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High-throughput genotyping in citrus accessions using an SNP genotyping array

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Abstract

We developed a 384 multiplexed SNP array, named CitSGA-1, for the genotyping of Citrus cultivars, and evaluated the performance and reliability of the genotyping. SNPs were surveyed by direct sequence comparison of the sequence tagged site (STS) fragment amplified from genomic DNA of cultivars representing the genetic diversity of citrus breeding in Japan. Among 1497 SNPs candidates, 384 SNPs for a high-throughput genotyping array were selected based on physical parameters of Illumina’s bead array criteria. The assay using CitSGA-1 was applied to a hybrid population of 88 progeny and 103 citrus accessions for breeding in Japan, which resulted in 73,726 SNP calls. A total of 351 SNPs (91 %) could call different genotypes among the DNA samples, resulting in a success rate for the assay comparable to previously reported rates for other plant species. To confirm the reliability of SNP genotype calls, parentage analysis was applied, and it indicated that the number of reliable SNPs and corresponding STSs were 276 and 213, respectively. The multiplexed SNP genotyping array reported here will be useful for the efficient construction of linkage map, for the detection of markers for marker-assisted breeding, and for the identification of cultivars.

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References

  1. Close TJ, Wanamaker S, Lyon M, Mei G, Davies C, Roose ML (2006) A GeneChip® for citrus. In: Plant & Animal Genome XIV Conference, San Diego, CA, W82

  2. Close TJ, Bhat PR, Lonardi S et al (2009) Development and implementation of high-throughput SNP genotyping in barley. BMC Genom 10:582

  3. Eckert AJ, Pande B, Ersoz ES et al (2009) High-throughput genotyping and mapping of single nucleotide polymorphisms in loblolly pine (Pinus taeda L.). Tree Genet Genom 5(1):225–234

  4. Fan JB, Oliphant A, Shen R et al (2003) Highly parallel SNP genotyping. Cold Spring Harb Symp Quant Biol 68:69–78

  5. Federici CT, Fang DQ, Scora RW, Roose ML (1998) Phylogenetic relationships within the genus Citrus (Rutaceae) and related genera as revealed by RFLP and RAPD analysis. Theor Appl Genet 96:812–822

  6. Feltus FA, Wan J, Schulze SR, Estill JC, Jiang N, Paterson AH (2004) An SNP resource of rice genetics and breeding based on subspecies indica and japonica genome alignment. Genome Res 14:1812–1819

  7. Fujii H, Shimada T, Endo T, Omura M (2003) Development of relational database system for Citrus ESTs. Bull Natl Inst Fruit Tree Sci 2:91–99

  8. Fujii H, Ogata T, Shimada T, Endo T, Shimizu T, Omura M (2007) Development of a novel algorithm and the computer program for the identification of minimal marker sets of discriminating DNA markers for efficient cultivar identification. In: Plant & Animal Genomes XV Conference, San Diego, CA, P322

  9. Fujii H, Ogata T, Sugiyama A, Shimada T, Endo T, Shimizu T, Omura M (2010a) Development of software to improve the design efficiency of the intron-spanning PCR primer from EST utilizing genomic information of Arabidopsis thaliana. In: Plant & Animal Genomes XVIII Conference, San Diego, CA, P860: Software

  10. Fujii H, Yamashita H, Hosaka F, Terakami S, Yamamoto T (2010b) Development of a software to presume the parent–child relationship using the result of DNA maker typing. Hort Res (Japan) 9(suppl1):34

  11. Goff SA, Ricke D, Lan TH et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296:92–100

  12. Hyten DL, Song Q, Choi IY et al (2008) High-throughput genotyping with the GoldenGate® assay in the complex genome of soybean. Theor Appl Genet 116:945–952

  13. Jiang D, Ye Q, Wang F, Cao L (2010) The mining of citrus EST-SNP and its application in cultivar discrimination. Agr Sci China 9:179–190

  14. Kato M, Ikoma Y, Matsumoto H, Sugiura M, Hyodo H, Yano M (2004) Accumulation of carotenoids and expression of carotenoid biosynthetic genes during maturation in citrus fruit. Plant Physiol 134:824–837

  15. Kwok PY (2001) Methods for genotyping single nucleotide polymorphisms. Ann Rev Hum Genet 2:235–258

  16. Lam LKT, Hasegawa S (1989) Inhibition of benzo[α]pyrene-induced fore-stomach neoplasia in mice by citrus limonoids. Nutr Canc 12:4347

