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

Hiraoka, Yoko; Ferrante, Sergio Pietro; Wu, Guohong Albert; Federici, Claire T.; Roose, Mikeal L.

doi:10.3390/plants13050691

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

Journal Article · 28 February 2024 · Plants

DOI: https://doi.org/10.3390/plants13050691 · OSTI ID:2370973

Hiraoka, Yoko ^[1]; Ferrante, Sergio Pietro ^[1]; Wu, Guohong Albert ^[2]; Federici, Claire T. ^[1];

^[1]

Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA

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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institute of Food and Agriculture

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 2370973

Journal Information:: Plants, Journal Name: Plants Journal Issue: 5 Vol. 13; ISSN 2223-7747

Publisher:: MDPICopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
citrus
genotyping array
plant breeding
germplasm
single nucleotide polymorphism

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

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