Methods and compositions for producing brachytic corn plants
The present disclosure is in the field of plant breeding. The disclosure provides methods for breeding corn plants having a brachytic trait using marker-assisted selection. The disclosure further provides brachytic germplasm, markers associated with a brachytic trait for introgressing the trait into elite germplasm in a breeding program. This disclosure also provides brachytic or dwarf elite corn varieties having yield equal to or higher than conventional non-brachytic corn varieties.
1. A method for selecting a corn plant or seed, said method comprising:
a. crossing a first corn plant comprising at least one brachytic allele at a polymorphic locus with a second corn plant to produce a progeny population of corn plants or progeny seeds;
b. conducting a marker assay to detect in said progeny population of corn plants or progeny seeds a corn plant or seed comprising a brachytic allele at a polymorphic locus selected from the group consisting of SEQ ID NOs: 5, 6, 8, 11 to 22, and 86 to 95; and
c. selecting said corn plant or seed comprising said brachytic allele;
and wherein:
said brachytic allele at SEQ ID NO:5 comprises a 3 nucleotide deletion beginning at position 70,
said brachytic allele at SEQ ID NO:6 comprises a G nucleotide at position 70,
said brachytic allele at SEQ ID NO:8 comprises a GTCCGT nucleotide insertion beginning at position 72,
said brachytic allele at SEQ ID NO:11 comprises an A nucleotide at position 62,
said brachytic allele at SEQ ID NO:12 comprises a T nucleotide at position 70,
said brachytic allele at SEQ ID NO:13 comprises a T nucleotide at position 72,
said brachytic allele at SEQ ID NO:14 comprises a G nucleotide at position 72,
said brachytic allele at SEQ ID NO:15 comprises a G nucleotide at position 72,
said brachytic allele at SEQ ID NO:16 comprises an A nucleotide at position 72,
said brachytic allele at SEQ ID NO:17 comprises a C nucleotide at position 72,
said brachytic allele at SEQ ID NO:18 comprises a G nucleotide at position 72,
said brachytic allele at SEQ ID NO:19 comprises a C nucleotide at position 72,
said brachytic allele at SEQ ID NO:20 comprises a T nucleotide at position 72,
said brachytic allele at SEQ ID NO:21 comprises a C nucleotide at position 72,
said brachytic allele at SEQ ID NO:22 comprises a CTCG nucleotide insertion beginning at position 72,
said brachytic allele at SEQ ID NO:86 comprises a 6 nucleotide deletion beginning at position 72,
said brachytic allele at SEQ ID NO:87 comprises a TG nucleotide insertion beginning at position 76,
said brachytic allele at SEQ ID NO:88 comprises a GGTA nucleotide insertion beginning at position 66,
said brachytic allele at SEQ ID NO:89 comprises a 6 nucleotide deletion beginning at position 71,
said brachytic allele at SEQ ID NO:90 comprises a T nucleotide at position 77,
said brachytic allele at SEQ ID NO:91 comprises a TT nucleotide insertion beginning at position 60,
said brachytic allele at SEQ ID NO:92 comprises a multi-kilobase insertion beginning at position 63,
said brachytic allele at SEQ ID NO:93 comprises an 85 nucleotide deletion beginning at position 51,
said brachytic allele at SEQ ID NO:94 comprises an 18 nucleotide insertion beginning at position 52, or
said brachytic allele at SEQ ID NO:95 comprises a 579 nucleotide insertion beginning at position 66.
2. The method of claim 1 , wherein said method further comprises backcrossing said selected corn plant or a corn plant grown from said seed with said second corn plant.
3. The method of claim 1 , wherein said selected corn plant or seed is homozygous for said brachytic allele.
4. The method of claim 3 , wherein the height at maturity of said selected corn plant or a corn plant grown from said seed is reduced to between 10% and 70% compared to a control plant not having said brachytic allele.
5. The method of claim 3 , wherein the yield of said selected corn plant or a corn plant grown from said seed is equal to or more than the yield of a control plant not having said brachytic allele.
6. The method of claim 3 , wherein said selected corn plant or a corn plant grown from said seed requires between 5% and 25% fewer heat units to reach anthesis than a control plant not having said brachytic allele.
7. The method of claim 3 , wherein said selected corn plant or a corn plant grown from said seed has a relative maturity of between 10% and 45% fewer days than a control plant not having said brachytic allele.