  17. Lam LKT, Li Y, Hasegawa S (1989) Effects of citrus limonoids on glutathione S-transferase activity in mice. J Agric Food Chem 37:878–880

  18. Masouleh AK, Waters DL, Reinke RF, Henry RJ (2009) A high-throughput assay for rapid and simultaneous analysis of perfect markers for important quality and agronomic traits in rice using multiplexed MALDI-TOF mass spectrometry. Plant Biotechnol J 7:355–363

  19. Murakami A, Nakamura Y, Torikai K et al (2000) Inhibitory effect of citrus nobiletin on phorbol ester-induced skin inflammation, oxidative stress, and tumor-promotion in mice. Cancer Res 60:5059–5066

  20. Oiyama I, Kobayashi S (1993) Haploids obtained from diploid X triploid crosses of citrus. J Japan Soc Hort Sci 62:89–93

  21. Ollitrault P, Terol J, Chen C et al (2011) A reference linkage map of C. clementina based on SNPs, SSRs and InDels. Plant & Animal Genome XIV Conference, January 15–19, 2011, San Diego, CA

  22. Omura M, Ueda T, Kita M, Komatsu A, Takanokura Y, Shimada T, Endo T, Nesumi H, Yoshida T (2003) EST mapping of Citrus. Proc Intl Soc Citricult IX Congr 2000:71–74

  23. Pavy N, Pelgas B, Beauseigle S, Blais S, Gagnon F, Gosselin I, Lamothe M, Isabel N, Bousquet J (2008) Enhancing genetic mapping of complex genomes through the design of highly-multiplexed SNP arrays: application to the large and unsequenced genomes of white spruce and black spruce. BMC Genom 9:21

  24. Rickert AM, Kim JH, Meyer S, Nagel A, Ballvora A, Oefner PJ, Gebhardt C (2003) First-generation SNP/InDel markers tagging loci for pathogen resistance in the potato genome. Plant Biotechnol J 1:399–410

  25. Rostoks N, Ramsay L, Mackenzie K et al (2006) Recent history of artificial outcrossing facilitates whole-genome association mapping in elite inbred crop varieties. Proc Natl Acad Sci USA 103:18656–18661

  26. Russell J, Booth A, Fuller J, Horrower B, Hedley P, Machery G, Powell W (2004) A comparison of sequence-based polymorphism and haplotype content in transcribed and anonymous regions of the barley genome. Genome 47:389–398

  27. Steemers FJ, Chang W, Lee G, Barker DL, Shen R, Gunderson KL (2006) Whole-genome genotyping with the single-base extension assay. Nat Methods 3:31–33

  28. Sugiyama A, Omura M, Matsumoto H, Shimada T, Fujii H, Endo T, Shimizu T, Nesumi H, Ikoma Y (2011) Quantitative trait loci (QTL) analysis of carotenoid content in Citrus fruit. J Japan Soc Hort Sci 80:136–144

  29. Syvänen AC (2005) Toward genome-wide SNP genotyping. Nat Genet 37(Suppl):S5–S10

  30. Tsushima M, Maoka T, Katsuyama M, Kozuka M, Matsuno T, Tokuda H, Nishino H, Iwashima A (1995) Inhibitory effect of natural carotenoids on Epstein–Barr virus activation activity of a tumor promoter in Raji cells. A screening study for anti-tumor promoters. Biol Pharm Bull 18:227–233

  31. Tung CW, Zhao K, Wright MH et al (2010) Development of a research platform for dissecting phenotype–genotype associations in rice (Oryza spp.). Rice 3:205–217

  32. Uchiyama K, Ujino-Ihara T, Ueno S et al (2011) Single nucleotide polymorphism in Cryptomeria japonica: their discovery and validation for genome mapping and diversity studies. Tree Genet Genom. doi:10.1007/s11295-012-0508-5

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Acknowledgment

This work was funded by the National Agriculture and Bio-oriented Research Organization, Japan.

Author information

Correspondence to Hiroshi Fujii.

Additional information

Communicated by W. Guo

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Fujii, H., Shimada, T., Nonaka, K. et al. High-throughput genotyping in citrus accessions using an SNP genotyping array. Tree Genetics & Genomes 9, 145–153 (2013). https://doi.org/10.1007/s11295-012-0542-3

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Keywords

  • High throughput
  • SNP
  • Genotyping
  • Citrus
  • Parentage