Identification of marker-trait associations in the German winter barley breeding gene pool (Hordeum vulgare L.)

Molecular Breeding

Volumn 30, Issue 2, 2012, Pages 831-843

  Rode, Jeannette ^a,b   Ahlemeyer, Jutta ^c,d   Friedt, Wolfgang ^c   Ordon, Frank ^a  

^a INSTITUTE FOR EPIDEMIOLOGY AND PATHOGEN DIAGNOSTICS   (Germany)

^b MARTIN LUTHER UNIVERSITY HALLE WITTENBERG   (Germany)

^c JUSTUS LIEBIG UNIVERSITY   (Germany)

^d Deutsche Saatveredelung AG (DSV)   (Germany)

Author keywords

Association genetics studies; Barley; Linkage disequilibrium; Marker assisted selection; Population structure; SNPs

Indexed keywords

DNA SEQUENCES; GENES;

ASSOCIATION GENETIC STUDY; BARLEY; BARLEY BREEDING; GENETIC STUDIES; GRAIN YIELD; HORDEUM VULGARE L; LINKAGE DISEQUILIBRIUM; MARKER-ASSISTED SELECTION; POPULATION STRUCTURES; SNP;

GRAIN (AGRICULTURAL PRODUCT);

EID: 84865405975     PISSN: 13803743     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11032-011-9667-6     Document Type: Article

References (58)

