Bayesian mapping of quantitative trait loci (QTL) controlling soybean cyst nematode resistant

Euphytica

Volumn 186, Issue 3, 2012, Pages 907-917

  Arriagada, Osvin ^a   Mora, Freddy ^b   Dellarossa, Joaquín C ^a   Ferreira, Marcia F S ^c   Cervigni, Gerardo D L ^d   Schuster, Ivan ^e  

^a UNIVERSITY OF CONCEPCIÓN   (Chile)

^b UNIVERSIDAD DE TALCA   (Chile)

^c FEDERAL UNIVERSITY OF ESPÍRITO SANTO   (Brazil)

^d UNIVERSIDAD NACIONAL DEL SUR   (Argentina)

^e Cooperativa Central de Pesquisa Agrícola ^*  (Brazil)

Author keywords

Linkage group; Marker assisted selection; MCMC algorithm; RIL

Indexed keywords

GLYCINE MAX; HETERODERA GLYCINES;

EID: 84864378614     PISSN: 00142336     EISSN: 15735060     Source Type: Journal    
DOI: 10.1007/s10681-012-0696-y     Document Type: Article

References (76)

1. Afzal AJ, Natarajan A, Saini N, Iqbal MJ, Geisler M, Shemy HA, Mungur R, Willmitzer L, Lightfoot DA (2009) The nematode resistance allele at the rhg1 locus alters the proteome and primary metabolism of soybean roots. Plant Physiol 151: 1264-1280.
2. Ball RA, McNew RW, Vories ED, Keisling TC, Purcell LC (2001) Path analyses of population density effects on short-season soybean yield. Agron J 93: 187-195.
3. Baudouin L, Piry S, Cornuet JM (2004) Analytical Bayesian approach for assigning individuals to populations. J Hered 95: 217-224.
4. Blasco A (2001) The Bayesian controversy in animal breeding. J Anim Sci 79: 2023-2046.
5. Brucker E, Carlson S, Wright E, Niblack T, Diers B (2005) Rhg1 alleles from soybean PI 437654 and PI 88788 respond differentially to isolates of Heterodera glycines in the greenhouse. Theor Appl Genetics 111: 44-49.
6. Carvalho G, Nepstad D, McGrath D, Vera-Diaz MDC, Santilli M, Barros AC (2002) Frontier expansion in the amazon: balancing development and sustainability. Environment 44: 34-45.
7. Cervigini GDL, Schuster I, Silva MF, Sediyama CS, de Barros EG, Moreira MA (2007) A common QTL for resistance to races 3 and 9 of soybean cyst nematode. Revista de la Facultad de Agronomía 106: 137-144.
8. Chang W, Dong L, Wang Z, Hu H, Han Y, Teng W, Zhang H, Guo M, Li W (2011) QTL underlying resistance to two HG types of Heterodera glycines found in soybean cultivar 'L-10'. BMC Genomics 12: 233-243.
9. Concibido VC, Diers BW, Arelli PR (2004) A decade of QTL mapping for cyst nematode resistance in soybean. Crop Sci 44: 1121-1131.
10. Cornelious B, Chen P, Chen Y, de Leon N, Shannon JG, Wang D (2005) Identification of QTLs underlying water-logging tolerance in soybean. Mol Breed 16: 103-112.
11. Dong K, Baker KR, Opperman CH (1997) Genetics of soybean-Heterodera glycines interactions. J Nematol 29: 509-522.
12. Embrapa (2007) Tecnologia de produção de soja: região central do Brasil, Londrina: Embrapa Soja, Embrapa Cerrados, Embrapa Agropecuária Oeste, 2006. 225 p.
13. Faghihi J, Vierling RA, Halbrendt JM, Ferris VR, Ferris JM (1995) Resistance genes in a 'Williams 82 × 'Hartwig' soybean cross to an inbred line of Heterodera glycines. J Nematol 27: 418-421.
14. Faria CU, Magnabosco CU, Reyes A, Lôbo RB, Bezerra LAF, Sainz RD (2007) Bayesian inference in a quantitative genetic study of growth traits in Nelore cattle (Bos indicus). Genetics Mol Biol 30: 545-551.
15. Ferreira MF, Cervigni GDL, Ferreira A, Schuster I, Santana FA, Pereira WD, Barros EG, Moreira MA (2011) QTLs for resistance to soybean cyst nematode, races 3, 9, and 14 in cultivar Hartwig. Pesquisa Agropecuária Brasileira 46: 420-428.
16. Figueiredo MG, Barros ALM, Guilhoto JJM (2005) Relação econômica dos setores agrícolas do Estado do Mato Grosso com os demais setores pertencentes tanto ao Estado quanto ao restante do Brasil. Revista de Economia e Sociologia Rural 43: 557-575.
