Development and Assessment of SNP Genotyping Arrays for Citrus and Its Close Relatives
Rapid advancements in technologies provide various tools to analyze fruit crop genomes to better understand genetic diversity and relationships and aid in breeding. Genome-wide single nucleotide polymorphism (SNP) genotyping arrays offer highly multiplexed assays at a relatively low cost per data po...
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| Format: | Article |
| Language: | English |
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MDPI AG
2024-02-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/13/5/691 |
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| author | Yoko Hiraoka Sergio Pietro Ferrante Guohong Albert Wu Claire T. Federici Mikeal L. Roose |
| author_facet | Yoko Hiraoka Sergio Pietro Ferrante Guohong Albert Wu Claire T. Federici Mikeal L. Roose |
| author_sort | Yoko Hiraoka |
| collection | DOAJ |
| description | Rapid advancements in technologies provide various tools to analyze fruit crop genomes to better understand genetic diversity and relationships and aid in breeding. Genome-wide single nucleotide polymorphism (SNP) genotyping arrays offer highly multiplexed assays at a relatively low cost per data point. We report the development and validation of 1.4M SNP Axiom<sup>®</sup> Citrus HD Genotyping Array (Citrus 15AX 1 and Citrus 15AX 2) and 58K SNP Axiom<sup>®</sup> Citrus Genotyping Arrays for <i>Citrus</i> and close relatives. SNPs represented were chosen from a citrus variant discovery panel consisting of 41 diverse whole-genome re-sequenced accessions of <i>Citrus</i> and close relatives, including eight progenitor citrus species. SNPs chosen mainly target putative genic regions of the genome and are accurately called in both <i>Citrus</i> and its closely related genera while providing good coverage of the nuclear and chloroplast genomes. Reproducibility of the arrays was nearly 100%, with a large majority of the SNPs classified as the most stringent class of markers, “<i>PolyHighResolution</i>” (PHR) polymorphisms. Concordance between SNP calls in sequence data and array data average 98%. Phylogenies generated with array data were similar to those with comparable sequence data and little affected by 3 to 5% genotyping error. Both arrays are publicly available. |
| first_indexed | 2024-04-25T00:21:47Z |
| format | Article |
| id | doaj.art-08f67430fe7f444cb8ff1d44ac515143 |
| institution | Directory Open Access Journal |
| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-04-25T00:21:47Z |
| publishDate | 2024-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Plants |
| spelling | doaj.art-08f67430fe7f444cb8ff1d44ac5151432024-03-12T16:52:59ZengMDPI AGPlants2223-77472024-02-0113569110.3390/plants13050691Development and Assessment of SNP Genotyping Arrays for Citrus and Its Close RelativesYoko Hiraoka0Sergio Pietro Ferrante1Guohong Albert Wu2Claire T. Federici3Mikeal L. Roose4Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USADepartment of Botany and Plant Sciences, University of California, Riverside, CA 92521, USAUS Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USADepartment of Botany and Plant Sciences, University of California, Riverside, CA 92521, USADepartment of Botany and Plant Sciences, University of California, Riverside, CA 92521, USARapid advancements in technologies provide various tools to analyze fruit crop genomes to better understand genetic diversity and relationships and aid in breeding. Genome-wide single nucleotide polymorphism (SNP) genotyping arrays offer highly multiplexed assays at a relatively low cost per data point. We report the development and validation of 1.4M SNP Axiom<sup>®</sup> Citrus HD Genotyping Array (Citrus 15AX 1 and Citrus 15AX 2) and 58K SNP Axiom<sup>®</sup> Citrus Genotyping Arrays for <i>Citrus</i> and close relatives. SNPs represented were chosen from a citrus variant discovery panel consisting of 41 diverse whole-genome re-sequenced accessions of <i>Citrus</i> and close relatives, including eight progenitor citrus species. SNPs chosen mainly target putative genic regions of the genome and are accurately called in both <i>Citrus</i> and its closely related genera while providing good coverage of the nuclear and chloroplast genomes. Reproducibility of the arrays was nearly 100%, with a large majority of the SNPs classified as the most stringent class of markers, “<i>PolyHighResolution</i>” (PHR) polymorphisms. Concordance between SNP calls in sequence data and array data average 98%. Phylogenies generated with array data were similar to those with comparable sequence data and little affected by 3 to 5% genotyping error. Both arrays are publicly available.https://www.mdpi.com/2223-7747/13/5/691<i>Citrus</i>genotyping arrayplant breedinggermplasmsingle nucleotide polymorphism |
| spellingShingle | Yoko Hiraoka Sergio Pietro Ferrante Guohong Albert Wu Claire T. Federici Mikeal L. Roose Development and Assessment of SNP Genotyping Arrays for Citrus and Its Close Relatives Plants <i>Citrus</i> genotyping array plant breeding germplasm single nucleotide polymorphism |
| title | Development and Assessment of SNP Genotyping Arrays for Citrus and Its Close Relatives |
| title_full | Development and Assessment of SNP Genotyping Arrays for Citrus and Its Close Relatives |
| title_fullStr | Development and Assessment of SNP Genotyping Arrays for Citrus and Its Close Relatives |
| title_full_unstemmed | Development and Assessment of SNP Genotyping Arrays for Citrus and Its Close Relatives |
| title_short | Development and Assessment of SNP Genotyping Arrays for Citrus and Its Close Relatives |
| title_sort | development and assessment of snp genotyping arrays for citrus and its close relatives |
| topic | <i>Citrus</i> genotyping array plant breeding germplasm single nucleotide polymorphism |
| url | https://www.mdpi.com/2223-7747/13/5/691 |
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