A super-pangenome of the North American wild grape species
Abstract Background Capturing the genetic diversity of wild relatives is crucial for improving crops because wild species are valuable sources of agronomic traits that are essential to enhance the sustainability and adaptability of domesticated cultivars. Genetic diversity across a genus can be capt...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-12-01
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| Series: | Genome Biology |
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| Online Access: | https://doi.org/10.1186/s13059-023-03133-2 |
| _version_ | 1797376986537000960 |
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| author | Noé Cochetel Andrea Minio Andrea Guarracino Jadran F. Garcia Rosa Figueroa-Balderas Mélanie Massonnet Takao Kasuga Jason P. Londo Erik Garrison Brandon S. Gaut Dario Cantu |
| author_facet | Noé Cochetel Andrea Minio Andrea Guarracino Jadran F. Garcia Rosa Figueroa-Balderas Mélanie Massonnet Takao Kasuga Jason P. Londo Erik Garrison Brandon S. Gaut Dario Cantu |
| author_sort | Noé Cochetel |
| collection | DOAJ |
| description | Abstract Background Capturing the genetic diversity of wild relatives is crucial for improving crops because wild species are valuable sources of agronomic traits that are essential to enhance the sustainability and adaptability of domesticated cultivars. Genetic diversity across a genus can be captured in super-pangenomes, which provide a framework for interpreting genomic variations. Results Here we report the sequencing, assembly, and annotation of nine wild North American grape genomes, which are phased and scaffolded at chromosome scale. We generate a reference-unbiased super-pangenome using pairwise whole-genome alignment methods, revealing the extent of the genomic diversity among wild grape species from sequence to gene level. The pangenome graph captures genomic variation between haplotypes within a species and across the different species, and it accurately assesses the similarity of hybrids to their parents. The species selected to build the pangenome are a great representation of the genus, as illustrated by capturing known allelic variants in the sex-determining region and for Pierce’s disease resistance loci. Using pangenome-wide association analysis, we demonstrate the utility of the super-pangenome by effectively mapping short reads from genus-wide samples and identifying loci associated with salt tolerance in natural populations of grapes. Conclusions This study highlights how a reference-unbiased super-pangenome can reveal the genetic basis of adaptive traits from wild relatives and accelerate crop breeding research. |
| first_indexed | 2024-03-08T19:46:27Z |
| format | Article |
| id | doaj.art-84eb690b79804b74a3c49bd82f60a7ed |
| institution | Directory Open Access Journal |
| issn | 1474-760X |
| language | English |
| last_indexed | 2024-03-08T19:46:27Z |
| publishDate | 2023-12-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj.art-84eb690b79804b74a3c49bd82f60a7ed2023-12-24T12:20:19ZengBMCGenome Biology1474-760X2023-12-0124113110.1186/s13059-023-03133-2A super-pangenome of the North American wild grape speciesNoé Cochetel0Andrea Minio1Andrea Guarracino2Jadran F. Garcia3Rosa Figueroa-Balderas4Mélanie Massonnet5Takao Kasuga6Jason P. Londo7Erik Garrison8Brandon S. Gaut9Dario Cantu10Department of Viticulture and Enology, University of California DavisDepartment of Viticulture and Enology, University of California DavisDepartment of Genetics, Genomics and Informatics, University of Tennessee Health Science CenterDepartment of Viticulture and Enology, University of California DavisDepartment of Viticulture and Enology, University of California DavisDepartment of Viticulture and Enology, University of California DavisCrops Pathology and Genetics Research Unit, United States Department of Agriculture–Agricultural Research ServiceHorticulture Section, School of Integrative Plant Science, Cornell AgriTech, Cornell UniversityDepartment of Genetics, Genomics and Informatics, University of Tennessee Health Science CenterDepartment of Ecology and Evolutionary Biology, University of California IrvineDepartment of Viticulture and Enology, University of California DavisAbstract Background Capturing the genetic diversity of wild relatives is crucial for improving crops because wild species are valuable sources of agronomic traits that are essential to enhance the sustainability and adaptability of domesticated cultivars. Genetic diversity across a genus can be captured in super-pangenomes, which provide a framework for interpreting genomic variations. Results Here we report the sequencing, assembly, and annotation of nine wild North American grape genomes, which are phased and scaffolded at chromosome scale. We generate a reference-unbiased super-pangenome using pairwise whole-genome alignment methods, revealing the extent of the genomic diversity among wild grape species from sequence to gene level. The pangenome graph captures genomic variation between haplotypes within a species and across the different species, and it accurately assesses the similarity of hybrids to their parents. The species selected to build the pangenome are a great representation of the genus, as illustrated by capturing known allelic variants in the sex-determining region and for Pierce’s disease resistance loci. Using pangenome-wide association analysis, we demonstrate the utility of the super-pangenome by effectively mapping short reads from genus-wide samples and identifying loci associated with salt tolerance in natural populations of grapes. Conclusions This study highlights how a reference-unbiased super-pangenome can reveal the genetic basis of adaptive traits from wild relatives and accelerate crop breeding research.https://doi.org/10.1186/s13059-023-03133-2Super-pangenomeGrapevineWild speciesVitis genusPan-GWAS |
| spellingShingle | Noé Cochetel Andrea Minio Andrea Guarracino Jadran F. Garcia Rosa Figueroa-Balderas Mélanie Massonnet Takao Kasuga Jason P. Londo Erik Garrison Brandon S. Gaut Dario Cantu A super-pangenome of the North American wild grape species Genome Biology Super-pangenome Grapevine Wild species Vitis genus Pan-GWAS |
| title | A super-pangenome of the North American wild grape species |
| title_full | A super-pangenome of the North American wild grape species |
| title_fullStr | A super-pangenome of the North American wild grape species |
| title_full_unstemmed | A super-pangenome of the North American wild grape species |
| title_short | A super-pangenome of the North American wild grape species |
| title_sort | super pangenome of the north american wild grape species |
| topic | Super-pangenome Grapevine Wild species Vitis genus Pan-GWAS |
| url | https://doi.org/10.1186/s13059-023-03133-2 |
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