17. Glover KD, Wang D, Arelli PR, Carlson SR, Cianzio SR, Diers BW (2004) Near isogenic lines confirm a soybean cyst nematode resistance gene from PI 88788 on linkage group. J Crop Sci 44: 936-941.
18. Guo Z (2007) Novel methods for increasing efficiency of quantitative trait locus mapping. Doctoral thesis, College of Agriculture, Kansas State University, Manhattan, Kansas, 55 pp.
19. Guo B, Sleper DA, Arelli PR, Shannon JG, Nguyen HT (2005) Identification of QTLs associated with resistance to soybean cyst nematode races 2, 3 and 5 in soybean PI 90763. Theor Appl Genetics 111: 965-971.
20. Guo B, Sleper DA, Nguyen HT, Arelli PR, Shannon JG (2006) Quantitative trait loci underlying resistance to three soybean cyst nematode populations in soybean PI 404198A. Crop Sci 46: 224-233.
21. Handoo ZA, Anand SC (1993) Biological manifestation of resistance to soybean cyst nematode development in Hartwig soybean. Crop Prot 12: 371-372.
22. Hayashi T, Awata T (2008) A Bayesian method for simultaneously detecting mendelian and imprinted quantitative trait loci in experimental crosses of outbred species. Genetics 178: 527-538.
23. Heidelberger P, Welch PD (1983) Simulation run length control in the presence of an initial transient. Oper Res 31: 1109-1144.
24. Henning JA, Townsend MS, Gent DH, Bassil N, Matthews P, Buck E, Beatson R (2011) QTL mapping of powdery mildew susceptibility in hop (Humulus lupulus L.). Euphytica 180: 411-420.
25. Jackson EW, Feng C, Fenn P, Chen P (2009) Genetic mapping of resistance to purple seed stain in PI 80837 soybean. J Hered 100: 777-783.
26. Kao CH, Zeng ZB, Teasdale R (1999) Multiple interval mapping for quantitative trait loci. Genetics 152: 1203-1216.
27. Kazi S, Shultz J, Afzal J, Hashmi R, Jasim M, Bond J, Arelli PR, Lightfoot DA (2010) Iso-lines and inbred-lines confirmed loci that underlie resistance from cultivar 'Hartwig' to three soybean cyst nematode populations. Theor Appl Genetics 120: 633-644.
28. Keim P, Olson TC, Shoemaker RC (1988) A rapid protocol for isolating soybean DNA. Soybean Genetics Newslett 15: 150-152.
29. Kosambi DD (1944) The estimation of map distances from recombination values. Ann Eugen 12: 173-175.
30. Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE, Newburg L (1987) Mapmaker: an interactive computer package for constructing genetic linkage maps of experimental and natural populations. Genomics 1: 174-181.
31. Li H, Ye G, Wang J (2007) A modified algorithm for the improvement of composite interval mapping. Genetics 175: 361-374.
32. Li H, Hearne S, Bänziger M, Li Z, Wang J (2010) Statistical properties of QTL linkage mapping in biparental genetic populations. Heredity 105: 257-267.
33. Lincoln SE, Lander SL (1993) Mapmaker/exp 3. 0 and mapmaker/qtl 1. 1. Technical report. Whitehead Institute of Medical Research, Cambridge, MA.
34. Liu MD, White TE, Litster DJ (2007) Dissolution behaviour of soy proteins and effect of initial concentration. J Agric Food Chem 55: 2467-2473.
35. Liu X, Liu S, Bendahmane AJA, Lightfoot DA, Mitchum MG, Meksem K (2011a) Soybean cyst nematode resistance in soybean is independent of the Rhg4 locus LRR-RLK gene. Funct Integr Genomics 11: 539-549.
36. Liu Y, Zhou X, Zhang J, Li H, Zhuang T, Yang R, Chen H (2011b) Bayesian analysis of interacting quantitative trait loci (QTL) for yield traits in tomato. Afr J Biotechnol 10: 13719-13723.
37. Mackay TFC, Stone EA, Ayroles JF (2009) The genetics of quantitative traits: challenges and prospects. Nat Rev Genetics 10: 565-577.
