Building pan-genome infrastructures for crop plants and their use in association genetics
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...
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| Published in: | DNA research Vol. 28; no. 1 |
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| Main Authors: | , , , |
| Format: | Journal Article |
| Language: | English |
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Oxford University Press
19-01-2021
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| Abstract | 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. |
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| AbstractList | 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. 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. |
| Author | Jayakodi, Murukarthick Stein, Nils Schreiber, Mona Mascher, Martin |
| AuthorAffiliation | 1 Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben , Seeland, Germany 3 German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig , Leipzig, Saxony, Germany 2 Center for Integrated Breeding Research (CiBreed), Georg-August-University Göttingen , Göttingen, Germany |
| AuthorAffiliation_xml | – name: 1 Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben , Seeland, Germany – name: 2 Center for Integrated Breeding Research (CiBreed), Georg-August-University Göttingen , Göttingen, Germany – name: 3 German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig , Leipzig, Saxony, Germany |
| Author_xml | – sequence: 1 givenname: Murukarthick surname: Jayakodi fullname: Jayakodi, Murukarthick organization: Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany – sequence: 2 givenname: Mona surname: Schreiber fullname: Schreiber, Mona organization: Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany – sequence: 3 givenname: Nils surname: Stein fullname: Stein, Nils organization: Center for Integrated Breeding Research (CiBreed), Georg-August-University Göttingen, Göttingen, Germany – sequence: 4 givenname: Martin surname: Mascher fullname: Mascher, Martin organization: German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Saxony, Germany |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/33484244$$D View this record in MEDLINE/PubMed |
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| Copyright | The Author(s) 2021. Published by Oxford University Press on behalf of Kazusa DNA Research Institute. The Author(s) 2021. Published by Oxford University Press on behalf of Kazusa DNA Research Institute. 2021 |
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| Keywords | pan-genome genome sequencing genomics crop plants association genetics |
| Language | English |
| License | The Author(s) 2021. Published by Oxford University Press on behalf of Kazusa DNA Research Institute. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
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| Title | Building pan-genome infrastructures for crop plants and their use in association genetics |
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