Linkage disequilibrium and genome-wide association mapping in tetraploid wheat (Triticum turgidum L.)

PLoS ONE

Volumn 9, Issue 4, 2014, Pages

  Laidò, Giovanni ^a   Marone, Daniela ^a   Russo, Maria A ^a   Colecchia, Salvatore A ^a   Mastrangelo, Anna M ^a   De Vita, Pasquale ^a   Papa, Roberto ^a  

^a ISTITUTO NAZIONALE DELLA NUTRIZIONE   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; DOMESTICATION; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENE MAPPING; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOME; GENOTYPE; HEADING DATE; NONHUMAN; PHENOTYPE; PLANT BREEDING; PLANT HEIGHT; PLANT PARAMETERS; PROTEIN CONTENT; SIMPLE SEQUENCE REPEAT; TETRAPLOIDY; THOUSAND KERNEL WEIGHT; WHEAT; GENETICS; PLANT GENOME; QUANTITATIVE TRAIT LOCUS;

GENOME, PLANT; GENOME-WIDE ASSOCIATION STUDY; LINKAGE DISEQUILIBRIUM; QUANTITATIVE TRAIT LOCI; TETRAPLOIDY; TRITICUM;

EID: 84899757451     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0095211     Document Type: Article

References (73)

1. Börner A, Schumann E, Furste A, Coster H, Leithold B, et al. (2002) Mapping of quantitative trait loci determining agronomic important characters in hexaploid wheat (Triticum aestivum L.). Theor Appl Genet 105: 921-936. (Pubitemid 36080322)
2. Peng JH, Ronin Y, Fahima T, Röder MS, Li YC, et al. (2003) Domestication quantitative trait loci in Triticum dicoccoides, the progenitor of wheat. Proc Natl Acad Sci USA 100: 2489-2494. (Pubitemid 36297526)
3. Kumar N, Kulwal PL, Balyan HS, Gupta PK (2007) QTL mapping for yield and yield contributing traits in two mapping populations of bread wheat. Mol Breed 19(2): 63-177.
4. Maccaferri M, Sanguineti MC, Corneti S, Ortega JLA, Salem MB, et al. (2008). Quantitative trait loci for grain yield and adaptation of durum wheat (Triticum durum Desf.) across a wide range of water availability. Genetics 178: 489-511. (Pubitemid 351398764)
5. Olmos S, Distelfeld A, Chicaiza O, Schlatter AR, Fahima T, et al. (2003) Precise mapping of a locus affecting grain protein content in durum wheat. Theor Appl Genet 107: 1243-1251. (Pubitemid 37425002)
6. Huang XQ, Cloutier S, Lycar L, Radovanovic N, Humphreys DG, et al. (2006) Molecular detection of QTLs for agronomic and quality traits in a double haploid population derived from two Canidian wheats (Triticum aestivum L.). Theor Appl Genet 113: 753-766. (Pubitemid 44127017)
7. Sun X, Marza F, Ma H, Carver BF, Bai G (2010) Mapping quantitative trait loci for quality factors in an inter-class cross of US and Chinese wheat. Theor Appl Genet 120: 1041-1051.
8. Tsilo TJ, Hareland GA, Simsek S, Chao S, Anderson JA (2010) Genome mapping of kernel characteristics in hard red spring wheat breeding lines. Theor Appl Genet 121: 717-730.
9. Blanco A, Simeone R, Gadaleta A (2006) Detection of QTL for grain protein content in durum wheat. Theor Appl Genet 112: 1195-1204.
10. Blanco A, Mangini G, Giancaspro A, Giove S, Colasuonno P, et al. (2012) Relationships between grain protein content and grain yield components through quantitative trait locus analyses in a recombinant inbred line population derived from two elite durum wheat cultivars. Mol Breed 30: 79-92.
11. Navabi A, Tewari JP, Singh RP, McCallum B, Laroche A, et al. (2005) Inheritance and QTL analysis of durable resistance to stripe and leaf rusts in an Australian cultivar, Triticum aestivum 'Cook'. Genome 48: 97-107. (Pubitemid 40748018)
12. Marone D, Del Olmo AI, Laidò G, Sillero JC, Emeran AA, et al. (2009) Genetic analysis of durable resistance against leaf rust in durum wheat. Mol Breed 24: 25-39.
