Methods and Compositions for Watermelon Firmness

Abstract

The invention provides for unique watermelon plants with an ultra-firm flesh phenotype and their progeny. Such plants may comprise an introgressed QTL associated with an ultra-firm flesh phenotype. In certain aspects, compositions, including distinct polymorphic molecular markers, and methods for producing, breeding, identifying, selecting, and the like of plants or germplasm with an ultra-firm flesh phenotype are provided.

1 . A watermelon plant comprising in its genome: i) at least one introgressed allele locus associated with an ultra-firm watermelon flesh phenotype wherein the locus is in a genomic region flanked by loci NW0251464 (SEQ ID NO: 1) and NW0250266 (SEQ ID NO: 18), and ii) one or more polymorphic loci comprising alleles or combinations of alleles that are not found in an ultra-firm watermelon flesh variety and that are linked to said locus associated with an ultra-firm watermelon flesh phenotype, or a progeny plant therefrom. 
     
     
         2 . The watermelon plant of  claim 1  wherein the fruit of said watermelon plant has flesh that resists a pressure of at least about 3.5 lb/F. 
     
     
         3 . The watermelon plant of  claim 1  wherein cut flesh from the fruit of said watermelon plant loses less than about four percent water after three days storage at 4° centigrade. 
     
     
         4 . The watermelon plant of  claim 1  wherein the locus is in a genomic region flanked by:
 a) loci NW0251464 (SEQ ID NO: 1) and NW0251011 (SEQ ID NO: 12); 
 b) loci NW0251464 (SEQ ID NO: 1) and NW0252274 (SEQ ID NO: 10); 
 c) loci NW0248953 (SEQ ID NO: 2) and NW0250266 (SEQ ID NO: 18); 
 d) loci NW0248953 (SEQ ID NO: 2) and NW0251011 (SEQ ID NO: 12); 
 e) loci NW0248953 (SEQ ID NO: 2) and NW0252274 (SEQ ID NO: 10); 
 f) loci NW0250301 (SEQ ID NO: 3) and NW0250266 (SEQ ID NO: 18); 
 g) loci NW0250301 (SEQ ID NO: 3) and NW0251011 (SEQ ID NO: 12); or 
 h) loci NW0250301 (SEQ ID NO: 3) and NW0252274 (SEQ ID NO: 10). 
 
     
     
         5 . A part of the watermelon plant of  claim 1 , wherein said part is selected from the group consisting of pollen, an ovule, a leaf, an embryo, a root, a root tip, an anther, a flower, a fruit, a stem, a shoot, a seed, a protoplast, a cell, and a callus. 
     
     
         6 . A method of detecting in at least one watermelon plant a genotype associated with an ultra-firm watermelon flesh phenotype, the method comprising the step of:
 (i) detecting in at least one watermelon plant an allele of at least one polymorphic nucleic acid that is associated with an ultra-firm watermelon flesh phenotype, wherein the polymorphic nucleic acid is in a genomic region flanked by loci NW0251464 (SEQ ID NO: 1) and NW0250266 (SEQ ID NO: 18).   
     
     
         7 . The method of  claim 6  further comprising the step of:
 (ii) identifying at least one watermelon plant in which a genotype associated with an ultra-firm flesh watermelon phenotype has been detected and denoting that the watermelon plant comprises a genotype associated with an ultra-firm watermelon flesh phenotype. 
 
     
     
         8 . The method of  claim 6  wherein the polymorphic nucleic acid is located in a genomic region flanked by:
 a) loci NW0251464 (SEQ ID NO: 1) and NW0251011 (SEQ ID NO: 12); 
 b) loci NW0251464 (SEQ ID NO: 1) and NW0252274 (SEQ ID NO: 10); 
 c) loci NW0248953 (SEQ ID NO: 2) and NW0250266 (SEQ ID NO: 18); 
 d) loci NW0248953 (SEQ ID NO: 2) and NW0251011 (SEQ ID NO: 12); 
 e) loci NW0248953 (SEQ ID NO: 2) and NW0252274 (SEQ ID NO: 10); 
 f) loci NW0250301 (SEQ ID NO: 3) and NW0250266 (SEQ ID NO: 18); 
 g) loci NW0250301 (SEQ ID NO: 3) and NW0251011 (SEQ ID NO: 12); or 
 h) loci NW0250301 (SEQ ID NO: 3) and NW0252274 (SEQ ID NO: 10). 
 
