Methods and Compositions for Haploid Mapping

• US 20090064361A1
• Filed: 08/29/2008
• Published: 03/05/2009
• Est. Priority Date: 08/29/2007
• Status: Abandoned Application

• Current Assignee: Monsanto Technology LLC (Bayer AG)
• Original Assignee: Monsanto Technology LLC (Bayer AG)
• Inventors: Grote, Karen, Eathington, Samuel, Weyhrich, Roger, Butruille, David, Carlson, Thomas, Bockelman, Donald, Kerns, Michael R., Frey, Travis J.
• Application Number:
  US12/201,485
• Publication Number:
  US 20090064361A1
• Time in Patent Office: Days
• US Class Current: 800/266
• CPC Class Codes: A01H 1/045 using molecular markers
• CPC Class Codes: A01H 5/10 Seeds
• CPC Class Codes: A01H 6/4684 Zea mays [maize]
• CPC Class Codes: C12N 15/8281 for bacterial resistance
• CPC Class Codes: C12N 15/8282 for fungal resistance
• CPC Class Codes: C12Q 1/6895 for plants, fungi or algae
• CPC Class Codes: C12Q 2600/13 Plant traits
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: C12Q 2600/172 Haplotypes

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 Gray Leaf Spot (GLS), a fungal disease associated with Cercospora spp. The invention further includes a method for breeding corn plants containing QTL that are associated with Goss'"'"' Wilt, a bacterial disease associated with Clavibacter michiganense spp.

Claims

1. A method for the association of at least one genotype with at least one phenotype using a haploid plant comprising:

a) assaying at least one genotype of at least one haploid plant with at least one genetic marker; and

b) associating the at least one marker with at least one phenotypic trait.

2. The method of claim 1, wherein the at least one genetic marker comprises a single nucleotide polymorphism (SNP), an insertion or deletion in DNA sequence (Indel), a simple sequence repeat of DNA sequence (SSR) a restriction fragment length polymorphism, a haplotype, or a tag SNP.

3. A method of claim 1, further comprising the step of using an association determined in step (b) to make a selection in a plant breeding program.

4. A method of claim 3, wherein said selection comprises selecting among breeding populations based on the at least one genotype.

5. The method of claim 3, wherein said selection comprises selecting progeny in one or more breeding populations based on the at least one genotype.

6. The method of claim 3, wherein said selection comprises selecting among parental lines based on prediction of progeny performance.

7. The method of claim 3, wherein said selection comprises selection of a line for advancement in a germplasm improvement activity based on the at least one genotype.

8. A method of claim 3, further comprising the step of doubling at least one haploid plant selected in said breeding program to obtain a doubled haploid plant.

10. The method of claim 1, wherein said haploid plant in step (a) is obtained from a haploid breeding population.

9. The method of claim 9, wherein the doubled haploid plant is used for introgression of the genotype of interest into at least a second plant for use in a plant breeding program.

11. A method for identifying an association of a plant genotype with one or more traits of interest comprising:

a) screening a plurality of haploid plants displaying heritable variation for at least one trait wherein the heritable variation is linked to at least one genotype; and

b) associating at least one genotype of at least one haploid plant to at least one trait.

12. The method of claim 11, wherein the genotype comprises a genetic marker.

13. The method of claim 11, further comprising the step of using an association determined in step (b) to make a selection in a plant breeding program.

14. The method of claim 13, wherein said selection comprises selecting among breeding populations based on the at least one genotype.

15. The method of claim 13, wherein said selection comprises selecting progeny in one or more breeding populations based on the at least one genotype.

16. The method of claim 13, wherein said selection comprises selecting among parental lines based on prediction of progeny performance.

17. The method of claim 13, wherein said selection comprises selection of a line for advancement in a germplasm improvement activity based on the at least one genotype.

18. The method of claim 13, further comprising the step of doubling at least one haploid plant selected in said breeding program to obtain a doubled haploid plant.

19. The method of claim 18, wherein the doubled haploid plant is used for introgressing the genotype of interest into a plant for use in a plant breeding program.

20. The method of claim 11, wherein said haploid plant or plants comprise an intact plant, a leaf, vascular tissue, flower, pod, root, stem, seed or portion thereof.

21. The method of claim 11, wherein the plants are selected from the group consisting of maize (Zea mays), soybean (Glycine max), cotton (Gossypium hirsutum), peanut (Arachis hypogaea), barley (Hordeum vulgare);

oats (Avena sativa);

orchard grass (Dactylis glomerata);

rice (Oryza sativa, including indica and japonica varieties);

sorghum (Sorghum bicolor);

sugar cane (Saccharum sp);

tall fescue (Festuca arundinacea);

turfgrass species (e.g. species;

Agrostis stolonifera, Poa pratensis, Stenotaphrum secundatum);

wheat (Triticum aestivum), and alfalfa (Medicago sativa), members of the genus Brassica, carrot, cucumber, dry bean, eggplant, fennel, garden beans, gourd, leek, lettuce, melon, okra, onion, pea, pepper, pumpkin, radish, spinach, squash, sweet corn, tomato, watermelon, and ornamental plants.

22. The method of claim 11, wherein the haploid plant is a fruit, vegetable, tuber, or root crop.

23. The method of claim 11, wherein the trait is selected from the group consisting of herbicide tolerance, disease resistance, insect or pest resistance, altered fatty acid, protein or carbohydrate metabolism, increased grain yield, increased oil, enhanced nutritional content, increased growth rates, enhanced stress tolerance, preferred maturity, enhanced organoleptic properties, altered morphological characteristics, sterility, a trait for industrial use, and a trait for consumer appeal.

24. A method for the association of at least one phenotype with at least one genetic marker using a haploid plant comprising:

a) assaying at least one phenotype of at least one haploid plant with at least one phenotypic marker to determine the presence or absence of said phenotype; and

b) associating the presence or absence of said phenotype with at least one genetic marker.

25. The method of claim 24, wherein said haploid plant is obtained from a haploid breeding population.

26. The method of claim 24, wherein the at least one genetic marker comprises a single nucleotide polymorphism (SNP), an insertion or deletion in DNA sequence (Indel), a simple sequence repeat of DNA sequence (SSR) a restriction fragment length polymorphism, a haplotype, or a tag SNP.

27. The method of claim 24, wherein the at least one phenotypic marker comprises at least one of a transcriptional profile, a metabolic profile, a nutrient composition profile, a protein expression profile, protein composition, protein levels, oil composition, oil levels, carbohydrate composition, carbohydrate levels, fatty acid composition, fatty acid levels, amino acid composition, amino acid levels, biopolymers, pharmaceuticals, starch composition, starch levels, fermentable starch, fermentation yield, fermentation efficiency, energy yield, secondary compounds, metabolites, morphological characteristics, or an agronomic characteristic.

28. The method of claim 24, further comprising the step of using an association determined in step (b) to make a selection in a plant breeding program.

29. The method of claim 28, further comprising the step of doubling at least one haploid plant selected in said breeding program to obtain a doubled haploid plant.

30. The method of claim 29, wherein the doubled haploid plant is used for introgression of the genotype of interest into at least a second plant for use in a plant breeding program.