13. Todorovska E, Christov N, Slavov S, Christova P, Vassilev D (2009) Biotic stress resistance in wheat - Breeding and genomic selection implications. Biotechnol. & Biotechnol EQ 23(4): 1417-1426.
14. Marone D, Russo MA, Laidò G, De Vita P, Papa R, et al. (2013) Genetic basis of qualitative and quantitative resistance to powdery mildew in wheat: from consensus regions to candidate genes. BMC Genomics 14: 562.
15. Toth B, Galiba G, Feher E, Sutka J, Snape JW (2003) Mapping genes affecting flowering time and frost resistance on chromosome 5B of wheat. Theor Appl Genet 107: 509-514. (Pubitemid 37007838)
16. Hanocq E, Niarquin M, Heumez E, Rousset M, Le Gouis J (2004) Detection and mapping of QTL for earliness components in bread wheat recombinant inbred lines population. Theor Appl Genet110(1): 106-115. (Pubitemid 40240642)
17. Båga M, Fowler DB, Chibbar RN (2009) Identification of genomic regions determining the phenological development leading to floral transition in wheat (Triticum aestivum L.). J. Exp Bot 60(12): 3575-3585.
18. Panio G, Motzo R, Mastrangelo AM, Marone D, Cattivelli L, et al. (2013) Molecular mapping of stomatal-conductance-related traits in durum wheat (Triticum turgidum ssp. durum). Ann Appl Biol 162: 258-270.
19. Flint-Garcia SA, Thornsberry JM, Buckler ES (2003) Structure of linkage disequilibrium in plants. Ann Rev Plant Biol 54:357-374. (Pubitemid 37399998)
20. Zhu C, Gore M, Buckler ES, Yu J (2008) Status and Prospects of Association Mapping in Plants. The Plant Genome 1(1): 5.
21. Breseghello F, Sorrells ME (2006) Association analysis as a strategy for improvement of quantitative traits in plants. Crop Sci 46: 1323-1330.
22. Somers DJ, Banks T, DePauw R, Fox S, Clarke J, et al. (2007) Genome-wide linkage disequilibrium analysis in bread wheat and durum wheat. Genome 50: 557-567. (Pubitemid 47309788)
23. Rafalski JA (2002) Novel genetic mapping tools in plant: SNP and LD-based approaches. Plant Sci 162: 329-333.
24. Rafalski JA (2010) Association genetics in crop improvement. Curr Opin Plant Biol 13(2): 174-180.
25. Neumann K, Kobiljski B, Denčić S, Varshney RK, Börner A (2010) Genome-wide association mapping: a case study in bread wheat (Triticum aestivum L.). Mol Breed 27: 37-58.
26. Hästbacka J, de la Chapelle A, Kaitila I, Sistonen P, Weaver A, et al. (1992) Linkage disequilbrium mapping in isolated founder populations: diastrophic dysplasia in Finland. Nat Genet 2: 204-211.
27. Lander ES, Schork NJ (1994) Genetic dissection of complex traits. Science 265: 2037-2048. (Pubitemid 24325685)
28. Gupta PK, Rustgi S, Kulwal PL (2005) Linkage disequilibrium and association studies in higher plants: Present status and future prospects. Plant Mol Biol 57(4): 461-485. (Pubitemid 40588706)
29. Mackay I, Powell W (2007) Methods for linkage disequilibrium mapping in crops. Trends Plant Sci 12(2):57-63. (Pubitemid 46241003)
30. Crossa J, Burgueno J, Dreisigacker S, Vargas M, Herrera-Foessel SA, et al. (2007) Association analysis of historical bread wheat germplasm using additive genetic covariance of relatives and population structure. Genetics 177: 1889-1913. (Pubitemid 350277080)
31. Atwell S, Huang YS, Vilhjalmsson BJ, Willems G, Horton M, et al. (2010) Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature 465(7298): 627-631.
32. Maccaferri M, Sanguineti MC, Demontis A, El-Ahmed A, Garcia del Moral L, et al. (2011) Association mapping in durum wheat grown across a broad range of water regimes. J Exp Bot 62(2): 409-438.
33. Le Gouis J, Bordes J, Ravel C, Heumez E, Faure S, et al. (2012) Genome-wide association analysis to identify chromosomal regions determining components of earliness in wheat. Theor Appl Genet 124: 597-611.
