DArT markers for the rye genome - genetic diversity and mapping
Tóm tắt
Implementation of molecular breeding in rye (Secale cereale L.) improvement programs depends on the availability of high-density molecular linkage maps. However, the number of sequence-specific PCR-based markers available for the species is limited. Diversity Arrays Technology (DArT) is a microarray-based method allowing for detection of DNA polymorphism at several thousand loci in a single assay without relying on DNA sequence information. The objective of this study was the development and application of Diversity Arrays technology for rye. Using the Pst I/Taq I method of complexity reduction we created a rye diversity panel from DNA of 16 rye varieties and 15 rye inbred lines, including parents of a mapping population consisting of 82 recombinant inbred lines. The usefulness of a wheat diversity panel for identification of DArT markers for rye was also demonstrated. We identified 1022 clones that were polymorphic in the genotyped ILs and varieties and 1965 clones that differentiated the parental lines L318 and L9 and segregated in the mapping population. Hierarchical clustering and ordination analysis were performed based on the 1022 DArT markers to reveal genetic relationships between the rye varieties and inbred lines included in the study. Chromosomal location of 1872 DArT markers was determined using wheat-rye addition lines and 1818 DArT markers (among them 1181 unique, non-cosegregating) were placed on a genetic linkage map of the cross L318 × L9, providing an average density of one unique marker every 2.68 cM. This is the most saturated rye linkage map based solely on transferable markers available at the moment, providing rye breeders and researches with a better choice of markers and a higher probability of finding polymorphic markers in the region of interest. The Diversity Arrays Technology can be efficiently and effectively used for rye genome analyses - assessment of genetic similarity and linkage mapping. The 11520-clone rye genotyping panel with several thousand markers with determined chromosomal location and accessible through an inexpensive genotyping service is a valuable resource for studies on rye genome organization and in molecular breeding of the species.
Tài liệu tham khảo
Devos KM, Atkinson MD, Chinoy CN, Francis HA, Harcourt RL, Koebner RMD, Liu CJ, Masojæ P, Xie DX, Gale MD: Chromosomal rearrangements in the rye genome relative to that of wheat. Theor Appl Genet. 1993, 85: 673-680. 10.1007/BF00225004.
Ma XF, Wanous MK, Houchins K, Rodriguez Milla MA, Goicoechea PG, Wang Z, Xie M, Gustafson JP: Molecular linkage mapping in rye (Secale cereale L). Theor Appl Genet. 2001, 102: 517-523. 10.1007/s001220051676.
Korzun V, Malyshev S, Voylokov AV, Börner A: A genetic map of rye (Secale cereale L.) combining RFLP, isozyme, protein, microsatellite and gene loci. Theor Appl Genet. 2001, 102: 709-717. 10.1007/s001220051701.
Khlestkina EK, Than MHM, Pestsova EG, Röder MS, Malyshev SV, Korzun V, Börner A: Mapping of 99 new microsatellite-derived loci in rye (Secale cereale L.) including 39 expressed sequence tags. Theor Appl Genet. 2004, 109: 725-732. 10.1007/s00122-004-1659-z.
Bednarek PT, Masojæ P, Lewandowska R, Myśków B: Saturating rye genomic map with amplified fragment length plymorphism (AFLP) and random amplified polymorphic DNA (RAPD) markers. J Appl Genet. 2003, 44: 21-33.
Saal B, Wricke G: Development of simple sequence repeat markers in rye (Secale cereale L.). Genome. 1999, 42: 964-972. 10.1139/gen-42-5-964.
Bolibok H, Gruszczyńska A, Hromada-Judycka A, Rakoczy-Trojanowska M: Identification of QTLs associated with the in vitro response of rye (Secale cereale L.). Cel Mol Biol Lett. 2007, 12: 523-535. 10.2478/s11658-007-0023-0.
Hackauf B, Wehling P: Development of microsatellite markers in rye: map construction. Plant Breed Seed Science. 2003, 48: 143-151.
