Pangenomes as a Resource to Accelerate Breeding of Under-Utilised Crop Species
Pangenomes are a rich resource to examine the genomic variation observed within a species or genera, supporting population genetics studies, with applications for the improvement of crop traits. Major crop species such as maize (<i>Zea mays</i>), rice (<i>Oryza sativa)</i>, &...
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2022-02-01
|
| Series: | International Journal of Molecular Sciences |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1422-0067/23/5/2671 |
| _version_ | 1797474905910935552 |
|---|---|
| author | Cassandria Geraldine Tay Fernandez Benjamin John Nestor Monica Furaste Danilevicz Mitchell Gill Jakob Petereit Philipp Emanuel Bayer Patrick Michael Finnegan Jacqueline Batley David Edwards |
| author_facet | Cassandria Geraldine Tay Fernandez Benjamin John Nestor Monica Furaste Danilevicz Mitchell Gill Jakob Petereit Philipp Emanuel Bayer Patrick Michael Finnegan Jacqueline Batley David Edwards |
| author_sort | Cassandria Geraldine Tay Fernandez |
| collection | DOAJ |
| description | Pangenomes are a rich resource to examine the genomic variation observed within a species or genera, supporting population genetics studies, with applications for the improvement of crop traits. Major crop species such as maize (<i>Zea mays</i>), rice (<i>Oryza sativa)</i>, <i>Brassica</i> (<i>Brassica</i> spp.), and soybean (<i>Glycine max</i>) have had pangenomes constructed and released, and this has led to the discovery of valuable genes associated with disease resistance and yield components. However, pangenome data are not available for many less prominent crop species that are currently under-utilised. Despite many under-utilised species being important food sources in regional populations, the scarcity of genomic data for these species hinders their improvement. Here, we assess several under-utilised crops and review the pangenome approaches that could be used to build resources for their improvement. Many of these under-utilised crops are cultivated in arid or semi-arid environments, suggesting that novel genes related to drought tolerance may be identified and used for introgression into related major crop species. In addition, we discuss how previously collected data could be used to enrich pangenome functional analysis in genome-wide association studies (GWAS) based on studies in major crops. Considering the technological advances in genome sequencing, pangenome references for under-utilised species are becoming more obtainable, offering the opportunity to identify novel genes related to agro-morphological traits in these species. |
| first_indexed | 2024-03-09T20:36:36Z |
| format | Article |
| id | doaj.art-1b6e588b6aac4c988b28da18edf31856 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T20:36:36Z |
| publishDate | 2022-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-1b6e588b6aac4c988b28da18edf318562023-11-23T23:07:46ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-02-01235267110.3390/ijms23052671Pangenomes as a Resource to Accelerate Breeding of Under-Utilised Crop SpeciesCassandria Geraldine Tay Fernandez0Benjamin John Nestor1Monica Furaste Danilevicz2Mitchell Gill3Jakob Petereit4Philipp Emanuel Bayer5Patrick Michael Finnegan6Jacqueline Batley7David Edwards8School of Biological Sciences, The University of Western Australia, Perth, WA 6009, AustraliaSchool of Biological Sciences, The University of Western Australia, Perth, WA 6009, AustraliaSchool of Biological Sciences, The University of Western Australia, Perth, WA 6009, AustraliaSchool of Biological Sciences, The University of Western Australia, Perth, WA 6009, AustraliaSchool of Biological Sciences, The University of Western Australia, Perth, WA 6009, AustraliaSchool of Biological Sciences, The University of Western Australia, Perth, WA 6009, AustraliaSchool of Biological Sciences, The University of Western Australia, Perth, WA 6009, AustraliaSchool of Biological Sciences, The University of Western Australia, Perth, WA 6009, AustraliaSchool of Biological Sciences, The University of Western Australia, Perth, WA 6009, AustraliaPangenomes are a rich resource to examine the genomic variation observed within a species or genera, supporting population genetics studies, with applications for the improvement of crop traits. Major crop species such as maize (<i>Zea mays</i>), rice (<i>Oryza sativa)</i>, <i>Brassica</i> (<i>Brassica</i> spp.), and soybean (<i>Glycine max</i>) have had pangenomes constructed and released, and this has led to the discovery of valuable genes associated with disease resistance and yield components. However, pangenome data are not available for many less prominent crop species that are currently under-utilised. Despite many under-utilised species being important food sources in regional populations, the scarcity of genomic data for these species hinders their improvement. Here, we assess several under-utilised crops and review the pangenome approaches that could be used to build resources for their improvement. Many of these under-utilised crops are cultivated in arid or semi-arid environments, suggesting that novel genes related to drought tolerance may be identified and used for introgression into related major crop species. In addition, we discuss how previously collected data could be used to enrich pangenome functional analysis in genome-wide association studies (GWAS) based on studies in major crops. Considering the technological advances in genome sequencing, pangenome references for under-utilised species are becoming more obtainable, offering the opportunity to identify novel genes related to agro-morphological traits in these species.https://www.mdpi.com/1422-0067/23/5/2671pangenome assemblygraph pangenomespresence absence variationQTLstrait discovery |
| spellingShingle | Cassandria Geraldine Tay Fernandez Benjamin John Nestor Monica Furaste Danilevicz Mitchell Gill Jakob Petereit Philipp Emanuel Bayer Patrick Michael Finnegan Jacqueline Batley David Edwards Pangenomes as a Resource to Accelerate Breeding of Under-Utilised Crop Species International Journal of Molecular Sciences pangenome assembly graph pangenomes presence absence variation QTLs trait discovery |
| title | Pangenomes as a Resource to Accelerate Breeding of Under-Utilised Crop Species |
| title_full | Pangenomes as a Resource to Accelerate Breeding of Under-Utilised Crop Species |
| title_fullStr | Pangenomes as a Resource to Accelerate Breeding of Under-Utilised Crop Species |
| title_full_unstemmed | Pangenomes as a Resource to Accelerate Breeding of Under-Utilised Crop Species |
| title_short | Pangenomes as a Resource to Accelerate Breeding of Under-Utilised Crop Species |
| title_sort | pangenomes as a resource to accelerate breeding of under utilised crop species |
| topic | pangenome assembly graph pangenomes presence absence variation QTLs trait discovery |
| url | https://www.mdpi.com/1422-0067/23/5/2671 |
| work_keys_str_mv | AT cassandriageraldinetayfernandez pangenomesasaresourcetoacceleratebreedingofunderutilisedcropspecies AT benjaminjohnnestor pangenomesasaresourcetoacceleratebreedingofunderutilisedcropspecies AT monicafurastedanilevicz pangenomesasaresourcetoacceleratebreedingofunderutilisedcropspecies AT mitchellgill pangenomesasaresourcetoacceleratebreedingofunderutilisedcropspecies AT jakobpetereit pangenomesasaresourcetoacceleratebreedingofunderutilisedcropspecies AT philippemanuelbayer pangenomesasaresourcetoacceleratebreedingofunderutilisedcropspecies AT patrickmichaelfinnegan pangenomesasaresourcetoacceleratebreedingofunderutilisedcropspecies AT jacquelinebatley pangenomesasaresourcetoacceleratebreedingofunderutilisedcropspecies AT davidedwards pangenomesasaresourcetoacceleratebreedingofunderutilisedcropspecies |