Single nucleotide polymorphism mapping and alignment of recombinant chromosome substitution lines in barley

Plant and Cell Physiology

Volumn 52, Issue 5, 2011, Pages 728-737

  Sato, Kazuhiro ^a   Close, Timothy J ^b   Bhat, Prasanna ^b   Muñoz Amatriaín, María ^c   Muehlbauer, Gary J ^c  

^a OKAYAMA UNIVERSITY   (Japan)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF MINNESOTA   (United States)

Author keywords

Barley; Expressed sequence tag; Hordeum vulgare; Mapping; Single nucleotide polymorphism

Indexed keywords

ARTICLE; BARLEY; CHROMOSOME MAP; CROSS BREEDING; GENETIC MARKER; GENETIC RECOMBINATION; GENETICS; GENOTYPE; HAPLOIDY; METHODOLOGY; PHYLOGENY; PLANT CHROMOSOME; PLANT GENOME; PLANT SEED; SINGLE NUCLEOTIDE POLYMORPHISM;

CHROMOSOME MAPPING; CHROMOSOMES, PLANT; CROSSES, GENETIC; GENETIC MARKERS; GENOME, PLANT; GENOTYPE; HAPLOIDY; HORDEUM; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE; RECOMBINATION, GENETIC; SEEDS;

HORDEUM; HORDEUM VULGARE;

EID: 79956136715     PISSN: 00320781     EISSN: 14719053     Source Type: Journal    
DOI: 10.1093/pcp/pcr024     Document Type: Article

References (37)

