Abstract
A high-density genetic map, an essential tool for comparative genomic studies and quantitative trait locus fine mapping, can also facilitate genome sequence assembly. The sequence-based marker technology known as restriction site-associated DNA (RAD) enables synchronous, single nucleotide polymorphism marker discovery, and genotyping using massively parallel sequencing. We constructed a high-density linkage map for carnation (Dianthus caryophyllus L.) based on simple sequence repeat (SSR) markers in combination with RAD markers developed by double-digest RAD sequencing (ddRAD-seq). A total of 2404 (285 SSR and 2119 RAD) markers could be assigned to 15 linkage groups spanning 971.5 cM, with an average marker interval of 0.4 cM. The total length of scaffolds with identified map positions was 95.6 Mb, which is equivalent to 15.4 % of the estimated genome size. The generated map is the first SSR and RAD marker-based high-density linkage map reported for carnation. The ddRAD-seq pipeline developed in this study should also help accelerate genetic and genomics analyses and molecular breeding of carnation and other non-model crops.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Agarwal M, Shrivastava N, Padh H (2008) Advances in molecular marker techniques and their applications in plant sciences. Plant Cell Rep 27:617–631
Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One 3:e3376
Barchi L, Lanteri S, Portis E, Acquadro A, Vale G, Toppino L, Rotino GL (2011) Identification of SNP and SSR markers in eggplant using RAD tag sequencing. BMC Genomics 12:304
Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633–2635
Cai C, Cheng YF, Wu J, Zhong Y, Liu G (2015) The first high-density genetic map construction in tree peony (Paeonia Sect. Moutan) using genotyping by specific-locus amplified fragment sequencing. PLoS One 10:e0128584
Davey JW, Blaxter ML (2010) RADSeq: next-generation population genetics. Brief Funct Genomics 9:416–423
Davey JW, Hohenlone PA, Etter PD, Boone JQ, Catchen JM, Blaxter ML (2011) Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev 12:499–510
Lashermes P, Combes MC, Prakash NS, Trouslot P, Lorieux M, Charrier A (2001) Genetic linkage map of Coffea canephora: effect of segregation distortion and analysis of recombination rate in male and female meioses. Genome 44:589–596
Li H, Kilian A, Zhou M, Wenzl P, Huttner E, Mendham N, McIntyre L, Vaillancourt RE (2010) Construction of a high-density composite map and comparative mapping of segregation distortion regions in barley. Mol Genet Genomics 284:319–331
Li C, Bai G, Chao S, Wang Z (2015) A high-density SNP and SSR consensus map reveals segregation distortion regions in wheat. Biomed Res Int 2015:830618
Onozaki T, Tanikawa N, Taneya M, Kudo K, Funayama T, Ikeda H, Shibata M (2004) A RAPD-derived STS marker is linked to a bacterial wilt (Burkholderia caryophylli) resistance gene in carnation. Euphytica 138:255–262
Onozaki T, Yagi M, Tanase K (2015) Selection of carnation line 806-46b with both ultra-long vase life and ethylene resistance. Hort J 84:58–68
Peterson BK, Weber JN, Kay EH, Fisher HS, Hoekstra HE (2012) Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS One 7:e37135
Scovel G, Ben-Meir H, Ovadis M, Itzhaki H, Vainstein A (1998) RAPD and RFLP markers tightly linked to the locus controlling carnation (Dianthus caryophyllus) flower type. Theor Appl Genet 96:117–122
Shirasawa K, Hirakawa H (2013) DNA marker applications to molecular genetics and genomics in tomato. Breed Sci 63:21–30
Shirasawa K, Hirakawa H, Isobe S (2016) Analytical workflow of double-digest restriction site-associated DNA sequencing based on empirical and in silico optimization in tomato. DNA Res. doi:10.1093/dnares/dsw004
Sun R, Chang Y, Yang F, Wang Y, Li H, Zhao Y, Chen D, Wu T, Zhang X, Han Z (2015) A dense SNP genetic map constructed using restriction site-associated DNA sequencing enables detection of QTLs controlling apple fruit quality. BMC Genomics 16:747
Tanase K, Nishitani C, Hirakawa H, Isobe S, Tabata S, Ohmiya A, Onozaki T (2012) Transcriptome analysis of carnation (Dianthus caryophyllus L.) based on next-generation sequencing technology. BMC Genomics 13:292
Wu J, Li LT, Li M, Khan MA, Li XG, Chen H, Yin H, Zhang SL (2014) High-density genetic linkage map construction and identification of fruit-related QTLs in pear using SNP and SSR markers. J Exp Bot 65:5771–5781
Yagi M (2015) Recent progress in genomic analysis of ornamental plants, with a focus on carnation. Hort J 84:2–13
Yagi M, Onozaki T, Taneya M, Watanabe H, Yoshimura T, Yoshinari T, Ochiai Y, Shibata M (2006) Construction of a genetic linkage map for the carnation by using RAPD and SSR markers and mapping quantitative trait loci (QTL) for resistance to bacterial wilt caused by Burkholderia caryophylli. J Japan Soc Hort Sci 75:166–172
Yagi M, Kimura T, Yamamoto T, Isobe S, Tabata S, Onozaki T (2012) QTL analysis for resistance to bacterial wilt (Burkholderia caryophylli) in carnation (Dianthus caryophyllus) using an SSR-based genetic linkage map. Mol Breed 30:495–509
Yagi M, Yamamoto T, Isobe S, Tabata S, Hirakawa H, Yamaguchi H, Tanase K, Onozaki T (2013) Construction of a reference genetic linkage map in carnation (Dianthus caryophyllus L.). BMC Genomics 14:734
Yagi M, Kosugi S, Hirakawa H, Ohmiya A, Tanase K, Harada T, Kishimoto K, Nakayama M, Ichimura K, Onozaki T, Yamaguchi H, Sasaki N, Miyahara T, Nishizaki Y, Ozeki Y, Nakamura N, Suzuki T, Tanaka Y, Sato S, Shirasawa K, Isobe S, Miyamura Y, Watanabe A, Nakayama S, Kishida Y, Kohara M, Tabata S (2014a) Sequence analysis of the genome of carnation (Dianthus caryophyllus L.). DNA Res 21:231–241
Yagi M, Yamamoto T, Isobe S, Tabata S, Hirakawa H, Yamaguchi H, Tanase K, Onozaki T (2014b) Identification of tightly linked SSR markers for flower type in carnation (Dianthus caryophyllus L.). Euphytica 198:175–183
Yamamoto T, Terakami S (2016) Genomics of pear and other Rosaceae fruit trees. Breed Sci 66:148–159
Acknowledgments
We thank Dr. Shingo Terakami, Institute of Fruit Tree and Tea Science, NARO, who gave us helpful advice and provided data processing support. We are grateful to Miss Y. Yamazaki and Miss M. Nakazawa for technical assistance. This work was funded by a genome-support grant from the National Institute of Agrobiological Sciences (NIAS), JSPS KAKENHI (grant no. 26850022) and a grant from the Ministry of Agriculture, Forestry, and Fisheries of Japan (Genomics-based Technology for Agricultural Improvement, DHR4).
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Yagi, M., Shirasawa, K., Waki, T. et al. Construction of an SSR and RAD Marker-Based Genetic Linkage Map for Carnation (Dianthus caryophyllus L.). Plant Mol Biol Rep 35, 110–117 (2017). https://doi.org/10.1007/s11105-016-1010-2
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11105-016-1010-2