Building pan-genome infrastructures for crop plants and their use in association genetics

Murukarthick Jayakodi, Mona Schreiber, Nils Stein, Martin Mascher

Research output: Contribution to journalReview article

2 Citations (Scopus)


Pan-genomic studies aim at representing the entire sequence diversity within a species to provide useful resources for evolutionary studies, functional genomics and breeding of cultivated plants. Cost reductions in high-throughput sequencing and advances in sequence assembly algorithms have made it possible to create multiple reference genomes along with a catalogue of all forms of genetic variations in plant species with large and complex or polyploid genomes. In this review, we summarize the current approaches to building pan-genomes as an in silico representation of plant sequence diversity and outline relevant methods for their effective utilization in linking structural with phenotypic variation. We propose as future research avenues (i) transcriptomic and epigenomic studies across multiple reference genomes and (ii) the development of user-friendly and feature-rich pan-genome browsers.

Original languageEnglish
JournalDNA research : an international journal for rapid publication of reports on genes and genomes
Issue number1
Publication statusPublished - 19 Jan 2021
Externally publishedYes


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