1. Agrama HA, Eizenga GC, Yan W (2007) Association mapping of yield and its components in rice cultivars. Mol Breed 19: 341-356.
2. Beattie AD, Edney MJ, Scoles GJ, Rossnagel BG (2010) Association mapping of malting quality data from western Canadian two-row barley cooperative trails. Crop Sci 50: 1649-1663.
3. Brantestam AK, von Bothmer R, Dayteg C, Rashal I, Tuvesson S, Weibull J (2007) Genetic diversity changes and relationships in spring barley (Hordeum vulgare L.) germplasm of nordic and baltic areas as shown by SSR markers. Genet Resour Crop Evol 54: 749-758.
4. Breseghello F, Sorrells ME (2006) Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics 172: 1165-1177.
5. Caldwell KS, Russell J, Langridge P, Powell W (2006) Extreme population-dependent linkage disequilibrium detected in an inbreeding plant species, Hordeum vulgare. Genetics 172: 557-567.
6. Cardon LR, Bel JI (2001) Association study designs for complex diseases. Nat Rev Genet 2: 91-99.
7. Chaabane R, El Felah M, Salah HB, Naceur MB, Abdelly C, Ramla D, Nada A, Saker M (2009) Molecular characterization of tunisian barley (Hordeum vulgare L.) genotypes using microsatellites (SSRs) markers. Eur J Sci Res 36: 6-15.
8. Close TJ, Bhat PR, Lonardi S, Wu Y, Rostoks N, Ramsay L, Druka A, Stein N, Svensson JT, Wanamaker S, Bozdag S, Roose ML, Moscou MJ, Chao S, Varshney RK, Szu{double acute}cs P, Sato K, Hayes PM, Matthews DE, Kleinhofs A, Muehlbauer GJ, De Young J, Marshall DF, Madishetty K, Fenton RD, Condamine P, Graner A, Waugh R (2009) Development and implementation of high-throughput SNP genotyping in barley. BMC Genomics 10: 582.
9. Cockram J, White J, Leigh FJ, Lea VJ, Chiapparino E, Laurie DA, Mackay IJ, Powell W, O'Sullivan DM (2008) Association mapping of partitioning loci in barley. BMC Genet 9: 16.
10. Cockram J, White J, Zuluaga DL, Smith D, Comadran J, Macaulay M, Luo Z, Kearsey MJ, Werner P, Harrap D, Tapsell C, Liu H, Hedley PE, Stein N, Schulte D, Steuernagel B, Marshall DF, Thomas WTB, Ramsay L, Mackay I, Balding DJ, The AGOUEB Consortium, Waugh R, O'Sullivan DM (2010) Genome-wide association mapping to candidate polymorphism resolution in the unsequenced barley genome. Proc Natl Acad Sci USA 107: 21611-21616.
11. Comadran J, Thomas WTB, van Eeuwijk FÁ, Ceccarelli S, Grando S, Stanca AM, Pecchioni N, Akar T, Al-Yassin A, Benbelkacem A, Ouabbou H, Bort J, Romagosa I, Hackett CA, Russell JR (2009) Patterns of genetic diversity and linkage disequilibrium in a highly structured Hordeum vulgare association-mapping population for the Mediterranean basin. Theor Appl Genet 119: 175-187.
12. Dice LR (1945) Measures of the amount of ecological association between species. Ecology 26: 297-302.
13. Flint-Garcia SA, Thornsberry JM, Buckler ES (2003) Structure of linkage disequilibrium in plants. Annu Rev Plant Biol 54: 357-374.
14. Friedt W, Ordon F (2008) Molecular markers for gene pyramiding and resistance breeding in barley. In: Varshney R, Tuberosa R (eds) Genomics-assisted crop improvement, vol 2. Genomics applications in crops. Springer, Berlin, pp 81-101.
15. Garris AJ, Tai TH, Coburn J, Kresovich S, McCouch S (2005) Genetic structure and diversity in Oryza sativa L. Genetics 169: 1631-1638.
16. Hamblin MT, Close TJ, Bhat PR, Chao S, Kling JG, Abraham KJ, Blake T, Brooks WS, Cooper B, Griffey CA, Hayes PM, Hole DJ, Horsley RD, Obert DE, Smith KP, Ullrich SE, Muehlbauer GJ, Jannink J-L (2009) Population structure and linkage disequilibrium in US barley germplasm: implications for association mapping. Crop Sci 50: 556-566.
17. Hayes P, Szucs P (2006) Disequilibrium and association in barley: thinking outside the glass. Proc Natl Acad Sci USA 103: 18385-18386.
18. Igartua E, Casas AM, Ciudadà F, Montoyaà JL, Romagosa I (1999) RFLP markers associated with major genes controlling heading date evaluated in a barley germ plasm pool. Heredity 83: 551-559.
