# US 2013/0160170 A1 · Methods and Compositions for Goss' Wilt Resistance in Corn

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- Number: US 2013/0160170 A1
- Document ID: US20130160170A1
- Status: Published application
- Kind: A1
- Application number: 13/742,042
- Filed: 2013-01-15
- Published: 2013-06-20
- Earliest claimed: 2007-08-29
- Assignees: Monsanto Technology LLC
- Inventors: Michael R. Kerns; Hongwu Jia; David Butruille; Travis J. Frey; Kevin Cook; Laron Peters
- Web page: https://patentgrep.com/patent/US20130160170A1

## CPC

- C12N 15/8282: {for fungal resistance}
- A01H 1/045: {using molecular markers}
- A01H 5/10: Seeds
- A01H 6/4684: {Zea mays [maize]}
- C12N 15/8281: {for bacterial resistance}
- C12Q 1/6895: for plants, fungi or algae
- C12Q 2600/13: Plant traits
- C12Q 2600/156: Polymorphic or mutational markers
- C12Q 2600/172: Haplotypes
- C12N: MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA (microbiological testing media C12Q1/00)
- A01H: NEW PLANTS OR {NON-TRANSGENIC} PROCESSES FOR OBTAINING THEM; PLANT REPRODUCTION BY TISSUE CULTURE TECHNIQUES
- C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES

## Abstract

The present invention relates to the field of plant breeding. More specifically, the present invention includes a method of using haploid plants for genetic mapping of traits of interest such as disease resistance. Further, the invention includes a method for breeding corn plants containing quantitative trait loci (QTL) that are associated with resistance to Goss' Wilt, a bacterial disease associated with Clavibacter michiganense spp.

## Claims

### Claim 1

A method of identifying a corn plant comprising at least one allele associated with Goss' Wilt resistance in a corn plant comprising:
a) genotyping at least one corn plant with at least one nucleic acid marker selected from the group consisting of SEQ ID NOs: 13, 19, 24, 27, 36, 50, 53, 90, 94, 95, 97, 99, 101, 102, 106, 110, 111, 119, 121, 122, 124, 128, 130-132, 136, 138, 141, 146, 153, 158-160, 162, 164, 166, 169, 172, 175, 177, 186, 200, 202, 203, 207, 208, 215, 216, 218, 220, 224, 228, 231-236, 244, 248, 250, 252, 256, 257, 260, 265-267, 271-274, 278, 279, 282, 287, 289, 294-296, 299, 317, 320, 332-334, 337, 347, 355, 362, 363, 366-368, 370, 371, 375, 381, 382, 392, 395, 401, 408, 409, 411, 412, 422, 423, 429, 430, 433, 438, 440, 447, 474, 476, 479, 480, 482, 486, 490, 493, 498, 500, 525, 530, 533, 556, 566, 582, 585, 587, 589, 593, 594, 599, 611, 618, 621, 623, 629, 630, 632, 637, 639, 646, 649, 650, 657, 665, 669, 678, 679, 688, 690, 704, 709, 710, 717, 719-721, 726, 727, 733, 734, 744, 746, 758, 760, 764, 768, 773, 792, 793, 812, 821, 825, 835, 844, 846, 850, 854, 856-858, 874, 876, 880, 882, 885, 893, 896, 897, 915, 926, 940, 942, 949, 951, 957, 963, 964, 974, 976, 981, 983, 990, 997, 999, 1000, 1015, 1016, 1027, 1043, 1049, 1053, 1054, 1056, 1075, 1081, 1087, 1088, 1098-1100, 1104, 1105, 1108, 1110, 1115, 1122, 1131, 1133, 1142, 1143, 1145, 1146, 1148, 1149, 1159, 1168, 1174, 1184, 1186, 1196, 1204, 1212, 1215, 1229, 1234-1302, and 1303, and
b) selecting at least one corn plant comprising an allele of at least one of said markers that is associated with resistance to Goss' Wilt.

### Claim 2 (depends on 1)

The method according to claim 1, wherein the at least one corn plant genotyped in step (a) and/or the at least one corn plant selected in step (b) is a corn plant from a population generated by a cross.