Hackauf B, Wehling P: Identification of microsatellite polymorphisms in expressed portion of the rye genome. Plant Breed. 2002, 121: 17-25. 10.1046/j.1439-0523.2002.00649.x.
Chebotar S, Röder MS, Korzun V, Saal B, Weber WE, Börner A: Molecular studies on genetic integrity of open-pollinating species rye (Secale cereale L.) after long-term genebank maintenance. Theor Appl Genet. 2003, 107: 1469-1476. 10.1007/s00122-003-1366-1.
Matos M, Camacho MV, Perez-Flores V, Pernaute B, Pinto-Carnide O, Benito C: A new aluminum tolerance gene located on rye chromosome arm 7RS. Theor Appl Genet. 2005, 111: 360-369. 10.1007/s00122-005-2029-1.
Simkova H, Safar J, Suchankova P, Kovarova P, Bartos J, Kubalakova M, Janda J, Cihalikova J, Mago R, Lelley T, Dolezel J: A novel resource for genomic of Triticeae; BAC library specific for the short arm of rye (Secale cereale L.) chromosome 1R (1RS). BMC Genomics. 2008, 9: 237-10.1186/1471-2164-9-237.
Kofler R, Bartos J, Gong L, Stift G, Suchankova P, Simkova H, Berenyi M, Burg K, Dolezel J, Lelley T: Development of microsatellite markers specific for the short arm of rye (Secale cereale L.) chromosome 1. Theor Appl Genet. 2008, 117: 915-926. 10.1007/s00122-008-0831-2.
Jaccoud D, Peng K, Feinstein D, Kilian A: Diversity arrays: a solid state technology for sequence independent genotyping. Nucleic Acids Res. 2001, 29: e25-10.1093/nar/29.4.e25.
Wenzl P, Carling J, Kudrna D, Jaccoud D, Huttner E, Kleinhofs A, Kilian A: Diversity arrays technology (DArT) for whole-genome profiling of barley. Proc Natl Acad Sci USA. 2004, 101: 9915-9920. 10.1073/pnas.0401076101.
Akbari M, Wenzl P, Caig V, Carling J, Xia L, Yang S, Uszynski G, Mohler V, Lehmensiek A, Kuchel H, Hayden MJ, Howes N, Sharp P, Vaughan P, Rathmell B, Huttner E, Kilian A: Diversity arrays technology (DArT) for high-throughput profiling of the hexaploid wheat genome. Theor Appl Genet. 2006, 113: 1409-1420. 10.1007/s00122-006-0365-4.
Mace ES, Xia L, Jordan DR, Halloran K, Parh DK, Huttner E, Wenzl P, Kilian A: DArT markers: diversity analyses and mapping in Sorghum bicolor. BMC Genomics. 2008, 9: 26-10.1186/1471-2164-9-26.
Kilian A, Huttner E, Wenzl P, Jaccoud D, Carling J, Caig V, Evers M, Heller-Uszynska K, Cayla C, Patarapuwadol S, Xia L, Yang S, Thomson B: The fast and the cheap: SNP and DArT-based whole genome profiling for crop improvement. Proceedings of the International Congress In the Wake of the Double Helix: From the Green Revolution to the Gene Revolution May 27-31, 2003, Bologna, Italy. Edited by: Tuberosa R, Phillips RL, Gale M. 2005, Avenue Media, 443-461.
Wenzl P, Li H, Carling J, Zhou M, Raman H, Paul E, Hearnden P, Maier C, Xia L, Caig V, Ovesná J, Cakir M, Poulsen D, Wang J, Raman R, Smith KP, Muehlbauer GJ, Chalmers KJ, Kleinhofs A, Huttner E, Kilian A: A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and phenotypic traits. BMC Genomics. 2006, 7: 206-10.1186/1471-2164-7-206.
Crossa J, Burgueno J, Dreisigacker S, Vargas M, Herrera-Foessel SA, Lillemo M, Singh RP, Trethowan R, Warburton M, Franco J, Reynolds M: Association analysis of historical bread wheat germplasm using additive genetic covariance of relatives and population structure. Genetics. 2007, 177: 1889-1913. 10.1534/genetics.107.078659.
