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: Genes, Genomes, Genetics

Volumn 4, Issue 10, 2014, Pages 1971-1979

  Li, Xuehui ^a   Wei, Yanling ^a   Acharya, Ananta ^a   Jiang, Qingzhen ^a   Kang, Junmei ^b   Charles Brummer, E ^c  

^a PLANT BIOLOGY DIVISION   (United States)

^b INSTITUTE OF PLANT PROTECTION   (China)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Autotetraploid alfalfa; Genetic linkage map; Genotyping bysequencing

Indexed keywords

ALFALFA; ARTICLE; AUTOTETRAPLOID; BARREL MEDIC; BREEDING; COST CONTROL; GENE ASSIGNMENT; GENE FREQUENCY; GENETIC LINKAGE; GENETIC MARKER; GENOME ANALYSIS; GENOTYPE; GENOTYPING BY SEQUENCING; HAPLOTYPE; HAPLOTYPE MAP; HETEROZYGOTE; HIGH THROUGHPUT SEQUENCING; HOMOZYGOTE; NONHUMAN; PLANT CHROMOSOME; PLANT GENOME; POPULATION GENETICS; SEGREGATION DISTORTION; SIMPLE SEQUENCE REPEAT; SINGLE NUCLEOTIDE POLYMORPHISM; TETRAPLOIDY; CHROMOSOME MAP; CHROMOSOME SEGREGATION; DNA SEQUENCE; GENETICS;

MEDICAGO SATIVA; MEDICAGO TRUNCATULA;

MICROSATELLITE DNA;

CHROMOSOME MAPPING; CHROMOSOME SEGREGATION; GENETIC LINKAGE; GENOME, PLANT; GENOTYPE; HAPLOTYPES; MEDICAGO SATIVA; MEDICAGO TRUNCATULA; MICROSATELLITE REPEATS; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA; TETRAPLOIDY;

EID: 84908459291     PISSN: None     EISSN: 21601836     Source Type: Journal    
DOI: 10.1534/g3.114.012245     Document Type: Article

References (43)

