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ARS Home » Midwest Area » St. Paul, Minnesota » Plant Science Research » Research » Publications at this Location » Publication #414611
Research Project: Expanding Resiliency and Utility of Alfalfa in Agroecosystems

Location: Plant Science Research

Title: A stepwise guide for pangenome development in crop plants: An alfalfa (Medicago sativa) case study

Author
item KAUR, HARPEET - University Of Minnesota
item SHANNON, LAURA - University Of Minnesota
item Samac, Deborah - Debby

Submitted to: BMC Genomics
Publication Type: Review Article
Publication Acceptance Date: 10/21/2024
Publication Date: 10/31/2024
Citation: Kaur, H., Shannon, L.M., Samac, D.A. 2024. A stepwise guide for pangenome development in crop plants: An alfalfa (Medicago sativa) case study. BMC Genomics. 25. Article 1022. https://doi.org/10.1186/s12864-024-10931-w.
DOI: https://doi.org/10.1186/s12864-024-10931-w

Interpretive Summary:

Technical Abstract: The concept of pangenomics and the importance of structural variants is gaining recognition within the plant genomics community. Due to advancements in sequencing and computational technology, it has become feasible to sequence the entire genome of numerous individuals of a single species at a reasonable cost. Pangenomes have been constructed for many major diploid crops, including rice, maize, soybean, sorghum, pearl millet, peas, sunflower, grapes, and mustards. However, pangenomes for polyploid species are relatively scarce and are available in only few crops including wheat, cotton, rapeseed, and potatoes. Among these polyploids, apart from potatoes, all species are allopolyploids. Alfalfa, a highly heterozygous, cross pollinated and autotetraploid forage crop species, is used as an example to discuss the concerns and challenges offered by polyploid crop species. In this review, we delve into the diverse methods employed for crop pangenome development and discuss the challenges and implications of these methods. We offer a systematic guide and discuss the tools available for constructing a pangenome and conducting downstream analyses. We conducted a comparative analysis using graph-based methods by constructing an alfalfa graph pangenome using three publicly available genome assemblies. To illustrate the intricacies captured by pangenome graphs for a complex crop genome, we focused on a locus associated with male sterility in alfalfa. The comparison of the three graph pangenome methods reveals significant differences in the genomic sequence of this region at different scales.