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. 2024 Feb 29;13(5):691.
doi: 10.3390/plants13050691.

Development and Assessment of SNP Genotyping Arrays for Citrus and Its Close Relatives

Yoko Hiraoka  1 , Sergio Pietro Ferrante  1 , Guohong Albert Wu  2 , Claire T Federici  1 , Mikeal L Roose  1
Affiliations

Development and Assessment of SNP Genotyping Arrays for Citrus and Its Close Relatives

Yoko Hiraoka et al. Plants (Basel). .

Abstract

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® Citrus HD Genotyping Array (Citrus 15AX 1 and Citrus 15AX 2) and 58K SNP Axiom® Citrus Genotyping Arrays for Citrus and close relatives. SNPs represented were chosen from a citrus variant discovery panel consisting of 41 diverse whole-genome re-sequenced accessions of Citrus and close relatives, including eight progenitor citrus species. SNPs chosen mainly target putative genic regions of the genome and are accurately called in both Citrus 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, "PolyHighResolution" (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.

Keywords: Citrus; genotyping array; germplasm; plant breeding; single nucleotide polymorphism.

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Conflict of interest statement

The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript; or in the decision to publish the results.

Figures

Figure 1
Figure 1
Proportion of markers on the Axiom® Citrus HD Genotyping Array (a) and the Axiom® Citrus Genotyping Array (b) classified in 6 categories by the Axiom Analysis Suite with default settings. Categories of markers are PolyHighResolution (yellow), OTV (Off Target Variant, gray), CallRateBelowThreshold (orange), Hemizygous (Red), other (green), and MonoHighResolution (blue).
Figure 2
Figure 2
Genome-wide SNP distributions for the Axiom® Citrus HD Genotyping Array, the Axiom® Citrus Genotyping Array, and heterozygous marker distribution of selected accessions. Gene density of C. clementina was binned in 50 kb windows (blue), SNP density distribution of the Axiom® Citrus Genotyping Array (red), and the Axiom® Citrus HD Genotyping Array (yellow) on each of nine chromosomes from data binned in non-overlapping 50 kb windows. Distributions of heterozygous markers for Chandler pummelo (green), sweet orange (purple), and Pomeroy trifoliate (dark blue) on the Axiom® Citrus Genotyping Array data were binned in 50 kb windows. There are 4554 heterozygous markers in Chandler pummelo, 18,159 heterozygous markers in sweet orange, and 1293 heterozygous markers in Pomeroy trifoliate.
Figure 3
Figure 3
Comparison of percent heterozygosity estimated with sequence data and array data. Percent heterozygosity (proportion of 19 million variable sites called heterozygous in sequence data) was estimated for 38 accessions included in the citrus discovery panel (see Table S1 for abbreviations). The correlation between sequence data and array data for estimated percent heterozygosity is shown in the plot (upper right corner) with an R2 value of 0.7516.
Figure 4
Figure 4
Genotyping call comparison between sequencing data and Axiom® Citrus HD Genotyping Array data for 17 accessions from citrus variant discovery panel that were also genotyped with the Axiom® Citrus HD Genotyping Array. Genotyping calls at 635,809 PHR loci were considered.
Figure 5
Figure 5
Reproducibility of genotyping data between the Axiom® Citrus HD Genotyping Array and the Axiom® Citrus Genotyping Array was assessed using 36 accessions that were analyzed with both arrays. Genotyping calls at 51,296 PHR loci were considered. Figure shows X-axis ranging from 93% to 100%.
Figure 6
Figure 6
PCA of citrus variant discovery panel and accessions genotyped with the Axiom® Citrus HD Genotyping Array. (a) PCA was carried out with 196 genomic DNA samples from the CVC (gray) genotyped at PHR loci with the Axiom® Citrus HD Genotyping Array. Accessions representing the citrus variant discovery panel are highlighted in yellow. PC1 (35.6%), PC2 (22.5%), and PC3 (4.1%) explained 62.2% of the total variation that exists in the data. The individuals in the citrus variant discovery panel are shown (orange). (b) Cumulative proportion calculated for PCs.
Figure 7
Figure 7
PCA of 871 diploid accessions in the CVC genotyped with the Axiom® Citrus Genotyping Array at PHR loci. Accessions included 20 citrons (orange), 94 mandarins (light blue), 58 pummelos (blue), 7 papedas (yellow), 6 kumquats (pink), 11 kumquat hybrids (brown), 33 trifoliates (red), 44 trifoliate hybrids (purple), 4 citrus relatives (green), and 594 others (gray). PC1 (30.1%), PC2 (18.5%), and PC3 (11.1%) explained 59.7% of the total variation that exists in the data. (a) PCA PC1 vs. PC2. (b) PCA PC2 vs. PC3. (c) PCA PC1 vs. PC3. (d) PCA of clonally propagated accessions: navel oranges (orange), Valencia oranges (dark blue), sweet oranges (red), satsuma mandarins (purple), clementine mandarins (green), and Eureka/Lisbon lemons (blue). (e) Eigenvalues calculated for PCA.
Figure 8
Figure 8
Maximum likelihood phylogeny trees of 26 accessions of Citrus and close relatives in the citrus variant discovery panel. Maximum likelihood trees were generated by pipeline SNPhylo and visualized by FigTree v1.4.3. Bootstrap values based on 1000 replications. Bootstrap values above 90% are indicated as bold lines. Tree generated by Axiom® Citrus Genotyping Array data with 41,626 concatenated SNPs on the left and tree generated from sequence data with 32,754 SNPs that were also analyzed with Axiom® Citrus Genotyping Array on the right.
Figure 9
Figure 9
Maximum likelihood phylogeny tree of 87 non-admixed accessions in Citrus and close relatives with the Axiom® Citrus Genotyping Array data on 41,626 concatenated SNPs. Bootstrap values of above 90% are indicated by bold lines.
Figure 10
Figure 10
Workflow for citrus variant discovery panel selection, SNP detection, filtering, validation, and final selection of SNPs for Axiom® Citrus HD Genotyping Array and Axiom® Citrus Genotyping Array.
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References

    1. FAO . FAO Statistical Yearbook: World Food and Agriculture. FAO; Roma, Italy: 2013.
    1. FAO FAOstat. 2020. [(accessed on 23 December 2023)]. Available online: https://www.fao.org/faostat/
    1. United Nations . Food and Agriculture Organization of the United Nations (FAO) In: United Nations, editor. Yearbook of the United Nations 1995 (UN) United Nations; New York, NY, USA: 1995. pp. 1469–1472.
    1. Tripoli E., Guardia M.L., Giammanco S., Majo D.D., Giammanco M. Citrus flavonoids: Molecular structure, biological activity and nutritional properties: A review. Food Chem. 2007;104:466–479. doi: 10.1016/j.foodchem.2006.11.054. - DOI
    1. Xu Q., Chen L.L., Ruan X., Chen D., Zhu A., Chen C., Bertrand D., Jiao W.B., Hao B.H., Lyon M.P., et al. The draft genome of sweet orange (Citrus sinensis) Nat. Genet. 2013;45:59–66. doi: 10.1038/ng.2472. - DOI - PubMed

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