1. Antanaviciute, L., F. Fernandez-Fernandez, J. Jansen, E. Banchi, K. M. Evans et al., 2012 Development of a dense SNP-based linkage map of an apple rootstock progeny using the Malus Infinium whole genome genotyping array. BMC Genomics 13: 203.
2. Arends, D., P. Prins, R. C. Jansen, and K. W. Broman, 2010 R/qtl: highthroughput multiple QTL mapping. Bioinformatics 26: 2990-2992.
3. Blondon, F., D. Marie, S. Brown, and A. Kondorosi, 1994 Genome size and base composition in Medicago sativa and M. truncatula species. Genome 37: 264-270.
4. Bowers, J. E., E. Bachlava, R. L. Brunick, L. H. Rieseberg, S. J. Knapp et al., 2012 Development of a 10,000 locus genetic map of the sunflower genome based on multiple crosses. G3: Genes, Genomes. Genetics 2: 721-729.
5. Brouwer, D. J., and T. C. Osborn, 1999 A molecular marker linkage map of tetraploid alfalfa (Medicago sativa L.). Theor. Appl. Genet. 99: 1194-1200.
6. Chancerel, E., J. B. Lamy, I. Lesur, C. Noirot, C. Klopp et al., 2013 Highdensity linkage mapping in a pine tree reveals a genomic region associated with inbreeding depression and provides clues to the extent and distribution of meiotic recombination. BMC Biol. 11: 50.
7. Choi, H. K., D. Kim, T. Uhm, E. Limpens, H. Lim et al., 2004 A sequencebased genetic map of Medicago truncatula and comparison of marker colinearity with M. sativa. Genetics 166: 1463-1502.
8. Delourme, R., C. Falentin, B. F. Fomeju, M. Boillot, G. Lassalle et al., 2013 High-density SNP-based genetic map development and linkage disequilibrium assessment in Brassica napus L. BMC Genomics 14: 120.
9. Elshire, R. J., J. C. Glaubitz, Q. Sun, J. A. Poland, K. Kawamoto et al., 2011 A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One 6: e19379.
10. Felcher, K. J., J. J. Coombs, A. N. Massa, C. N. Hansey, J. P. Hamilton et al., 2012 Integration of two diploid potato linkage maps with the potato genome sequence. PLoS One 7: e36347.
11. Grattapaglia, D., and R. Sederoff, 1994 Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudo-testcross: mapping strategy and RAPD markers. Genetics 137: 1121-1137.
12. Griffiths, A. G., B. A. Barrett, D. Simon, A. K. Khan, P. Bickerstaff et al., 2013 An integrated genetic linkage map for white clover (Trifolium repens L.) with alignment to Medicago. BMC Genomics 14: 388.
13. Hackett, C. A., and L. B. Broadfoot, 2003 Effects of genotyping errors, missing values and segregation distortion in molecular marker data on the construction of linkage maps. Heredity 90: 33-38.
14. Hackett, C. A., I. Milne, J. E. Bradshaw, and Z. Luo, 2007 TetraploidMap for Windows: linkage map construction and QTL mapping in autotetraploid species. J. Hered. 98: 727-729.
15. Han, Y., Y. Kang, I. Torres-Jerez, F. Cheung, C. D. Town et al., 2011 Genome-wide SNP discovery in tetraploid alfalfa using 454 sequencing and high resolution melting analysis. BMC Genomics 12: 350.
16. Julier, B., S. Flajoulot, P. Barre, G. Cardinet, S. Santoni et al., 2003 Construction of two genetic linkage maps in cultivated tetraploid alfalfa (Medicago sativa) using microsatellite and AFLP markers. BMC Plant Biol. 3: 9.
17. Kamphuis, L. G., A. H. Williams, N. K. D'Souza, T. Pfaff, S. R. Ellwood et al., 2007 The Medicago truncatula reference accession A17 has an aberrant chromosomal configuration. New Phytol. 174: 299-303.
18. Khu, D. M., R. Reyno, Y. Han, P. X. Zhao, J. H. Bouton et al., 2013 Identification of aluminum tolerance quantitative trait loci in tetraploid alfalfa. Crop Sci. 53: 148-163.
19. Langmead, B., C. Trapnell, M. Pop, and S. L. Salzberg, 2009 Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10: R25.
20. Li, X., and E. C. Brummer, 2012 Applied genetics and genomics in alfalfa breeding. Agronomy 2: 40-61.
21. Li, X., X. Wang, Y. Wei, and E. C. Brummer, 2011 Prevalence of segregation distortion in diploid alfalfa and its implications for genetics and breeding applications. Theor. Appl. Genet. 123: 667-679.
22. Li, X., A. Acharya, A. D. Farmer, J. A. Crow, A. K. Bharti et al., 2012 Prevalence of single nucleotide polymorphism among 27 diverse alfalfa genotypes as assessed by transcriptome sequencing. BMC Genomics 13: 568.
