ArticleAnnals of botany2013
Assignment of SNP allelic configuration in polyploids using competitive allele-specific PCR: application to citrus triploid progeny.
Article in Annals of botany, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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31 citing papers in PubMed, 73 citations in OpenAlex.
- Optimization of Microsatellite Multiplex PCRs for Triploidy Verification and Genetic Diversity Assessment in the Pacific Oyster, Crassostrea gigas.Marine biotechnology (New York, N.Y.) · 2025Article
- Development of multiplex allele-specific RT-qPCR assays for differentiation of SARS-CoV-2 Omicron subvariants.Applied microbiology and biotechnology · 2024Article
- Marine transmissible cancer navigates urbanized waters, threatening spillover.Proceedings. Biological sciences · 2024Article
- Insight into Physiological and Biochemical Determinants of Salt Stress Tolerance in Tetraploid Citrus.Antioxidants (Basel, Switzerland) · 2023Article
- Meiotic Behaviors of Allotetraploid Citrus Drive the Interspecific Recombination Landscape, the Genetic Structures, and Traits Inheritance in Tetrazyg Progenies Aiming to Select New Rootstocks.Plants (Basel, Switzerland) · 2023Article
- Genotyping by Sequencing for SNP-Based Linkage Analysis and the Development of KASPar Markers for Male Sterility and Polyembryony in Citrus.Plants (Basel, Switzerland) · 2023Article
- Prevalence and polymorphism of a mussel transmissible cancer in Europe.Molecular ecology · 2022Article
- Development of a panel of three multiplex allele-specific qRT-PCR assays for quick differentiation of recombinant variants and Omicron subvariants of SARS-CoV-2.Frontiers in cellular and infection microbiology · 2022Article
- Genotyping of polyploid plants using quantitative PCR: application in the breeding of white-fleshed triploid loquats (Eriobotrya japonica).Plant methods · 2021Article
- Localization and characterization of Citrus centromeres by combining half-tetrad analysis and CenH3-associated sequence profiling.Plant cell reports · 2020Article
- Male and female inheritance patterns in tetraploid 'Moncada' mandarin.Plant cell reports · 2020Article
- Development of a minimal KASP marker panel for distinguishing genotypes in apple collections.PloS one · 2020Article
- Preferential Disomic Segregation andFrontiers in plant science · 2020Article
- Article
- Development of a cost-effective single nucleotide polymorphism genotyping array for management of greater yam germplasm collections.Ecology and evolution · 2019Article
- Facing Climate Change: Biotechnology of Iconic Mediterranean Woody Crops.Frontiers in plant science · 2019Review
- Machine Learning Models for Genetic Risk Assessment of Infants with Non-syndromic Orofacial Cleft.Genomics, proteomics & bioinformatics · 2018Article
- Origin of C. latifolia and C. aurantiifolia triploid limes: the preferential disomic inheritance of doubled-diploid 'Mexican' lime is consistent with an interploid hybridization hypothesis.Annals of botany · 2018Article
- Preferential Homologous Chromosome Pairing in a Tetraploid Intergeneric Somatic Hybrid (Frontiers in plant science · 2018Article
- Molecular Characterization and Stress Tolerance Evaluation of New Allotetraploid Somatic Hybrids Between Carrizo Citrange andFrontiers in plant science · 2018Article
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4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundPolyploidy is a major component of eukaryote evolution. Estimation of allele copy numbers for molecular markers has long been considered a challenge for polyploid species, while this process is essential for most genetic research. With the increasing availability and whole-genome coverage of single nucleotide polymorphism (SNP) markers, it is essential to implement a versatile SNP genotyping method to assign allelic configuration efficiently in polyploids. SCOPE: This work evaluates the usefulness of the KASPar method, based on competitive allele-specific PCR, for the assignment of SNP allelic configuration. Citrus was chosen as a model because of its economic importance, the ongoing worldwide polyploidy manipulation projects for cultivar and rootstock breeding, and the increasing availability of SNP markers.
conclusionsFifteen SNP markers were successfully designed that produced clear allele signals that were in agreement with previous genotyping results at the diploid level. The analysis of DNA mixes between two haploid lines (Clementine and pummelo) at 13 different ratios revealed a very high correlation (average = 0·9796; s.d. = 0·0094) between the allele ratio and two parameters [θ angle = tan(-1) (y/x) and y' = y/(x + y)] derived from the two normalized allele signals (x and y) provided by KASPar. Separated cluster analysis and analysis of variance (ANOVA) from mixed DNA simulating triploid and tetraploid hybrids provided 99·71 % correct allelic configuration. Moreover, triploid populations arising from 2n gametes and interploid crosses were easily genotyped and provided useful genetic information. This work demonstrates that the KASPar SNP genotyping technique is an efficient way to assign heterozygous allelic configurations within polyploid populations. This method is accurate, simple and cost-effective. Moreover, it may be useful for quantitative studies, such as relative allele-specific expression analysis and bulk segregant analysis.
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