRA PRATAP - Texas A&M University
item Mendu, Lavanya
item THUDI, MAHENDAR - Fort Valley State University
item MENDU, VENUGOPAL - Texas A&M University

Submitted to: Elsevier
Publication Type: Book / Chapter
Publication Acceptance Date: 6/19/2025
Publication Date: 9/26/2025
Citation: Singh, N., Mendu, L., Thudi, M., Mendu, V. 2025. Technological development for analyzing and constructing plant pangenomes. Elsevier. p. 1-24. https://doi.org/10.1016/B978-0-443-26791-8.00001-7.
DOI: https://doi.org/10.1016/B978-0-443-26791-8.00001-7

Interpretive Summary:

Technical Abstract: Advances in genomics and computational biology have revolutionized our understanding of plant genomes, genetics of complex traits, and evolutionary processes. The limitations of using a single reference genome to capture the genetic diversity within a species led to the development of the pangenome concept. Consequently, pangenomes serve as comprehensive genetic references, enabling the identification of genetic variation across multiple genomes with higher resolution for the entire species, effectively replacing reference genomes. Pangenomes offer a holistic view of the genome diversity of species by representing the core genome present in all the sequenced individuals and accessory genome restricted to some individuals. Core genes of the core genome are necessary for essential functions, while variable genes/unique genes present in the accessory genome play a key role in evolutionary adaptation and environmental interactions. Crop domestication and breeding for yield improvement resulted in gene erosion, making these genes part of the accessory genome. Pangenome construction using wild species will help in the development of accessory genomes and identify novel genetic variations for crop improvement. This chapter aims to explore the latest technological innovations driving the analysis and construction of plant pangenomes and focus on the complex genomic landscapes of diverse plant species. Specifically, we will delve into three distinct methods for pangenome construction: iterative mapping and assembly, de novo genome assembly of individual genomes, and graph-based pangenome approaches. Furthermore, we provide insights into various next-generation sequencing platforms, spanning from short-read to long-read sequencing technologies, elucidating their respective strengths and limitations in advancing pangenome research. In summary, the advancements detailed in this chapter have markedly improved the quality and continuity of plant pangenomes, enabling more profound insights into plant genomic diversity and evolution. These breakthroughs not only bolster our understanding of plant genetics but also pave the way for future research and applications in plant biology and agriculture.