     
     
         9 . The method of  claim 6  wherein at least one of said polymorphic nucleic acid is selected from the group consisting of NW0248953 (SEQ ID NO: 2), NW0250301 (SEQ ID NO: 3), NW0248949 (SEQ ID NO: 4), NW0248646 (SEQ ID NO: 5), NW0249077 (SEQ ID NO: 6), NW0249132 (SEQ ID NO: 7), NW0252494 (SEQ ID NO: 8), NW0248163 (SEQ ID NO: 9), NW0252274 (SEQ ID NO: 10), NW0248905 (SEQ ID NO: 11), NW0251011 (SEQ ID NO: 12), NW0248869 (SEQ ID NO: 13), NW0251470 (SEQ ID NO: 14), NW0251308 (SEQ ID NO: 15), NW0250718 (SEQ ID NO: 16), and NW0248059 (SEQ ID NO: 17). 
     
     
         10 . The method of  claim 6 , wherein the genotype associated with an ultra-firm watermelon flesh genotype comprises having at least one of: at least one allele of the C allelic state of the polymorphic nucleic acid of NW0252274 (SEQ ID NO: 10); at least one allele of the C allelic state of the polymorphic nucleic acid of NW0248646 (SEQ ID NO: 5); or at least one allele of the G allelic state of the polymorphic nucleic acid of NW0250301 (SEQ ID NO: 3). 
     
     
         11 . A method for introgressing a locus associated with an ultra-firm watermelon flesh phenotype into a watermelon plant, the method comprising:
 (i) crossing a first watermelon plant lacking a locus associated with an ultra-firm watermelon flesh phenotype with a second watermelon plant comprising: (a) an allele of at least one polymorphic nucleic acid that is associated with an ultra-firm watermelon flesh phenotype located in a genomic region flanked by loci NW0251464 (SEQ ID NO: 1) and NW0250266 (SEQ ID NO: 18), and (b) at least one additional polymorphic locus located outside of said region that is not present in said first watermelon plant, to obtain a population of watermelon plants segregating for the polymorphic locus that is associated with an ultra-firm watermelon flesh phenotype and said additional polymorphic locus; and   (ii) detecting said polymorphic locus in at least one watermelon plant from said population of watermelon plants.   
     
     
         12 . The method of  claim 11  wherein the fruit of said selected watermelon plant comprising an introgressed locus associated with an ultra-firm watermelon flesh phenotype has flesh that resists a pressure of at least about 3.5 lb/F. 
     
     
         13 . The method of  claim 11  wherein cut flesh from the fruit of said selected watermelon plant loses less than about four percent water after three days storage at 4° centigrade. 
     
     
         14 . The method of  claim 11  wherein the polymorphic nucleic acid is located in a genomic region flanked by:
 a) loci NW0251464 (SEQ ID NO: 1) and NW0251011 (SEQ ID NO: 12); 
 b) loci NW0251464 (SEQ ID NO: 1) and NW0252274 (SEQ ID NO: 10); 
 c) loci NW0248953 (SEQ ID NO: 2) and NW0250266 (SEQ ID NO: 18); 
 d) loci NW0248953 (SEQ ID NO: 2) and NW0251011 (SEQ ID NO: 12); 
 e) loci NW0248953 (SEQ ID NO: 2) and NW0252274 (SEQ ID NO: 10); 
 f) loci NW0250301 (SEQ ID NO: 3) and NW0250266 (SEQ ID NO: 18); 
 g) loci NW0250301 (SEQ ID NO: 3) and NW0251011 (SEQ ID NO: 12); or 
 h) loci NW0250301 (SEQ ID NO: 3) and NW0252274 (SEQ ID NO: 10). 
 