8. The method of claim 1 , wherein said brachytic allele predicts a brachytic trait with a accuracy of at least 50%.
9. A method of creating a population of corn plants, said method comprising:
a. genotyping a first population of corn plants, said population comprising at least one brachytic allele of a polymorphic locus, wherein said polymorphic locus is selected from the group consisting of SEQ ID NOs: 5, 6, 8, 11 to 22, and 86 to 95;
b. selecting from said first population one or more corn plants containing said at least one brachytic allele; and
c. crossing or selfing said selected one or more corn plants to produce a second population, wherein said second population of corn plants comprises said at least one brachytic allele; and
wherein:
said brachytic allele at SEQ ID NO:5 comprises a 3 nucleotide deletion beginning at position 70,
said brachytic allele at SEQ ID NO:6 comprises a G nucleotide at position 70,
said brachytic allele at SEQ ID NO:8 comprises a GTCCGT nucleotide insertion beginning at position 72,
said brachytic allele at SEQ ID NO:11 comprises an A nucleotide at position 62,
said brachytic allele at SEQ ID NO:12 comprises a T nucleotide at position 70,
said brachytic allele at SEQ ID NO:13 comprises a T nucleotide at position 72,
said brachytic allele at SEQ ID NO:14 comprises a G nucleotide at position 72,
said brachytic allele at SEQ ID NO:15 comprises a G nucleotide at position 72,
said brachytic allele at SEQ ID NO:16 comprises an A nucleotide at position 72,
said brachytic allele at SEQ ID NO:17 comprises a C nucleotide at position 72,
said brachytic allele at SEQ ID NO:18 comprises a G nucleotide at position 72,
said brachytic allele at SEQ ID NO:19 comprises a C nucleotide at position 72,
said brachytic allele at SEQ ID NO:20 comprises a T nucleotide at position 72,
said brachytic allele at SEQ ID NO:21 comprises a C nucleotide at position 72,
said brachytic allele at SEQ ID NO:22 comprises a CTCG nucleotide insertion beginning at position 72,
said brachytic allele at SEQ ID NO:86 comprises a 6 nucleotide deletion beginning at position 72,
said brachytic allele at SEQ ID NO:87 comprises a TG nucleotide insertion beginning at position 76,
said brachytic allele at SEQ ID NO:88 comprises a GGTA nucleotide insertion beginning at position 66,
said brachytic allele at SEQ ID NO:89 comprises a 6 nucleotide deletion beginning at position 71,
said brachytic allele at SEQ ID NO:90 comprises a T nucleotide at position 77,
said brachytic allele at SEQ ID NO:91 comprises a TT nucleotide insertion beginning at position 60,
said brachytic allele at SEQ ID NO:92 comprises a multi-kilobase insertion beginning at position 63,
said brachytic allele at SEQ ID NO:93 comprises an 85 nucleotide deletion beginning at position 51,
said brachytic allele at SEQ ID NO:94 comprises an 18 nucleotide insertion beginning at position 52, or
said brachytic allele at SEQ ID NO:95 comprises a 579 nucleotide insertion beginning at position 66.
10. The method of claim 1 , wherein said first corn plant, said second corn plant, or both are a hybrid dwarf or hybrid semi-dwarf variety.
11. The method of claim 1 , wherein said selected corn plant or seed is a hybrid.
12. The method of claim 9 , wherein said first population of corn plants is a hybrid dwarf or hybrid semi-dwarf variety.
13. The method of claim 9 , wherein said selected corn plant or seed is a hybrid.
14. The method of claim 9 , wherein said method further comprises backcrossing at least one corn plant from said second population with a corn plant from said first population.
15. The method of claim 9 , wherein said genotyping comprises a marker assay.
16. The method of claim 9 , wherein said second population of corn plants is homozygous for said brachytic allele.
17. The method of claim 16 , wherein the height at maturity of a corn plant from said second population is reduced between 10% and 70% compared to a control plant not having said brachytic allele.
18. The method of claim 16 , wherein the yield of, a corn plant from said second population is equal to or more than the yield of a control plant not having said brachytic allele.
19. The method of claim 16 , wherein a corn plant from said second population requires between 5% and 25% fewer heat units to reach anthesis than a control plant not having said brachytic allele.
20. The method of claim 16 , wherein a corn plant from said second population has a relative maturity of between 10% and 45% fewer days than a control plant not having said brachytic allele.