### Claim 3 (depends on 2)

The method of claim 2, wherein said cross is effected by mechanical emasculation, chemical sterilization, or genetic sterilization of a pollen acceptor.

### Claim 4 (depends on 1)

The method of claim 1, wherein said genotyping is effected in step (a) by determining the allelic state of at least one of said corn genomic DNA markers.

### Claim 5 (depends on 1)

The method according to claim 1, wherein said selected corn plant(s) of step (b) exhibit at least partial resistance to a Goss' Wilt-inducing bacteria or at least substantial resistance to a Goss' Wilt-inducing bacteria.

### Claim 6 (depends on 1)

The method according to claim 1, wherein said nucleic acid marker is selected from the group consisting of SEQ ID NOs: 27, 121, 141, 175, 177, 220, 224, 234, 248, 252, 381, 440, 479, 480, 533, 582, 585, 639, 721, 727, 733, 746, 768, 773, 940, 1053, 1054, 1122, 1186, 1246, 1250, and 1251.

### Claim 7 (depends on 6)

The method according to claim 6, wherein said nucleic acid marker is selected from the group consisting of SEQ ID NOs: 234 and 1250.

### Claim 8 (depends on 2)

The method of claim 2, wherein said population is generated by a cross of at least one Goss' Wilt resistant corn plant with at least one Goss' Wilt sensitive corn plant.

### Claim 9 (depends on 2)

The method of claim 2, wherein said population is a segregating population.

### Claim 10 (depends on 2)

The method of claim 2, wherein said cross is a back cross of at least one Goss' Wilt resistant corn plant with at least one Goss' Wilt sensitive corn plant to introgress Goss' Wilt resistance into a corn germplasm.

### Claim 11 (depends on 2)

The method of claim 2, wherein said population is a haploid breeding population.

### Claim 12

A method of introgressing a Goss' Wilt resistance QTL into a corn plant comprising:
a) screening a population of corn plants with at least one nucleic acid marker to determine if one or more corn plants from the population contains a Goss' Wilt resistance QTL, wherein the Goss' Wilt resistance QTL is a QTL selected from the group consisting of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, and 131 as provided in FIGS. 1; and
b) selecting from said population of corn plants at least one corn plant comprising an allele of said marker associated with Goss' Wilt resistance.

### Claim 13 (depends on 12)

The method according to claim 12, wherein at least one of the markers is located within 5 cM of said Goss' Wilt resistance QTL.

### Claim 14 (depends on 13)

The method according to claim 13, wherein at least one of the markers is located within 2 cM of said Goss' Wilt resistance QTL.

### Claim 15 (depends on 14)

The method according to claim 14, wherein at least one of the markers is located within 1 cM of said Goss' Wilt resistance QTL.

### Claim 16 (depends on 12)

The method according to claim 12, wherein at least one of the markers exhibits a LOD score of greater than 4.0 with said Goss' Wilt resistance QTL.

### Claim 17 (depends on 16)

The method according to claim 16, wherein said nucleic acid marker is selected from the group consisting of SEQ ID NOs: 27, 121, 141, 175, 177, 220, 224, 234, 248, 252, 381, 440, 479, 480, 533, 582, 585, 639, 721, 727, 733, 746, 768, 773, 940, 1053, 1054, 1122, 1186, 1246, 1250, and 1251.

### Claim 18 (depends on 17)

The method according to claim 17, wherein said nucleic acid marker is selected from the group consisting of SEQ ID NOs: 234 and 1250.

### Claim 19 (depends on 12)

The method of claim 12, wherein said population is a segregating population.

