Methods for producing cotton plants with enhanced drought tolerance and compositions thereof

A method of creating a population of cotton plants or seeds, said method comprising the steps of:

• a. identifying in a first population of staygreen (STG) cotton plants or seeds, cotton plants having at least one marker linked within 3.0 cM to at least one haplotype comprising three or more representative STG alleles in at least one polymorphic locus;
• b. selecting from said first population one or more cotton plants or seeds comprising said at least one marker linked to said at least one haplotype comprising three or more representative STG alleles;
• and
• c. crossing said selected one or more cotton plants or seeds to produce a second population of cotton plants or seeds comprising an STG phenotype and said at least one haplotype comprising three or more representative STG alleles;
• wherein said haplotype comprises three representative STG alleles of the haplotype of quantitative trail locus (QTL) 1 selected from the group consisting of:
• an A nucleotide at position 61 of SEQ ID NO:1,
• an A nucleotide at position 61 of SEQ ID NO:2,
• an A nucleotide at position 61 of SEQ ID NO:3,
• a T nucleotide at position 440 of SEQ ID NO:4,
• a C nucleotide at position 61 of SEQ ID NO:5,
• an A nucleotide at position 61 of SEQ ID NO:6, and
• an A nucleotide at position 61 of SEQ ID NO:7,
• the haplotype of QTL 2 selected from the group consisting of:
• an A nucleotide at position 61 of SEQ ID NO:8,
• a G nucleotide at position 61 of SEQ ID NO:9,
• a G nucleotide at position 61 of SEQ ID NO:10,
• an insertion beginning at position 224 of SEQ ID NO:11,
• an A nucleotide at position 61 of SEQ ID NO:12,
• a G nucleotide at position 61 of SEQ ID NO:13,
• a G nucleotide at position 61 of SEQ ID NO:14,
• a C nucleotide at position 61 of SEQ ID NO:15,
• a T nucleotide at position 292 of SEQ ID NO:16, and
• a C nucleotide at position 104 of SEQ ID NO:17;
• the haplotype of QTL 3 selected from the group consisting of:
• an A nucleotide at position 61 of SEQ ID NO:18,
• a C nucleotide at position 61 of SEQ ID NO:19,
• a G nucleotide at position 50 of SEQ ID NO:20, and
• an A nucleotide at position 61 of SEQ ID NO:21;
• the haplotype of QTL 4 selected from the group consisting of:
• an A nucleotide at position 61 of SEQ ID NO:22,
• a G nucleotide at position 61 of SEQ ID NO:23,
• a T nucleotide at position 230 of SEQ ID NO:24,
• a G nucleotide at position 61 of SEQ ID NO:25,
• an A nucleotide at position 61 of SEQ ID NO:26,
• a C nucleotide at position 150 of SEQ ID NO:27, and
• an A nucleotide at position 391 of SEQ ID NO:28;
• the haplotype of QTL 5 selected from the group consisting of:
• a C nucleotide at position 61 of SEQ ID NO:29,
• a C nucleotide at position 61 of SEQ ID NO:30,
• a T nucleotide at position 61 of SEQ ID NO:31,
• and an A nucleotide at position 230 of SEQ ID NO:32;
• the haplotype of QTL 6 selected from the group consisting of:
• a C nucleotide at position 61 of SEQ ID NO:33,
• a T nucleotide at position 61 of SEQ ID NO:34,
• a G nucleotide at position 61 of SEQ ID NO:35,
• a T nucleotide at position 156 of SEQ ID NO:36,
• an A nucleotide at position 61 of SEQ ID NO:37,
• a T nucleotide at position 61 of SEQ ID NO:38,
• a C nucleotide at position 61 of SEQ ID NO:39, and
• a C nucleotide at position 61 of SEQ ID NO:40;
• or
• the haplotype of QTL 7 selected from the group consisting of:
• an A nucleotide at position 61 of SEQ ID NO:41;
• an A nucleotide at position 61 of SEQ ID NO:42,
• an A nucleotide at position 61 of SEQ ID NO:43;
• and
• a C nucleotide at position 61 of SEQ ID NO:44.