A high-density SNP genetic map consisting of a complete set of homologous groups in autohexaploid sweetpotato (Ipomoea batatas)

Scientific Reports

Volumn 7, Issue , 2017, Pages

  Shirasawa, Kenta ^a   Tanaka, Masaru ^b   Takahata, Yasuhiro ^b   Ma, Daifu ^c   Cao, Qinghe ^c   Liu, Qingchang ^d   Zhai, Hong ^d   Kwak, Sang Soo ^e   Cheol Jeong, Jae ^e   Yoon, Ung Han ^f   Lee, Hyeong Un ^f   Hirakawa, Hideki ^a   Isobe, Sachiko ^a  

^a KAZUSA DNA RESEARCH INSTITUTE   (Japan)

^b NATIONAL AGRICULTURAL RESEARCH CENTER FOR KYUSHU OKINAWA REGION   (Japan)

^c INSTITUTE OF PLANT PROTECTION   (China)

^d CHINA AGRICULTURAL UNIVERSITY   (China)

^e Korea Research Institute of Bioscience and Biotechnology (KRIBB)   (South Korea)

^f National Institute of Animal Science   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

CLINICAL ARTICLE; CROP; DIPLOIDY; DNA SEQUENCE; GENE MAPPING; GENE MUTATION; GENETIC LINKAGE; HUMAN; NEXT GENERATION SEQUENCING; NONHUMAN; POLYPLOIDY; PROGENY; RESTRICTION SITE; SELFING; SINGLE NUCLEOTIDE POLYMORPHISM; SINGLE PARENT; SPECIES; SWEET POTATO; GENETICS; PLANT GENOME;

GENOME, PLANT; IPOMOEA BATATAS; POLYMORPHISM, SINGLE NUCLEOTIDE; POLYPLOIDY;

EID: 85014953118     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep44207     Document Type: Article

References (36)

1. Deschamps, S., Llaca, V. & May, G. D. Genotyping-by-sequencing in plants. Biology 1, 460-483 (2012).
2. Poland, J. A. & Rife, T. W. Genotyping-by-sequencing for plant breeding and genetics. Plant Genome 5, 92-102 (2012).
3. Kalia, R. K., Rai, M. K., Kalia, S., Singh, R. & Dhawan, A. K. Microsatellite markers: an overview of the recent progress in plants. Euphytica 117, 309-334 (2011).
4. Kumar, S., Banks, T. W. & Cloutier, S. SNP discovery through next-generation sequencing and its applications. Int. J. Plant Genomics 2012, 831460 (2012).
5. Elshire, R. J. et al. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One 6, e19379 (2011).
6. Baird, N. A. et al. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One 3, e3376 (2008).
7. Davey, J. W. et al. Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat. Rev. Genet. 12, 499-510 (2011).
8. Comai, L. The advantages and disadvantages of being polyploid. Nat. Rev. Genet. 6, 836-846 (2005).
9. Leal-Bertioli, S. et al. Tetrasomic recombination is surprisingly frequent in allotetraploid Arachis. Genetics 199, 1093-1105 (2015).
10. Gar, O. et al. An autotetraploid linkage map of rose (Rosa hybrida) validated using the strawberry (Fragaria vesca) genome sequence. PLoS One 6, e20463 (2011).
11. Hackett, C. A., McLean, K. & Bryan, G. J. Linkage analysis and QTL mapping using SNP dosage data in a tetraploid potato mapping population. PLoS One 8, e63939 (2013).
12. Li, X. et al. A saturated genetic linkage map of autotetraploid alfalfa (Medicago sativa L.) developed using genotyping-by-sequencing is highly syntenous with the Medicago truncatula genome. G3 4, 1971-1979 (2014).
13. McCallum, S. et al. Construction of a SNP and SSR linkage map in autotetraploid blueberry using genotyping by sequencing. Mol. Breed. 36, 41 (2016).
14. Hackett, C. A. & Luo, Z. W. TetraploidMap: construction of a linkage map in autotetraploid species. J. Hered. 94, 358-359 (2003).
15. Cervantes-Flores, J. C. et al. Development of a genetic linkage map and identification of homologous linkage groups in sweetpotato using multiple-dose AFLP markers. Mol. Breed. 21, 511-532 (2008).
16. Zhao, N. et al. A genetic linkage map based on AFLP and SSR markers and mapping of QTL for dry-matter content in sweetpotato. Mol. Breed. 32, 807-820 (2013).
17. Kriegner, A., Cervantes, J. C., Burg, K., Mwanga, R. O. M. & Zhang, D. A genetic linkage map of sweetpotato [Ipomoea batatas (L.) Lam. ] based on AFLP markers. Mol. Breed. 11, 169-185 (2003).
18. Li, A. X. et al. Construction of molecular linkage maps using SRAP markers in sweetpotato. Acta Agron. Sin. 36, 1286-1295 (2010).
19. Monden, Y. et al. Construction of a linkage map based on retrotransposon insertion polymorphisms in sweetpotato via highthroughput sequencing. Breed. Sci. 65, 145-153 (2015).
20. Ukoskit, K. & Thompson, P. G. Autopolyploidy versus allopolyploidy and low-density randomly amplified polymorphic DNA linkage maps of sweetpotato. J. Amer. Soc. Hort. Sci. 122, 822-828 (1997).
21. Hirakawa, H. et al. Survey of genome sequences in a wild sweet potato, Ipomoea trifida (H. B. K.) G. Don. DNA Res. 22, 171-179 (2015).
22. Peterson, B. K., Weber, J. N., Kay, E. H., Fisher, H. S. & Hoekstra, H. E. Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS One 7, e37135 (2012).
23. Shirasawa, K., Hirakawa, H. & Isobe, S. Analytical workflow of double-digest restriction site-associated DNA sequencing based on empirical and in silico optimization in tomato. DNA Res. 23, 145-153 (2016).
24. Ward, J. A. et al. Saturated linkage map construction in Rubus idaeus using genotyping by sequencing and genome-independent imputation. BMC Genomics 14, 2 (2013).
25. Bertioli, D. J. et al. The use of SNP markers for linkage mapping in diploid and tetraploid peanuts. G3 4, 89-96 (2014).
26. Shirasawa, K. et al. Integrated consensus map of cultivated peanut and wild relatives reveals structures of the A and B genomes of Arachis and divergence of the legume genomes. DNA Res. 20, 173-184 (2013).
27. Cartwright, D. A., Troggio, M., Velasco, R. & Gutin, A. Genetic mapping in the presence of genotyping errors. Genetics 176, 2521-2527 (2007).
28. Garcia, A. A. et al. SNP genotyping allows an in-depth characterisation of the genome of sugarcane and other complex autopolyploids. Sci. Rep. 3, 3399 (2013).
29. Schmieder, R. & Edwards, R. Quality control and preprocessing of metagenomic datasets. Bioinformatics 27, 863-864 (2011).
30. Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357-359 (2012).
31. Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
32. Koboldt, D. C. et al. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res. 22, 568-576 (2012).
33. Cingolani, P. et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly 6, 80-92 (2012).
34. Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156-2158 (2011).
35. Margarido, G. R., Souza, A. P. & Garcia, A. A. OneMap: software for genetic mapping in outcrossing species. Hereditas 144, 78-79 (2007).
36. Voorrips, R. E. MapChart: software for the graphical presentation of linkage maps and QTLs. J. Hered. 93, 77-78 (2002).