34. Zhao K, Aranzana MJ, Kim S, Lister C, Shindo C, et al. (2007) An Arabidopsis example of association mapping in structured samples. Plos Genet 3(1): 71-82.
35. Pritchard JK, Stephens M, Donnelly PJ (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-959. (Pubitemid 30397141)
36. Yu J, Pressoir G, Briggs WH, Vroh BI, Yamasaki M, et al. (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 38: 203-208. (Pubitemid 43177234)
37. Vigouroux Y, McMullen M, Hittinger CT, Houchins K, Schulz L, et al. (2002) Identifying genes of agronomic importance in maize by screening microsatellites for evidence of selection during domestication. PNAS 99: 9650-9655. (Pubitemid 34831102)
38. Papa R, Bellucci E, Rossi M, Leonardi S, Rau D, et al. (2007) Tagging the signatures of domestication in common bean (Phaseolus vulgaris) by means of pooled DNA samples. Ann Bot 100: 1039-1051. (Pubitemid 47614328)
39. Maccaferri M, Sanguineti MC, Noli E, Tuberosa R (2005) Population structure and long-range linkage disequilibrium in a durum wheat elite collection. Mol Breed 15: 271-289. (Pubitemid 41201793)
40. Fu YB, Peterson GW, Clarke JM, Richards KW, Somers DJ (2005) Allelic reduction and genetic shift in the Canadian red hard spring wheat germplasm released from 1886 to 2004. Theor Appl Genet 110: 1505-1516.
41. Fu YB, Peterson GW, Yu JK, Gao LJJ, Richards KW (2006) Impact of plant breeding on genetic diversity of the Canadian hard red spring wheat germplasm as revealed by EST-derived SSR markers. Theor Appl Genet 112: 1239-1247.
42. Haudry A, Cenci A, Ravel C, Bataillon T, Brunel D, et al. (2007) Grinding up wheat: a massive loss of nucleotide diversity since domestication. Mol Biol Evol 24: 1506-1517. (Pubitemid 47216606)
43. Laidò G, Mangini G, Taranto F, Gadaleta A, Blanco A, et al. (2013) Genetic diversity and population structure of tetraploid wheats (Triticum turgidum L.) Estimated by SSR, DArT and Pedigree Data. Plos One 8(6): e67280.
44. Marone D, Laidò G, Gadaleta A, Colasuonno P, Ficco DBM, et al. (2012) A high-density consensus map of A and B wheat genomes. Theor Appl Genet 125: 1619-1638.
45. Nei M (1973) Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci USA 70: 3321-3323.
46. Weir BS (1996) Genetic data analysis II: methods for discrete population genetic data. Sinauer Associates Inc., Sunderland.
47. Breseghello F, Sorrells ME (2006) Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics 172: 1165-1177. (Pubitemid 43345448)
48. Cleveland WS (1979) Robust locally weighted regression and smoothing scatterplots. J. Am Stat Assoc 74: 829-836.
49. Zadoks JC, Chang TT, Konzak CF (1974) A decimal code for the growth stage of cereals. Weed Res 14: 415-421.
50. Benjamini Y, Hockberg Y (1995) Controlling the False Discovery Rate: a practical and powerful approach to multiple testing. J R Statist Soc B 57(1): 289-300.
51. Excoffier L, Laval G, Schneider S (2005) Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol Bioinf Online 1: 47-50.
52. Zhang J, Hao C, Ren Q, Chang X, Liu G, et al. (2011) Association mapping of dynamic developmental plant height in common wheat. Planta 234: 891-902.
53. Griffiths S, Simmonds J, Leverington M, Wang Y, Fish L, et al. (2009) Meta-QTL analy control of ear emergence in elite European winter wheat germplasm. Theor Appl Genet 119: 383-395.
54. Uauy C, Brevis JC, Dubcovsky J (2006) The high grain protein content gene Gpc-B1 accelerates senescence and has pleiotropic effects on protein content in wheat. J Exp Bot 57(11): 2785-2794. (Pubitemid 44290309)