### Claim 20 (depends on 1)

A corn plant obtained by the method of claim 1, wherein said corn plant comprises at least one allele of a nucleic acid marker selected from the group consisting of SEQ ID NOs: 13, 19, 24, 27, 36, 50, 53, 90, 94, 95, 97, 99, 101, 102, 106, 110, 111, 119, 121, 122, 124, 128, 130-132, 136, 138, 141, 146, 153, 158-160, 162, 164, 166, 169, 172, 175, 177, 186, 200, 202, 203, 207, 208, 215, 216, 218, 220, 224, 228, 231-236, 244, 248, 250, 252, 256, 257, 260, 265-267, 271-274, 278, 279, 282, 287, 289, 294-296, 299, 317, 320, 332-334, 337, 347, 355, 362, 363, 366-368, 370, 371, 375, 381, 382, 392, 395, 401, 408, 409, 411, 412, 422, 423, 429, 430, 433, 438, 440, 447, 474, 476, 479, 480, 482, 486, 490, 493, 498, 500, 525, 530, 533, 556, 566, 582, 585, 587, 589, 593, 594, 599, 611, 618, 621, 623, 629, 630, 632, 637, 639, 646, 649, 650, 657, 665, 669, 678, 679, 688, 690, 704, 709, 710, 717, 719-721, 726, 727, 733, 734, 744, 746, 758, 760, 764, 768, 773, 792, 793, 812, 821, 825, 835, 844, 846, 850, 854, 856-858, 874, 876, 880, 882, 885, 893, 896, 897, 915, 926, 940, 942, 949, 951, 957, 963, 964, 974, 976, 981, 983, 990, 997, 999, 1000, 1015, 1016, 1027, 1043, 1049, 1053, 1054, 1056, 1075, 1081, 1087, 1088, 1098-1100, 1104, 1105, 1108, 1110, 1115, 1122, 1131, 1133, 1142, 1143, 1145, 1146, 1148, 1149, 1159, 1168, 1174, 1184, 1186, 1196, 1204, 1212, 1215, 1229, 1234-1302, and 1303, wherein said allele is associated with Goss' Wilt resistance.

### Claim 21 (depends on 20)

The corn plant according to claim 20, wherein said nucleic acid marker is selected from the group consisting of SEQ ID NOs: 27, 121, 141, 175, 177, 220, 224, 234, 248, 252, 381, 440, 479, 480, 533, 582, 585, 639, 721, 727, 733, 746, 768, 773, 940, 1053, 1054, 1122, 1186, 1246, 1250, and 1251.

### Claim 22 (depends on 20)

The corn plant of claim 20, wherein the corn plant exhibits at least partial resistance to a Goss' Wilt-inducing bacterium or at least substantial resistance to a Goss' Wilt-inducing bacterium.

### Claim 23 (depends on 20)

The corn plant according to claim 20 a nucleic acid marker selected from the group consisting of SEQ ID NOs: 234 and 1250.

### Claim 24 (depends on 20)

The corn plant of claim 20, wherein said corn plant is a haploid corn plant.

### Claim 25 (depends on 12)

A corn plant obtained by the method of claim 12, wherein said corn plant comprises a Goss' Wilt resistance QTL selected from the group consisting of QTL numbers 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, and 131 as provided in FIG. 1.

### Claim 26

An isolated nucleic acid molecule for detecting a molecular marker representing a polymorphism in corn DNA, wherein said nucleic acid molecule comprises at least 15 nucleotides that include or are immediately adjacent to said polymorphism, wherein said nucleic acid molecule is at least 90 percent identical to a sequence of the same number of consecutive nucleotides in either strand of DNA that include or are immediately adjacent to said polymorphism, and wherein said molecular marker is selected from the group consisting of SEQ ID NOs: 27, 121, 141, 175, 177, 220, 224, 234, 248, 252, 440, 479, 480, 533, 582, 585, 639, 721, 727, 733, 746, 768, 773, 940, 1053, 1054, 1122, 1186, 1234-1302, and 1303.

### Claim 27 (depends on 26)

The isolated nucleic acid according to claim 26, wherein said molecular marker is selected from the group consisting of SEQ ID NOs: 27, 121, 141, 175, 177, 220, 224, 234, 248, 252, 381, 440, 479, 480, 533, 582, 585, 639, 721, 727, 733, 746, 768, 773, 940, 1053, 1054, 1122, 1186, 1246, 1250, and 1251.

### Claim 28 (depends on 27)

The isolated nucleic acid of claim 27, wherein said molecular marker is selected from the group consisting of SEQ ID NOs: 1250.