Soybean Polymorphisms And Methods Of Genotyping

• US 20100275286A1
• Filed: 05/29/2008
• Published: 10/28/2010
• Est. Priority Date: 05/31/2007
• Status: Active Grant

• Current Assignee: Monsanto Technology LLC (Bayer AG)
• Original Assignee: Monsanto Technology LLC (Bayer AG)
• Inventors: McLaird, Paul, Edwards, Marlin, Butruille, David, Wu, Kunsheng, Bull, Jason, Gupta, Anju, Eathington, Sam, LeDeaux, John, Johnson, Richard
• Granted Patent: US 9,271,455 B2
• Time in Patent Office: Days
• US Class Current: 800/260
• CPC Class Codes: A01H 1/045 using molecular markers

Abstract

Polymorphic soybean DNA loci useful for genotyping between at least two varieties of soybean. Sequences of the loci are useful for providing the basis for designing primers and probe oligonucleotides for detecting polymorphisms in soybean DNA. Polymorphisms are useful for genotyping applications in soybean. The polymorphic markers are useful to establish marker/trait associations, e.g. in linkage disequilibrium mapping and association studies, positional cloning and transgenic applications, marker-aided breeding and marker-assisted selection, hybrid prediction and identity by descent studies. The polymorphic markers are also useful in mapping libraries of DNA clones, e.g. for soybean QTLs and genes linked to polymorphisms.

Claims

1-36. -36. (canceled)

37. A method of genotyping a soybean plant to select a parent plant, a progeny plant or a tester plant for breeding, said method comprising the steps of:

a. obtaining a DNA or RNA sample from a tissue of at least one soybean plant;

b. determining an allelic state of at least one soybean genomic DNA polymorphism identified in Table 1 or Table 3 for said sample from step (a); and

c. using said allelic state determination of step (b) to select a parent plant, a progeny plant or a tester plant for breeding.

38. The method of genotyping according to claim 37 wherein said polymorphism is a mapped polymorphism identified in Table 3.

39. The method according to claim 37 wherein said polymorphism is used to identify plants for breeding with a preferred yield trait and wherein said polymorphism can be selected from the group consisting of SEQ ID NO:

3122, 2914, 3984, 3608, 1448, 69, 1261, 3436, 1142, 80, 88, 980, 538, 1925, 3669, 2270, 1397, 3747, 888, 365, 2132, 1972, 459, 762, and SEQ ID NO;

1094.

41. The method according to claim 37, wherein an allelic state of at least 8 distinct polymorphisms identified in Table 1 or Table 3 is determined.

45. The method according to claim 37, further comprising the step of using said allelic state determination of step (b) to select a parent plant, a progeny plant or a tester plant for breeding.

40. (canceled)

42-44. -44. (canceled)

46-50. -50. (canceled)

51. A method of breeding soybean plants comprising the steps of:

(a) identifying trait values for at least one trait associated with at least two haplotypes in at least two genomic windows of up to 10 centimorgans for a breeding population of at least two soybean plants;

(b) breeding two soybean plants in said breeding population to produce a population of progeny seed;

(c) identifying an allelic state of at least one polymorphism identified in Table 1 or Table 3 in each of said windows in said progeny seed to determine the presence of said haplotypes; and

(d) selecting progeny seed having a higher trait value for at least one trait associated with the determined haplotypes in said progeny seed, thereby breeding a soybean plant.

52-53. -53. (canceled)

55. (canceled)

56. A method of claim 55 wherein said polymorphisms in said haplotypes are in a set of DNA sequences that comprises all of the DNA sequences of SEQ ID NO:

1 through SEQ ID NO;

7800.

57-60. -60. (canceled)

61. A method of genotyping a soybean plant to select a parent plant, a progeny plant or a tester plant for breeding, said method comprising the steps of:

a. obtaining a DNA or RNA sample from a tissue of at least one soybean plant;

b. determining an allelic state of a set of soybean genomic DNA polymorphisms comprising at least two polymorphisms identified in Table 1 or Table 3 for said sample from step (a), wherein said allelic state is determined with a set of nucleic acid molecules that provide for typing of said soybean genomic DNA polymorphisms; and

c. using said allelic state determination of step (b) to select a parent plant, a progeny plant or a tester plant for breeding.

62. The method of genotyping a soybean plant of claim 61, wherein said set of soybean genomic DNA polymorphisms comprise at least 5 polymorphisms identified in Table 1 or Table 3.

65. The method of genotyping a soybean plant of claim 61, wherein said set of soybean genomic DNA polymorphisms comprise at least 2 polymorphisms selected from the group consisting of SEQ ID NO:

3122, 2914, 3984, 3608, 1448, 69, 1261, 3436, 1142, 80, 88, 980, 538, 1925, 3669, 2270, 1397, 3747, 888, 365, 2132, 1972, 459, 762, and 1094, wherein said set of soybean genomic DNA polymorphisms are associated with a trait value for yield.

66. The method of genotyping a soybean plant of claim 65, wherein said set of soybean genomic DNA polymorphisms comprise at least 2 polymorphisms selected from the group consisting of SEQ ID NO:

3122, 2914, 3984, 3608, 1448, 69, 1261, 3436, 1142, and 80.

69. The method of genotyping a soybean plant of claim 61, wherein said set of soybean genomic DNA polymorphisms are associated with a trait values identified for at least one of yield, lodging, maturity, plant height, drought tolerance and cold germination.

70. The method of genotyping a soybean plant of claim 69, wherein said set of soybean genomic DNA polymorphisms are associated with a trait value for yield.

63-64. -64. (canceled)

67-68. -68. (canceled)

71-100. -100. (canceled)