38. Maliepaard C, Sillanpää MJ, van Ooijen J, Jansen RC, Arjas E (2001) Bayesian versus frequentist analysis of multiple quantitative trait loci with an application to an outbred apple cross. Theor Appl Genetics 103: 1243-1253.
39. Mauro AO, Unêda-Trevisoli SH, Mauro SMZ, Costa MM, Oliveira RC, Arantes NE (2004) Efficiency of microsatellite markers in assisted selection for resistance to soybean cyst nematode (race 3). Crop Breed Appl Biotechnol 4: 28-34.
40. Mayer M, Yuefu L, Freyer G (2004) A simulation study on the accuracy of position and effect estimates of linked QTL and their asymptotic standard deviations using multiple interval mapping in an F2 scheme. Genetics Sel Evol 36: 455-479.
41. Minuzzi A, Mora F, Sedrez-Rangel MA, De Lucca e Braccini A, Scapim CA (2007) Características fisiológicas, contenido de aceite y proteína en genotipos de soya, evaluadas en diferentes sitios y épocas de cosecha, Brasil. Agricultura Técnica 67: 353-361.
42. Minuzzi A, Sedrez-Rangel MA, De Lucca e Braccini A, Scapim CA, Mora F, Dias Robaina A (2009) Yield, oil and protein content of four soybean cultivars produced in two locations of Mato Grosso do Sul State. Ciência e Agrotecnologia 33: 1047-1054.
43. Mora F, Tapia F, Scapim CA, Martins EN, Pinto RJB, Ibacache A (2008) Early performance of Olea europaea cv. Arbequina, Picual and Frantoio in southern Atacama Desert. Crop Breed Appl Biotechnol 8: 30-38.
44. Mora F, Scapim CA, Baharum A, Amaral AT (2010) Generalized composite interval mapping offers improved efficiency in the analysis of loci influencing non-normal continuous traits. Ciencia e Investigación Agraria 37: 83-89.
45. Noor MAF, Cunningham AL, Larkin JC (2001) Consequences of recombination rate variation on quantitative trait locus mapping studies: simulations based on the Drosophila melanogaster genome. Genetics 159: 581-588.
46. Pfalz M, Vogel H, Mitchell-Olds T, Kroymann J (2007) Mapping of QTL for resistance against the crucifer specialist herbivore Pieris brassicae in a new arabidopsis inbred line population, Da(1)-12 × Ei-2. Plos One. doi: 10. 1371/journal. pone. 0000578.
47. Piepho HP (2000) Optimal marker density for interval mapping in a backcross population. Heredity 84: 437-440.
48. Qi Z, Wu Q, Han X, Sun Y, Du X, Liu C, Jiang H, Hu G, Chen Q (2011) Soybean oil content QTL mapping and integrating with meta-analysis method for mining genes. Euphytica 179: 499-514.
49. Riggs RD, Schmidt DP (1988) Complete characterization of the race scheme for Heterodera glycines. J Nematol 20: 392-395.
50. Ruben E, Aziz J, Afzal J, Njiti VN, Triwitayakorn K, Iqbal MJ, Yaegashi S, Arelli P, Town C, Meksem K, Lightfoot DA (2006) Genomic analysis of the 'Peking' rhg1 locus: candidate genes that underlie soybean resistance to the cyst nematode. Mol Genetics Genomics 276: 320-330.
51. Santos AI, Ribeiro RP, Vargas L, Mora F, Filho LA, Fornari DC, Oliveira SN (2011) Bayesian genetic parameters for body weight and survival of Nile tilapia farmed in Brazil. Pesquisa Agropecuária Brasileira 46: 33-43.
52. Satagopan JM, Yandell BS, Newton MA, Osborn TC (1996) A Bayesian approach to detect quantitative trait loci using Markov Chain Monte Carlo. Genetics 144: 805-816.
53. Schuster I, Cruz CD (2004) Estatística genômica aplicada a populações derivadas de cruzamentos controlados. Universidade Federal de Viçosa, Viçosa.
54. Shoemaker JS, Painter IS, Weir BS (1999) Bayesian statistics in genetics. A guide for the uninitiated. Trends Genetics 15: 354-358.
55. Silva JP, Leandro RA (2009) A bayesian approach to map QTLs using reversible jump MCMC. Ciência e Agrotecnologia 33: 1061-1070.