19. Inostroza L, del Pozo A, Matus I, Castillo D, Hayes P, Machado S, Corey A (2009) Association mapping of plant height, yield, and yield stability in recombinant chromosome substitution lines (RCSLs) using Hordeum vulgare subsp. spontaneum as a source of donor alleles in a Hordeum vulgare subsp. vulgare background. Mol Breed 23: 365-376.
20. Ivandic V, Thomas WTB, Nevo E, Zhang Z, Forster BP (2003) Associations of simple sequence repeats with quantitative trait variation including biotic and abiotic stress tolerance in Hordeum spontaneum. Plant Breed 122: 300-304.
21. Jannink J-L, Bink MCAM, Jansen RC (2001) Using complex plant pedigrees to map valuable genes. Trends Plant Sci 6: 337-342.
22. Jun T-H, van K, Kim MY, Lee S-H, Walker DR (2008) Association analysis using SSR markers to find QTL for seed protein content in soybean. Euphytica 162: 179-191.
23. Komatsuda T, Pourkheirandish M, He C, Azhaguvel P, Kanamori H, Perovic D, Stein N, Graner A, Wicker T, Tagiri A, Lundqvist U, Fujimura T, Matsuoka M, Matsumoto T, Yano M (2007) Six-rowed barley originated from a mutation in a homeodomain-leucine zipper I-class homeobox gene. Proc Natl Acad Sci USA 104: 1424-1429.
24. Kraakman ATW, Niks RE, van den Berg PMMM, Stam P, van Eeuwijk FA (2004) Linkage disequilibrium mapping of yield and yield stability in modern spring barley cultivars. Genetics 168: 435-446.
25. Kraakman ATW, Martinez F, Mussiraliev B, van Eeuwijk FA, Niks RE (2006) Linkage disequilibrium mapping of morphological, resistance, and other agronomically relevant traits in modern spring barley cultivars. Mol Breed 17: 41-58.
26. Kraft T, Hansen M, Nilsson N-O (2000) Linkage disequilibrium and fingerprinting in sugar beet. Theor Appl Genet 101: 323-326.
27. Laurie DA, Pratchett N, Bezant JH, Snape JW (1995) RFLP mapping of five major genes and eight quantitative trait loci controlling flowering time in a winter × spring barley (Hordeum vulgare L.) cross. Genome 38: 575-585.
28. Malysheva-Otto LV, Ganal MW, Röder MS (2006) Analysis of molecular diversity, population structure and linkage disequilibrium in a worldwide survey of cultivated barley germplasm (Hordeum vulgare L.). BMC Genet 7: 6.
29. Matsuoka Y, Vigouroux Y, Goodman M, Sanchez JG, Buckler E, Doebley J (2002) A single domestication for maize shown by multilocus microsatellite genotyping. Proc Natl Acad Sci USA 99: 6080-6084.
30. Matthies IE, Weise S, Roeder M (2009a) Association of haplotype diversity in the a-amylase gene amy1 with malting quality parameters in barley. Mol Breed 23: 139-152.
31. Matthies IE, Weise S, Foerster J, Roeder M (2009b) Association mapping and marker development of the candidate genes (1 → 3), (1 → 4)-β-d-glucan-4-glucanohydrolase and (1 → → → 4)-β-xylan-endohydrolase 1 for malting quality in barley. Euphytica 170: 109-122.
32. Mohlke KL, Lange EM, Valle TT, Ghosh S, Magnuson VL, Silander K, Watanabe RM, Chines PS, Bergman RN, Tuomilehto J, Collins FS, Boehnke M (2010) Linkage disequilibrium between microsatellite markers extends beyond 1 cM on chromosome 20 in finns. Genome Res 11: 1221-1226.
33. Morrell PL, Toleno DM, Lundy KE, Clegg MT (2005) Low levels of linkage disequilibrium in wild barley (Hordeum vulgare ssp. spontaneum) despite high rates of self-fertilization. Proc Natl Acad Sci USA 102: 2442-2447.
34. Neale DB, Savolainen O (2004) Association genetics of complex traits in conifers. Trends Plant Sci 9: 1360-1385.
35. Nordborg M, Borevitz JO, Bergelson J, Berry CC, Chory J, Hagenblad J, Kreitman M, Maloof JN, Noyes T, Oefner PJ, Stahl EA, Weigel D (2002) The extent of linkage disequilibrium in Arabidopsis thaliana. Nat Genet 30: 190-193.
36. Oliphant A, Barker DL, Stuelpnagel JR, Chee MS (2002) BeadArray technology: enabling an accurate, cost-effective approach to high-throughput genotyping. Biotechniques 32: 56-61.
37. Ordon F, Ahlemeyer J, Werner K, Koehler W, Friedt W (2005) Molecular assessment of genetic diversity in winter barley and its use in breeding. Euphytica 146: 21-28.
