Pool-seq of diverse apple germplasm reveals candidate loci underlying ripening time, phenolic content, and softening
Ripening time, softening, and phenolic content are phenotypes of considerable commercial importance in apples. Identifying causal genetic variants controlling these traits not only advances marker-assisted breeding, but it is also an essential step for the application of gene editing technologies in...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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Maximum Academic Press
2023-01-01
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| Series: | Fruit Research |
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| Online Access: | https://www.maxapress.com/article/doi/10.48130/FruRes-2023-0011 |
| _version_ | 1797293134502166528 |
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| author | Thomas Davies Sean Myles |
| author_facet | Thomas Davies Sean Myles |
| author_sort | Thomas Davies |
| collection | DOAJ |
| description | Ripening time, softening, and phenolic content are phenotypes of considerable commercial importance in apples. Identifying causal genetic variants controlling these traits not only advances marker-assisted breeding, but it is also an essential step for the application of gene editing technologies in apples. To advance the discovery of genetic variants associated with these phenotypes, we examined allele frequency differences between groups of phenotypically extreme individuals from Canada’s Apple Biodiversity Collection using pooled whole genome sequencing (pool-seq). We sequenced pooled DNA samples to an average read depth of 150x and scanned the genome for allelic differentiation between pools. For each phenotype, we identified >20 million genetic variants and identified numerous candidate genes. We identified loci on chromosomes 3 and 4 associated with ripening time, the former suggesting that regulatory variants upstream of a previously identified transcription factor NAC18.1 may be causal. Our analysis identified candidate regions on chromosomes 4, 8, and 16 associated with phenolic content, and suggested a cluster of UDP-Glycosyltransferase family genes as candidates for polyphenol production. Further, we identified regions on chromosomes 17 and 10 associated with softening and suggest a Long-chain fatty alcohol dehydrogenase family gene as putatively causal. |
| first_indexed | 2024-03-07T20:09:26Z |
| format | Article |
| id | doaj.art-f39d1aa787d24ff3806989aa57aa06cc |
| institution | Directory Open Access Journal |
| issn | 2769-4615 |
| language | English |
| last_indexed | 2024-03-07T20:09:26Z |
| publishDate | 2023-01-01 |
| publisher | Maximum Academic Press |
| record_format | Article |
| series | Fruit Research |
| spelling | doaj.art-f39d1aa787d24ff3806989aa57aa06cc2024-02-28T03:19:43ZengMaximum Academic PressFruit Research2769-46152023-01-013111210.48130/FruRes-2023-0011FruRes-2023-0011Pool-seq of diverse apple germplasm reveals candidate loci underlying ripening time, phenolic content, and softeningThomas Davies0Sean Myles1Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, Nova Scotia, CanadaDepartment of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, Nova Scotia, CanadaRipening time, softening, and phenolic content are phenotypes of considerable commercial importance in apples. Identifying causal genetic variants controlling these traits not only advances marker-assisted breeding, but it is also an essential step for the application of gene editing technologies in apples. To advance the discovery of genetic variants associated with these phenotypes, we examined allele frequency differences between groups of phenotypically extreme individuals from Canada’s Apple Biodiversity Collection using pooled whole genome sequencing (pool-seq). We sequenced pooled DNA samples to an average read depth of 150x and scanned the genome for allelic differentiation between pools. For each phenotype, we identified >20 million genetic variants and identified numerous candidate genes. We identified loci on chromosomes 3 and 4 associated with ripening time, the former suggesting that regulatory variants upstream of a previously identified transcription factor NAC18.1 may be causal. Our analysis identified candidate regions on chromosomes 4, 8, and 16 associated with phenolic content, and suggested a cluster of UDP-Glycosyltransferase family genes as candidates for polyphenol production. Further, we identified regions on chromosomes 17 and 10 associated with softening and suggest a Long-chain fatty alcohol dehydrogenase family gene as putatively causal.https://www.maxapress.com/article/doi/10.48130/FruRes-2023-0011applegenetic mappingripening timesofteningphenolic contentpooled sequencing |
| spellingShingle | Thomas Davies Sean Myles Pool-seq of diverse apple germplasm reveals candidate loci underlying ripening time, phenolic content, and softening Fruit Research apple genetic mapping ripening time softening phenolic content pooled sequencing |
| title | Pool-seq of diverse apple germplasm reveals candidate loci underlying ripening time, phenolic content, and softening |
| title_full | Pool-seq of diverse apple germplasm reveals candidate loci underlying ripening time, phenolic content, and softening |
| title_fullStr | Pool-seq of diverse apple germplasm reveals candidate loci underlying ripening time, phenolic content, and softening |
| title_full_unstemmed | Pool-seq of diverse apple germplasm reveals candidate loci underlying ripening time, phenolic content, and softening |
| title_short | Pool-seq of diverse apple germplasm reveals candidate loci underlying ripening time, phenolic content, and softening |
| title_sort | pool seq of diverse apple germplasm reveals candidate loci underlying ripening time phenolic content and softening |
| topic | apple genetic mapping ripening time softening phenolic content pooled sequencing |
| url | https://www.maxapress.com/article/doi/10.48130/FruRes-2023-0011 |
| work_keys_str_mv | AT thomasdavies poolseqofdiverseapplegermplasmrevealscandidatelociunderlyingripeningtimephenoliccontentandsoftening AT seanmyles poolseqofdiverseapplegermplasmrevealscandidatelociunderlyingripeningtimephenoliccontentandsoftening |