James KE, Schneider H, Ansell SW, Evers M, Robba L, Uszynski G, Pedersen N, Newton AE, Russell SJ, Vogel JC, Kilian A: Diversity arrays technology (DArT) for pan-genomic evolutionary studies of non-model organisms. PLoS ONE. 2008, 3 (2): e1682-10.1371/journal.pone.0001682.
Bonin A, Paris M, Despres L, Tetreau G, David JP, Kilian A: A MITE-based genotyping method to reveal hundreds of DNA polymorphisms in an animal genome after a few generations of artificial selection. BMC Genomics. 2008, 9 (1): 459-10.1186/1471-2164-9-459.
Masojc P, Banek-Tabor A, Milczarski P, Twardowska M: QTLs for resistance to preharvest sprouting in rye (Secale cereale L.). J Appl Genet. 2007, 48 (3): 211-217. 10.1007/BF03195215.
Ma R, Yli-Mattila T, Pulli S: Phylogenetic relationships among genotypes of worldwide collection of spring and winter ryes (Secale cereale L.) determined by RAPD-PCR markers. Hereditas. 2004, 140: 210-221. 10.1111/j.1601-5223.2004.01844.x.
Wilde K, Geiger HH, Miedaner T: Significance of host complexity and diversity for race-specific leaf-rust resistance in self-fertile synthetic rye populations. Plant Breeding. 2006, 125: 225-230. 10.1111/j.1439-0523.2006.01216.x.
Wenzl P, Raman H, Wang J, Zhou M, Huttner E, Kilian A: A DArT platform for quantitative bulked segregant analysis. BMC Genomics. 2007, 8: 196-10.1186/1471-2164-8-196.
Bolibok H, Rakoczy-Trojanowska M, Hromada A, Pietrzykowski R: Effciency of different PCR-based marker systems in assessing genetic diversity among winter rye (Secale sereale L.) inbred lines. Euphytica. 2005, 146: 109-216. 10.1007/s10681-005-0548-0.
Sigh A, Chaudhury A, Srivastava PS, Lakshmikumaran M: Comparison of AFLP and SAMPL markers for assessment of intra-population genetic variation in Azadirachta indica A. Juss. Plant Sci. 2002, 162: 17-25. 10.1016/S0168-9452(01)00503-9.
Myśków B, Masojæ P, Banek-Tabor A, Szołkowski A: Genetic diversity of inbred rye lines evaluated by RAPD analysis. J Appl Genet. 2001, 42 (1): 1-14.
Schlegel R, Melz G, Nestrowicz R: A universal reference karyotype in rye Secale cerale L. Theor Appl Genet. 1987, 74: 820-826. 10.1007/BF00247563.
Gustafson JP, Ma X-F, Korzun V, Snape JW: A consensus map of rye integrating mapping data from five mapping populations. Theor Appl Genet. 2009, 118: 793-800. 10.1007/s00122-008-0939-4.
Haldane JBS, Waddington CH: Inbreeding and linkage. Genetics. 1931, 16: 357-374.
Teuscher F, Guiard V, Rudolph PE, Brockmann GA: The map expansion obtained with recombinant inbred strains and intermated recombinant inbred populations for finite generation designs. Genetics. 2005, 170: 875-879. 10.1534/genetics.104.038026.
Sharopova N, McMullen MD, Schultz L, Schroeder S, Sanchez-Villeda H, Gardiner J, Bergstrom D, Houchins K, Melia-Hancock S, Musket T, Duru N, Polacco M, Edwards K, Ruff T, Register JC, Brouwer C, Thompson R, Velasco R, Chin E, Lee M, Woodman-Clikeman W, Long MJ, Liscum E, Cone K, Davis G, Coe EH: Development and mapping of SSR markers for maize. Plant Mol Biol. 2002, 48: 463-481. 10.1023/A:1014868625533.
Knox MR, Ellis THN: Excess heterozygosity contributes to genetic map expansion in pea recombinant inbred populations. Genetics. 2002, 162: 861-873.