23. Li, X., Y. Han, Y. Wei, A. Acharya, A. D. Farmer et al., 2014 Development of an alfalfa SNP array and its use to evaluate patterns of population structure and linkage disequilibrium. PLoS ONE 9: e84329.
24. Lu, F., A. E. Lipka, J. Glaubitz, R. Elshire, J. H. Cherney et al., 2013 Switchgrass genomic diversity, ploidy, and evolution: novel insights from a network-based SNP discovery protocol. PLoS Genet. 9: e1003215.
25. Michaud, R., W. F. Lehman, and M. D. Rumbaugh, 1988 World distribution and historical development, pp. 31-32 in Alfalfa and Alfalfa Improvement, edited by A. Hanson. American Society of Agronomy, Crop Science Society of America, Soil Science Society of America, Madison, WI.
26. Musial, J. M., J. M. Mackie, D. J. Armour, H. T. Phan, S. E. Ellwood et al., 2007 Identification of QTL for resistance and susceptibility to Stagonospora meliloti in autotetraploid lucerne. Theor. Appl. Genet. 114: 1427-1435.
27. Paterson, A. H., J. E. Bowers, R. Bruggmann, I. Dubchak, J. Grimwood et al., 2009 The Sorghum bicolor genome and the diversification of grasses. Nature 457: 551-556.
28. Poland, J. A., P. J. Brown, M. E. Sorrells, and J. L. Jannink, 2012a Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PLoS One 7: e32253.
29. Poland, J., J. Endelman, J. Dawson, J. Rutkoski, S. Y. Wu et al., 2012b Genomic selection in wheat breeding using genotyping-bysequencing. Plant Genome 5: 103-113.
30. Robins, J. G., D. Luth, I. A. Campbell, G. R. Bauchan, C. L. He et al., 2007 Genetic mapping of biomass production in tetraploid alfalfa. Crop Sci. 47: 1-10.
31. Schuelke, M., 2000 An economic method for the fluorescent labeling of PCR fragments. Nat. Biotechnol. 18: 233-234.
32. Sim, S. C., G. Durstewitz, J. Plieske, R. Wieseke, M. W. Ganal et al., 2012 Development of a large SNP genotyping array and generation of high-density genetic maps in tomato. PLoS One 7: e40563.
33. Sledge, M. K., I. M. Ray, and G. Jiang, 2005 An expressed sequence tag SSR map of tetraploid alfalfa (Medicago sativa L.). Theor. Appl. Genet. 111: 980-992.
34. Sonah, H., M. Bastien, E. Iquira, A. Tardivel, G. Legare et al., 2013 An improved genotyping by sequencing (GBS) approach offering increased versatility and efficiency of SNP discovery and genotyping. PLoS One 8: e54603.
35. Spindel, J., M. Wright, C. Chen, J. Cobb, J. Gage et al., 2013 Bridging the genotyping gap: using genotyping by sequencing (GBS) to add highdensity SNP markers and new value to traditional bi-parental mapping and breeding populations. Theor. Appl. Genet. 126: 2699-2716.
36. Tavoletti, S., F. Veronesi, and T. C. Osborn, 1996 RFLP linkage map of an alfalfa meiotic mutant based on an F1 population. J. Hered. 87: 167-170.
37. Teuber, L. R., K. L. Taggard, L. K. Gibbs, M. H. McCaslin, M. A. Peterson et al., 1998 Fall dormancy, in Standard Tests to Characterize Alfalfa Cultivars, Ed. 3, edited by C. C. Fox, L. Berberet, F. A. Gray, C. R. Grau, D. L. Jessen, et al. North America Alfalfa Improvement Conference, Beltsville, MD. Available at: http://www.naaic.org/stdtests/Dormancy2.html [Verified 07 September 2014].
38. Uitdewilligen, J. G., A. M. Wolters, B. D'Hoop, T. J. Borm, R. G. Visser et al., 2013 A next-generation sequencing method for genotyping-bysequencing of highly heterozygous autotetraploid potato. PLoS One 8: e62355.
39. Van Ooijen, J. W., 2011 Multipoint maximum likelihood mapping in a fullsib family of an outbreeding species. Genet. Res. 93: 343-349.
40. Voorrips, R. E., 2002 MapChart: software for the graphical presentation of linkage maps and QTLs. J. Hered. 93: 77-78.
41. Wickham, H., 2009. ggplot2: Elegant Graphics for Data Analysis. Springer, New York.
42. Yang, S. S., Z. J. Tu, F. Cheung, W. W. Xu, J. F. Lamb et al., 2011 Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems. BMC Genomics 12: 199.
43. Zhang, L., S. Wang, H. Li, Q. Deng, A. Zheng et al., 2010 Effects of missing marker and segregation distortion on QTL mapping in F2 populations. Theor. Appl. Genet. 121: 1071-1082.