Abstract
Marker-assisted selection (MAS) is fundamental for plant breeding programs, as it can identify desirable seedlings at a young stage and reduce the cost, time and space needed for plant maintenance, especially for perennial crops. To facilitate the process of genotyping, which is time consuming and laborious, we developed a simplified amplicon sequencing (simplified AmpSeq) library construction method for next-generation sequencing that can be applied to MAS in breeding programs. The method is based on one-step PCR with a mixture of two primer sets: the first consisting of tailed target primers, the second of primers that contain flow-cell binding sites, indexes and tail sequences complementary to those in the first set. To demonstrate the process of MAS using s implified AmpSeq, we created databases of genotypes for important traits by using cultivar collections including triploid cultivars and segregating seedlings of Japanese pear (Pyrus pyrifolia Nakai), Japanese chestnut (Castanea crenata Sieb. et Zucc.) and apple (Malus domestica Borkh.). Simplified AmpSeq has the advantages of high repeatability, ability to estimate allele number in polyploid species and semi-automatic evaluation using target allele frequencies. Because this method provides high flexibility for designing primer sets and targeting any variant, it will be useful for plant breeding programs.
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Claims 6
Claim · model-written summary
Simplified AmpSeq genotype databases were created for Japanese pear breeding material.
Not reportedMaterialGeneCompoundOrgan / stageInteractorInteractor roleSecond interactorSecond interactor roleTreatmentComparatorSettingDirectionQualifier
Verbatim
e0“created databases of genotypes for important traits by using cultivar collections including triploid cultivars and segregating seedlings of Japanese pear (Pyrus pyrifolia Nakai)”
Claim · model-written summary
Simplified AmpSeq genotype databases were created for Japanese chestnut breeding material.
- Taxon
- Japanese chestnut
Castanea crenatae0 - Outcome
- databases of genotypes for important traitse0
- Value
- triploid cultivarse0
Not reportedMaterialGeneCompoundOrgan / stageInteractorInteractor roleSecond interactorSecond interactor roleTreatmentComparatorSettingDirectionQualifier
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“created databases of genotypes for important traits by using cultivar collections including triploid cultivars and segregating seedlings of Japanese pear (Pyrus pyrifolia Nakai), Japanese chestnut (Castanea crenata Sieb. et Zucc.)”
Claim · model-written summary
Simplified AmpSeq genotype databases were created for apple breeding material.
- Taxon
- apple
Malus domesticae0 - Outcome
- databases of genotypes for important traitse0
- Value
- triploid cultivarse0
Not reportedMaterialGeneCompoundOrgan / stageInteractorInteractor roleSecond interactorSecond interactor roleTreatmentComparatorSettingDirectionQualifier
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“created databases of genotypes for important traits by using cultivar collections including triploid cultivars and segregating seedlings of Japanese pear (Pyrus pyrifolia Nakai), Japanese chestnut (Castanea crenata Sieb. et Zucc.) and apple (Malus domestica Borkh.)”
Claim · model-written summary
Simplified AmpSeq showed high repeatability.
Not reportedTaxonMaterialGeneCompoundOrgan / stageInteractorInteractor roleSecond interactorSecond interactor roleTreatmentComparatorSettingDirectionQualifier
Verbatim
e0“Simplified AmpSeq has the advantages of high repeatability”
Claim · model-written summary
Simplified AmpSeq could estimate allele number in polyploids.
Not reportedTaxonMaterialGeneCompoundOrgan / stageInteractorInteractor roleSecond interactorSecond interactor roleTreatmentComparatorSettingDirectionQualifier
Verbatim
e0“ability to estimate allele number in polyploid species”
Claim · model-written summary
Simplified AmpSeq allowed semi-automatic target-allele-frequency evaluation.
Not reportedTaxonMaterialGeneCompoundOrgan / stageInteractorInteractor roleSecond interactorSecond interactor roleTreatmentComparatorSettingDirectionQualifier
Verbatim
e0“semi-automatic evaluation using target allele frequencies”