Hackauf B, Wehling P: Approaching the self-incompatibility locus Z in rye (Secale cereale L.) via comparative genetics. Theor Appl Genet. 2005, 110: 832-845. 10.1007/s00122-004-1869-4.
Senft P, Wricke G: An extended genetic map of rye (Secale cereale L.). Plant Breeding. 1996, 115: 508-510. 10.1111/j.1439-0523.1996.tb00966.x.
Blair MW, Pedraza F, Buendia HF, Gaitan-Solis E, Beebe SE, Gepts P, Tohme J: Development of a genome-wide anchored microsatellite map for common bean (Phaseolus vulgaris L.). Theor Appl Genet. 2003, 107: 1362-1374. 10.1007/s00122-003-1398-6.
Li JZ, Sjakste TG, Röder MS, Röder MS, Ganal MW: Development and genetic mapping of 127 new microsatelllite markers in barley. Theor Appl Genet. 2003, 107: 1021-1027. 10.1007/s00122-003-1345-6.
Hackett CA, Broadfoot LB: Effects of genotyping errors, missing values and segregation distortion in molecular marker data on the construction of linkage maps. Heredity. 2003, 90: 33-38. 10.1038/sj.hdy.6800173.
Liu S-S, Kowalsky SP, Lan T-H, Feldmann KA, Peterson AH: Genome-wide high-resolution mapping by recurrent intermating using Arabidopsis thaliana as a model. Genetics. 1996, 142: 247-258.
Paux E, Sourdille P, Salse J, Saintenac C, Choulet F, Leroy P, Korol P, Michalak M, Kianian S, Spielmeyer W, Lagudah E, Somers D, Kilian A, Alaux M, Vautrin S, Bergès H, Eversole K, Appels R, Safar J, Simkova H, Dolezel J, Bernard M, Feuillet C: A physical map of the 1-Gigabase bread wheat chromosome 3B. Science. 2008, 322: 101-104. 10.1126/science.1161847.
Murray MG, Thompson WF: Rapid isolation of high molecular weight plant DNA. Nucleic Acid Res. 1980, 8: 4321-4325. 10.1093/nar/8.19.4321.
Yang S, Pang W, Ash G, Harper J, Carling J, Wenzl P, Huttner E, Zong X, Kilian A: Low level of genetic diversity in cultivated Pigeonpea compared to its wild relatives is revealed by Diversity Arrays Technology. Theor Appl Genet. 2006, 113: 585-595. 10.1007/s00122-006-0317-z.
Xia L, Peng K, Yang S, Wenzl P, Carmen de Vincente M, Fregene M, Kilian A: DArT for high-throughput genotyping of Cassava (Manihot esculenta) and its wild relatives. Theor Appl Genet. 2005, 110: 1092-1098. 10.1007/s00122-005-1937-4.
Jaccard P: Nouvelles recherches sur la distribution florale. Bull Soc Vaudoise Sc Nat. 1908, 44: 223-270.
Rohlf FJ: NTSYS-pc: numerical taxonomy and multivariate system. Version 2.1. 2000, Exeter Software, Setauket, NY
Mantel NA: The detection of disease clustering and a generalized regression approach. Cancer Res. 1967, 27: 209-220.
Buntjer JB: Phylogenetic Computer Tools v. 1.3. 1997, Wageningen University
Felsenstein J: PHYLIP - phylogeny inference package. Cladistics. 1989, 5: 164-166.
Van Os H, Stam P, Visser RGF, van Eck HJ: RECORD: a novel method for ordering loci on a genetic linkage map. Theor Appl Genet. 2005, 112: 30-40. 10.1007/s00122-005-0097-x.
Van Ooijen JW: JoinMap® 4, Software for the calculation of genetic linkage maps in experimental populations. Edited by: Kyazma BV. 2006, Wageningen, Netherlands
Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE, Newberg L: MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics. 1987, 1: 174-181. 10.1016/0888-7543(87)90010-3.
Voorrips RE: MapChart: Software for the graphical presentation of linkage maps and QTLs. J Hered. 2002, 93: 77-78. 10.1093/jhered/93.1.77.