Single‐nucleotide polymorphisms that uniquely identify cultivars of avocado (Persea americana)
Premise Progeny of avocado (Persea americana) are highly variable due to high levels of heterozygosity. Breeding programs need molecular resources to allow the assessment of genetic differences and the selection of genotypes. Polymorphisms that uniquely identify different avocado cultivars provide a...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2021-06-01
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| Series: | Applications in Plant Sciences |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/aps3.11440 |
| _version_ | 1818864759804526592 |
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| author | Wiebke Kämper Stephen J. Trueman Jade Cooke Naga Kasinadhuni Aaron J. Brunton Steven M. Ogbourne |
| author_facet | Wiebke Kämper Stephen J. Trueman Jade Cooke Naga Kasinadhuni Aaron J. Brunton Steven M. Ogbourne |
| author_sort | Wiebke Kämper |
| collection | DOAJ |
| description | Premise Progeny of avocado (Persea americana) are highly variable due to high levels of heterozygosity. Breeding programs need molecular resources to allow the assessment of genetic differences and the selection of genotypes. Polymorphisms that uniquely identify different avocado cultivars provide a valuable tool to accelerate avocado research and development, including, for example, genotype selection. Methods A double‐digest restriction site–associated DNA sequencing (ddRADseq) approach was used to screen 10 avocado cultivars for single‐nucleotide polymorphisms (SNPs). The fragments were size selected with Blue Pippin and PCR using universal Illumina primers, and catalog tags were then created with de novo alignment using Stacks software. Catalog tags were tabulated and filtered to identify alleles unique to each cultivar. Results A total of 104 million sequences were collected, and 52 homozygous SNPs were identified that uniquely distinguished nine avocado cultivars. The cultivars Carmen Hass and Hass have a strong genetic similarity and no homozygous SNPs distinguishing these cultivars could be identified; therefore, both cultivars were grouped together. Discussion The resource described here for cultivars of P. americana presents a new and significant molecular resource that can enable targeted genotype selection, paternity analysis, germplasm genotyping, pollination dynamics investigation, and crop improvement. |
| first_indexed | 2024-12-19T10:36:46Z |
| format | Article |
| id | doaj.art-3d2dee04de1348feb5e920d6a50e946c |
| institution | Directory Open Access Journal |
| issn | 2168-0450 |
| language | English |
| last_indexed | 2024-12-19T10:36:46Z |
| publishDate | 2021-06-01 |
| publisher | Wiley |
| record_format | Article |
| series | Applications in Plant Sciences |
| spelling | doaj.art-3d2dee04de1348feb5e920d6a50e946c2022-12-21T20:25:35ZengWileyApplications in Plant Sciences2168-04502021-06-0196n/an/a10.1002/aps3.11440Single‐nucleotide polymorphisms that uniquely identify cultivars of avocado (Persea americana)Wiebke Kämper0Stephen J. Trueman1Jade Cooke2Naga Kasinadhuni3Aaron J. Brunton4Steven M. Ogbourne5Food Security Platform Centre for Planetary Health and Food Security School of Environment and Science Griffith University Nathan Queensland4111AustraliaFood Security Platform Centre for Planetary Health and Food Security School of Environment and Science Griffith University Nathan Queensland4111AustraliaAustralian Genome Research Facility Melbourne Victoria3000AustraliaAustralian Genome Research Facility Brisbane Queensland4072AustraliaGeneCology Research Centre University of the Sunshine Coast Maroochydore DC Queensland4558AustraliaGeneCology Research Centre University of the Sunshine Coast Maroochydore DC Queensland4558AustraliaPremise Progeny of avocado (Persea americana) are highly variable due to high levels of heterozygosity. Breeding programs need molecular resources to allow the assessment of genetic differences and the selection of genotypes. Polymorphisms that uniquely identify different avocado cultivars provide a valuable tool to accelerate avocado research and development, including, for example, genotype selection. Methods A double‐digest restriction site–associated DNA sequencing (ddRADseq) approach was used to screen 10 avocado cultivars for single‐nucleotide polymorphisms (SNPs). The fragments were size selected with Blue Pippin and PCR using universal Illumina primers, and catalog tags were then created with de novo alignment using Stacks software. Catalog tags were tabulated and filtered to identify alleles unique to each cultivar. Results A total of 104 million sequences were collected, and 52 homozygous SNPs were identified that uniquely distinguished nine avocado cultivars. The cultivars Carmen Hass and Hass have a strong genetic similarity and no homozygous SNPs distinguishing these cultivars could be identified; therefore, both cultivars were grouped together. Discussion The resource described here for cultivars of P. americana presents a new and significant molecular resource that can enable targeted genotype selection, paternity analysis, germplasm genotyping, pollination dynamics investigation, and crop improvement.https://doi.org/10.1002/aps3.11440avocadobreedingddRADSeqgene flowpollination |
| spellingShingle | Wiebke Kämper Stephen J. Trueman Jade Cooke Naga Kasinadhuni Aaron J. Brunton Steven M. Ogbourne Single‐nucleotide polymorphisms that uniquely identify cultivars of avocado (Persea americana) Applications in Plant Sciences avocado breeding ddRADSeq gene flow pollination |
| title | Single‐nucleotide polymorphisms that uniquely identify cultivars of avocado (Persea americana) |
| title_full | Single‐nucleotide polymorphisms that uniquely identify cultivars of avocado (Persea americana) |
| title_fullStr | Single‐nucleotide polymorphisms that uniquely identify cultivars of avocado (Persea americana) |
| title_full_unstemmed | Single‐nucleotide polymorphisms that uniquely identify cultivars of avocado (Persea americana) |
| title_short | Single‐nucleotide polymorphisms that uniquely identify cultivars of avocado (Persea americana) |
| title_sort | single nucleotide polymorphisms that uniquely identify cultivars of avocado persea americana |
| topic | avocado breeding ddRADSeq gene flow pollination |
| url | https://doi.org/10.1002/aps3.11440 |
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