55. Yu H, Deng Z, Xiang C, Tian J (2012) Analysis of diversity and linkage disequilibrium mapping of agronomic traits on B-genome of wheat. J Genom 1: 78-88.
56. Peleg Z, Fahima T, Korol AB, Abbo S, Saranga Y (2011) Genetic analysis of wheat domestication and evolution under domestication. J Exp Bot 62(14): 5051-5061.
57. Pasam RK, Sharma R, Malosetti M, van Eeuwijk FA, Haseneyer G, et al. (2012) Genome-wide association studies for agronomical traits in a worldwide spring barley collection. Plant Biol 12: 16.
58. Chao S, Zhang W, Dubcovsky J, Sorrells M (2007) Evaluation of genetic diversity and genome-wide linkage disequilibrium among U.S. wheat (Triticum aestivum) germplasm representing different market classes. Crop Sci 47: 1018-1030. (Pubitemid 47309151)
59. Reif JC, Gowda M, Maurer HP, Longin CFH, Korzun V, et al. (2011) Association mapping for quality traits in soft winter wheat. Theor Appl Genet 122: 961-970.
60. Gupta PK, Langridge P, Mir RR (2010) Marker-assisted wheat breeding: present status and future possibilities. Mol Breed 26: 145-161.
61. Golovnina KA, Kondratenko EY, Blinov AG, Goncharov NP (2010) Molecular characterization of vernalization loci VRN1 in wild and cultivated wheats. BMC Plant Biol 10: 168.
62. Kraakman ATW, Niks RE, Van den Berg PM, Stam P, Van Eeuwijk FA (2004) Linkage disequilibrium mapping of yield and yield stability in modern spring barley cultivars. Genetics 168: 435-446. (Pubitemid 39346607)
63. Moerell PL, Toleno DM, Lundy EK, Clegg MT (2005) Low levels of linkage disequilibrium in wild barley (Hordeum vulgare ssp. spontaneum) despite high rates of self-fertilization. PNAS 102(7): 2442-2447. (Pubitemid 40279395)
64. Caldwell KS, Russell J, Langridge P, Powell W (2006) Extreme population-dependent linkage disequilibrium detected in an inbreeding plant species. Genetics 172: 557-567. (Pubitemid 43345515)
65. Rostoks N, Ramsay L, MacKenzie K, Cardle L, Bhat PR, et al. (2006) Recent history of artificial outcrossing facilitates whole-genome associ-ation mapping in elite inbred crop varieties. Proc Natl Acad Sci USA 103: 18656-18661. (Pubitemid 44913466)
66. Rossi M, Bitocchi E, Bellucci E, Nanni L, Rau D, et al. (2009) Linkage disequilibrium and population structure in wild and domesticated populations of Phaseolus vulgaris L. Evol Appl 2(4): 504-522.
67. Yu J, Zhang Z, Zhu C, Tabanao DA, Pressoir G, et al. (2009) Simulation appraisal of the adequacy of number of background markers for relationship estimation in association mapping. Plant Genome 2: 63-77.
68. Gervais L, Dedryver F, Morlais JY, Bodusseau V, Negre S, et al. (2003) Mapping of quantitative trait loci for field resistance to Fusarium head blight in an European winter wheat. Theor Appl Genet 106: 961-970. (Pubitemid 36599804)
69. Kohn MH, Pelz HJ, Wayne RK (2003) Locus-specific genetic differentiation at Rw among warfarin-resistance rat (Rattus noevegicus) populations. Genetics 164(3): 1055-1070. (Pubitemid 36935681)
70. Storz JF (2005) Using genome scan of DNA polymorphism to infer adaptive population divergence. Mol Ecol 14: 671-688.
71. Nielsen R (2005) Molecular signatures of natural selection. Ann Rev Genet 39: 197-218.
72. Schwarzenbacher H, Dolezal M, Flisikowski K, Seefried F, Wurmser C, et al. (2012) Combining evidence of selection with association analysis increases power to detect regions influencing complex traits in dairy cattle. BMC Genomics 13: 48.
73. Reif JC, Maurer HP, Korzun V, Ebmeyer E, Miedaner T, et al. (2011) Mapping QTLs with main and epistatici affects underlying grain yield and heading time in soft winter wheat. Theor Appl Genet 123: 283-292.