56. Silva JFV, Garcia A, Almeida AMR, Pereira JE (2002) Ecologia e controle do nematóide de cisto da soja. Resultados de Pesquisa da Embrapa Soja-2001: Doencas e Nematóides, Londrina, Embrapa Soja, pp. 8-9. Embrapa Soja, Documentos, 194.
57. Silva MF, Schuster I, Silva JFV, Ferreira A, Barros EG, Moreira MA (2007) Validation of microsatellite markers for assisted selection of soybean resistance to cyst nematode races 3 and 14. Pesquisa Agropecuária Brasileira 42: 1143-1150.
58. Stich B, Piepho HP, Schulz B, Melchinger AE (2008) Multi-trait association mapping in sugar beet (Beta vulgaris L.). Theor Appl Genetics 117: 947-954.
59. Studer AJ, Doebley JF (2011) Do large effect QTL fractionate? A case study at the maize domestication QTL teosinte branched1. Genetics 188: 673-681.
60. van Ooijen JW (1999) LOD significance thresholds for QTL analysis in experimental populations of diploid species. Heredity 83: 613-624.
61. Varona L, García-Cortes LA, Pérez-Enciso M (2001) Bayes factor for detection of quantitative trait loci. Genetics Sel Evol 33: 133-152.
62. Vierling RA, Faghihi J, Ferris VR, Ferris JM (1996) Association of RFLP markers conferring broad-based resistance to the soybean cyst nematode (Heterodera glycines). Theor Appl Genetics 92: 83-86.
63. Wang S, Basten CJ, Zeng ZB (2011) Windows QTL Cartographer 2. 5. Department of Statistics, North Carolina State University, Raleigh, NC. (http://statgen. ncsu. edu/qtlcart/WQTLCart. htm).
64. Watanabe S, Tajuddin T, Yamanaka N, Hayashi M, Harada K (2004) Analysis of QTLs for reproductive development and seed quality traits in soybean using recombinant inbred lines. Breed Sci 54: 399-407.
65. Webb DM (2003) (inventor), Pioneer Hi-Bred International Inc, assignee. Quantitative trait loci associated with cyst nematode resistance and uses thereof. US patent 6, 538, 175, 25 Mar 2003 (Issue date).
66. Webb DM, Baltazar BM, Rao-Arelli PA, Schupp J, Clayton K, Keim P, Beavis WD (1995) Genetic mapping of soybean cyst nematode race-3 resistance loci in soybean PI 437654. Theor Appl Genetics 91: 574-581.
67. Wei W, Li Y, Wang L, Liu S, Yan X, Mei D, Li Y, Xu Y, Peng P, Hu Q (2010) Development of a novel Sinapis arvensis disomic addition line in Brassica napus containing the restorer gene for Nsa CMS and improved resistance to Sclerotinia sclerotiorum and pod shattering. Theor Appl Genetics 120: 1089-1097.
68. Winter SMJ, Rajcan I, Shelp BJ (2006) Soybean cyst nematode: challenges and opportunities. Can J Plant Sci 86: 25-32.
69. Wu X, Blake S, Sleper DA, Shannon JG, Cregan P, Nguyen HT (2009) QTL, additive and epistatic effects for SCN resistance in PI 437654. Theor Appl Genetics 118: 1093-1105.
70. Yang J, Wu R, Casella G (2009) Nonparametric functional mapping of quantitative trait loci. Biometrics 65: 30-39.
71. Yi N, Shriner D (2008) Advances in Bayesian multiple QTL mapping in experimental designs. Heredity 100: 240-252.
72. Yi N, George V, Allison DB (2003) Stochastic search variable selection for identifying multiple quantitative trait loci. Genetics 164: 1129-1138.
73. Yue P, Arelli PR, Sleper DA (2001) Molecular characterization of resistance to Heterodera glycines in soybean PI 438489B. Theor Appl Genetics 102: 921-928.
74. Zeng ZB (1993) Theoretical basis for separation of multiple linked gene effects in mapping quantitative trait loci. Proc Nat Acad Sci 90: 10972-10976.
75. Zeng ZB (1994) Precision mapping of quantitative trait loci. Genetics 136: 1457-1468.
76. Zou W, Zeng ZB (2008) Statistical methods for mapping multiple QTL. Int J Plant Genomics. doi: 10. 1155/2008/286561.