1. Chono, M., Honda, I., Zeniya, H., Yoneyama, K., Saisho, D., Takeda, K. et al. (2003) A semidwarf phenotype of barley uzu results from a nucleotide substitution in the gene encoding a putative brassinos-teroid receptor. Plant Physiol. 133: 1209-1219. (Pubitemid 37458019)
2. Close, T.J., Bhat, P.R., Lonardi, S., Wu, Y., Rostoks, N., Ramsay, L. et al. (2009) Development and implementation of high-throughput SNP genotyping in barley. BMC Genomics 10: 582.
3. Costa, J.M., Corey, A., Hayes, P.M., Jobet, C., Kleinhofs, A., Kopsich-Obusch, A. et al. (2001) Molecular mapping of the Oregon Wolfe Barleys: a phenotypically polymorphic doubled-haploid population. Theor. Appl. Genet. 103: 415-424. (Pubitemid 32770195)
4. Fan, J.B., Oliphant, A., Shen, R., Kermani, B.G., Garcia, F., Gunderson, K.L. et al. (2003) Highly parallel SNP genotyping. Cold Spring Harbor Symp. Quant. Biol. 68: 69-78.
5. Fang, Z., Polacco, M., Chen, S., Schroeder, S., Hancock, D., Sanchez, H. et al. (2003) cMap: the comparative genetic map viewer. Bioinformatics 19: 416-417. (Pubitemid 36284940)
6. Gyenis, L., Yun, S.J., Smith, K.P., Steffenson, B.J., Bossolini, E. and Muehlbauer, G.J. (2007) Genetic architecture of quantitative trait loci associated with morphological and agronomic trait differences in a wild by cultivated barley cross. Genome 50: 714-723. (Pubitemid 350033230)
7. Hayes, P.M., Blake, T.K., Chen, T.H.H., Tragoonrung, S., Chen, F., Pan, A. et al. (1993) Quantitative trait loci on barley (Hordeum vulgare) chromosome 7 associated with components of winterhardiness. Genome 36: 66-71. (Pubitemid 23142709)
8. Hori, K., Sato, K. and Takeda, K. (2007) Detection of seed dormancy QTL in multiple mapping populations derived from crosses involving novel barley germplasm. Theor. Appl. Genet. 115: 869-876. (Pubitemid 47460481)
9. Inukai, T., Vales, M.I., Hori, K., Sato, K. and Hayes, P.M. (2006) RMo1 conferring blast resistance is located within the complex of resistance genes containing powdery mildew resistance locus Mla on chromosome 1H in barley. Mol. Plant-Microbe Interact. 19: 1034-1041. (Pubitemid 44260245)
10. Kleinhofs, A., Kilian, A., Saghai Maroof, M., Biyashev, R., Hayes, P., Chen, F.Q. et al. (1993) A molecular, isozyme and morphological map of the barley (Hordeum vulgare) genome. Theor. Appl. Genet. 86: 705-713.
11. Kosambi, D. (1944) The estimation of map distances from recombination values. Ann. Eugen. 12: 172-175.
12. Matus, I., Corey, A., Filichkin, T., Hayes, P.M., Vales, M.I., Kling, J. et al. (2003) Development and characterization of recombinant chromosome substitution lines (RCSLs) using Hordeum vulgare subsp. spon-taneum as a source of donor alleles in a Hordeum vulgare subsp. vulgare background. Genome 46: 1010-1023. (Pubitemid 38122442)
13. Moragues, M., Comadran, J., Waugh, R., Milne, I., Flavell, A.J. and Russell, J.R. (2010) Effects of ascertainment bias and marker number on estimations of barley diversity from high-throughput SNP genotype data. Theor. Appl. Genet. 120: 1525-1534.
14. Pillen, K., Zacharias, A. and Leon, J. (2003) Advanced backcross QTL analysis in barley (Hordeum vulgare L.). Theor. Appl. Genet. 107: 340-352. (Pubitemid 36922313)
15. Pillen, K., Zacharias, A. and Leon, J. (2004) Comparative AB-QTL analysis in barley using a single exotic donor of Hordeum vulgare ssp. spontaneum. Theor. Appl. Genet. 108: 1591-1601. (Pubitemid 38791267)
16. Rostoks, N., Mudie, S., Cardle, L., Russell, J., Ramsay, L., Booth, A. et al. (2005) Genome-wide SNP discovery and linkage analysis in barley based on genes responsive to abiotic stress. Mol. Genet. Genomics 274: 515-527. (Pubitemid 41721160)
17. Saisho, D., Myoraku, E., Kawasaki, S., Sato, K. and Takeda, K. (2007) Construction and characterization of a bacterial artificial chromosome (BAC) library for Japanese malting barley 'Haruna Nijo'. Breed. Sci. 57: 29-38. (Pubitemid 46434133)
18. Sakai, K., Nasuda, S., Sato, K. and Endo, T.R. (2009) Dissection of barley chromosome 3H in common wheat and a comparison of 3H physical and genetic maps. Genes Genet. Syst. 85: 25-34.
19. Sato, K., Matsumoto, T., Ooe, N. and Takeda, K. (2009a) Genetic analysis of seed dormancy QTL in barley. Breed. Sci. 59: 645-650.
20. Sato, K., Nankaku, N. and Takeda, K. (2009b) A high-density transcript linkage map of barley derived from a single population. Heredity 103: 110-117.
21. Sato, K. and Takeda, K. (2009) An application of high-throughput SNP genotyping for barley genome mapping and characterization of recombinant chromosome substitution lines. Theor. Appl. Genet. 119: 613-619.
22. Schmalenbach, I., Korber, N. and Pillen, K. (2008) Selecting a set of wild barley introgression lines and verification of QTL effects for resistance to powdery mildew and leaf rust. Theor. Appl. Genet. 117: 1093-1106.
23. Schmalenbach, I., Leon, J. and Pillen, K. (2009a) Identification and verification of QTLs for agronomic traits using wild barley intro-gression lines. Theor. Appl. Genet. 118: 483-497.
24. Schmalenbach, I. and Pillen, K. (2009b) Detection and verification of malting quality QTLs using wild barley introgression lines. Theor. Appl. Genet. 118: 1411-1427.
25. Stein, N., Prasad, M., Scholz, U., Thiel, T., Zhang, H., Wolf, M. et al. (2007) A 1,000-loci transcript map of the barley genome: new anchoring points for integrative grass genomics. Theor. Appl. Genet. 114: 823-839. (Pubitemid 46339689)
26. Szücs, P., Blake, V.C., Bhat, P.R., Chao, S., Close, T.J., Cuesta-Marcos, A. et al. (2009) An integrated resource for barley linkage map and malting quality QTL alignment. Plant Genome 2: 134-140.
27. Takahashi, H., Noda, M., Sakurai, K., Watanabe, A., Akagi, H., Sato, K. et al. (2008) QTLs in barley controlling seedling elongation of deep-sown seeds. Euphytica 164: 761-768.
28. Toojinda, T., Broers, L.H., Chen, X.M., Hayes, P.M., Kleinhofs, A., Korte, J. et al. (2000) Mapping quantitative and qualitative disease resistance genes in a doubled haploid population of barley (Hordeum vulgare). Theor. Appl. Genet. 101: 580-589.
29. Van Berloo, R. (2008) GGT 2.0: versatile software for visualization and analysis of genetic data. J. Hered. 99: 232-236. (Pubitemid 351430983)
30. Von Bothmer, R., Sato, K., Komatsuda, T., Yasuda, S. and Fischbeck, G. (2003) The domestication of cultivated barley. In Diversity in Barley (Hordeum vulgare). Edited by von Bothmer, R., Van Hintum, T., Knüpffer, H. and Sato, K. pp. 9-27. Elsevier Science, The Netherlands.
31. Von Korff, M., Wang, H., Leon, J. and Pillen, K. (2004) Development of candidate introgression lines using an exotic barley accession (Hordeum vulgare ssp. spontaneum) as donor. Theor. Appl. Genet. 109: 1736-1745. (Pubitemid 40024940)
32. Von Korff, M., Wang, H., Leon, J. and Pillen, K. (2005) AB-QTL analysis in spring barley. I. Detection of resistance genes against powdery mildew, leaf rust and scald introgressed from wild barley. Theor. Appl. Genet. 111: 583-590. (Pubitemid 41204241)
33. Von Korff, M., Wang, H., Leon, J. and Pillen, K. (2006) AB-QTL analysis in spring barley: II. Detection of favourable exotic alleles for agronomic traits introgressed from wild barley (H. vulgare ssp. sponta-neum). Theor. Appl. Genet. 112: 1221-1231.
34. Wenzl, P., Li, H., Carling, J., Zhou, M., Raman, H., Paul, E. et al. (2006) A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and agricultural traits. BMC Genomics 7: 206.
35. Wu, Y., Bhat, P.R., Close, T.J. and Lonardi, S. (2008) Efficient and accurate construction of genetic linkage maps from the minimum spanning tree of a graph. PLoS Genet. 4: e1000212.
36. Yun, S.J., Gyenis, L., Bossolini, E., Hayes, P.M., Matus, I., Smith, K.P. et al. (2006) Validation of quantitative trait loci for multiple disease resistance in barley using advanced backcross lines developed with a wild barley. Crop Sci. 46: 1179-1186.
37. Ziauddin, A., Simion, E. and Kasha, K.J. (1990) Improved plant regeneration from shed microspore culture in barley (Hordeum vulgare L.) cv. Igri. Plant Cell Rep. 9: 69-72.