38. Palaisa KA, Morgante M, Williams M, Rafalski A (2003) Contrasting effects of selection on sequence diversity and linkage disequilibrium at two phytoene synthase loci. Plant Cell 15: 1795-1806.
39. Pritchard JK, Przeworski M (2001) Linkage disequilibrium in humans: models and data. Am J Hum Genet 69: 1-14.
40. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
41. Pswarayi A, van Eeuwijk FA, Ceccarelli S, Grando S, Comadran J, Russell JR, Pecchioni N, Tondelli A, Akar T, Al-Yassin A, Benbelkacem A, Ouabbou H, Thomas WTB, Romagosa I (2008) Changes in allele frequencies in landraces, old and modern barley cultivars of marker loci close to QTL for grain yield under high and low input conditions. Euphytica 163: 435-447.
42. Qi X, Niks RE, Stam P, Lindhout P (1998) Identification of QTLs for partial resistance to leaf rust (Puccinia hordei) in barley. Theor Appl Genet 96: 1205-1215.
43. Ramsay L, Macaulay M, Degli Ivanissevich S, MacLean K, Cardle L, Fuller J, Edwards KJ, Tuvesson S, Morgante M, Massari A, Maestri E, Marmiroli N, Sjakste T, Ganal M, Powell W, Waugh R (2000) A simple sequence repeat-based linkage map of barley. Genetics 156: 1997-2005.
44. Remington DL, Thornsberry JM, Matsuola Y, Wilson LM, Whitt SR (2001) Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proc Natl Acad Sci USA 98: 11479-11484.
45. Rohlf FJ (2000) NTSYS-pc: numerical taxonomy and multivariate analysis system, version 2. 1. Exeter Software, Setauket.
46. Rostoks N, Ramsay L, MacKenzie K, Cardle L, Bhat PR, Roose ML, Svensson JT, Stein N, Varshney RK, Marshall DF, Graner A, Close TJ, Waugh R (2006) Recent history of artificial outcrossing facilitates whole genome association mapping in elite crop varieties. Proc Natl Acad Sci USA 103: 18656-18661.
47. Roy JK, Smith KP, Muehlbauer GJ, Chao S, Close TJ, Steffenson BJ (2010) Association mapping of spot blotch resistance in wild barley. Mol Breed 26: 243-256.
48. ® 9. 1. 2 qualification tools user's guide. SAS Institute, Cary.
49. Schmalenbach I, Léon J, Pillen K (2009) Identification and verification of QTLs for agronomic traits using wild barley introgression lines. Theor Appl Genet 118: 483-497.
50. Skøt L, Humphreys MO, Armstead I, Heywood S, Skøt KP, Sanderson R, Thomas ID, Chorlton KH, Hamilton NRS (2005) An association mapping approach to identify flowering time genes in natural populations of Lolium perenne (L.). Mol Breed 15: 233-245.
51. Sneath PHA, Sokal RR (1973) Numerical taxonomy: the principles and practice of numerical classification. W. H. Freeman, San Francisco.
52. Stein N, Herren G, Keller B (2001) A new DNA extraction method for high-throughput marker analysis in a large-genome species such as Triticum aestivum. Plant Breed 120: 354-356.
53. Stracke S, Prester T, Stein N, Perovic D, Ordon F, Graner A (2007) Effects of introgression and recombination on haplotype structure and linkage disequilibrium surrounding a locus encoding bymovirus resistance in barley. Genetics 175: 805-817.
54. Stracke S, Haseneyer G, Veyrieras J-B, Geiger HH, Sauer S, Graner A, Piepho HP (2009) Association mapping reveals gene action and interactions in the determination of flowering time in barley. Theor Appl Genet 118: 259-273.
55. Tenaillon MI, Sawkins MC, Long AD, Gaut RL, Doebley JF, Gaut BS (2001) Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.). Proc Natl Acad Sci USA 98: 9161-9166.
56. Thornsberry JM, Goodman MM, Doebley J, Kresovich S, Nielsen D, Buckler ES (2001) Dwarf8 polymorphisms associate with variation in flowering time. Nat Genet 28: 286-289.
57. Yan L, von Zitzewitz J, Skinner JS, Hayes PM, Dubcovsky J (2005) Molecular characterization of the duplicated meristem identity genes HvAP1a and HvAP1b in barley. Genome 48: 905-912.
58. Zhang LY, Marchand S, Tinker NA, Belzile F (2009) Population structure and linkage disequilibrium in barley assessed by DArT markers. Theor Appl Genet 119: 43-52.