     
     
         15 . The method of  claim 11  wherein the introgressed locus associated with an ultra-firm watermelon flesh phenotype comprises at least one polymorphic nucleic acid that is associated with an ultra-firm watermelon flesh phenotype selected from the group consisting of NW0248953 (SEQ ID NO: 2), NW0250301 (SEQ ID NO: 3), NW0248949 (SEQ ID NO: 4), NW0248646 (SEQ ID NO: 5), NW0249077 (SEQ ID NO: 6), NW0249132 (SEQ ID NO: 7), NW0252494 (SEQ ID NO: 8), NW0248163 (SEQ ID NO: 9), NW0252274 (SEQ ID NO: 10), NW0248905 (SEQ ID NO: 11), NW0251011 (SEQ ID NO: 12), NW0248869 (SEQ ID NO: 13), NW0251470 (SEQ ID NO: 14), NW0251308 (SEQ ID NO: 15), NW0250718 (SEQ ID NO: 16), and NW0248059 (SEQ ID NO: 17). 
     
     
         16 . The method of  claim 15  wherein at least one of said polymorphic nucleic acid that is associated with an ultra-firm watermelon flesh phenotype is selected from the group consisting of NW0250301 (SEQ ID NO: 3), NW0248646 (SEQ ID NO: 5), and NW0252274 (SEQ ID NO: 10). 
     
     
         17 . The method of  claim 11 , wherein the introgressed locus associated with an ultra-firm watermelon flesh phenotype comprises a genotype having at least one of: at least one allele of the C allelic state of the polymorphic nucleic acid of NW0252274 (SEQ ID NO: 10); at least one allele of the C allelic state of the polymorphic nucleic acid of NW0248646 (SEQ ID NO: 5); or at least one allele of the G allelic state of the polymorphic nucleic acid of NW0250301 (SEQ ID NO: 3). 
     
     
         18 . A watermelon plant produced by the method of  claim 11  or a progeny plant therefrom. 
     
     
         19 . A part of the watermelon plant of  claim 18 , wherein said part is selected from the group consisting of pollen, an ovule, a leaf, an embryo, a root, a root tip, an anther, a flower, a fruit, a stem, a shoot, a seed, a protoplast, a cell, and a callus. 
     
     
         20 . An isolated nucleic acid probe or primer of at least 12 nucleotides in length that hybridizes under conditions of 5×SSC, 50% formamide, and at 42° C. to a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1-18 or a fragment thereof, that contains a specific allelic variant. 
     
     
         21 . An isolated oligonucleotide comprising a nucleic acid molecule selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, and 18, and any specific allelic variants thereof. 
     
     
         22 . An isolated oligonucleotide comprising a nucleic acid fragment of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, or 18, that contains a specific allelic variant thereof and that is at least 12 nucleotides in length. 
     
     
         23 . The oligonucleotide of  claim 22  wherein the fragment that contains said allelic variant is at least 15, at least 18, at least 20, at least 22, at least 25, or at least 30 nucleotides in length. 
     
     
         24 . A method of introgressing an allele into a watermelon plant, the method comprising:
 (i) providing a population of watermelon plants;   (ii) genotyping at least one watermelon plant in the population with respect to at least one polymorphic nucleic acid located in a genomic region flanked by loci NW0251464 (SEQ ID NO: 1) and NW0250266 (SEQ ID NO: 18), and   (iii) selecting from the population at least one watermelon plant comprising at least one allele associated with an ultra-firm watermelon flesh phenotype.   
     
     
         25 . The method of  claim 24  wherein the fruit of the selected watermelon plant has flesh that resists a pressure of at least about 3.5 lb/F. 
     
     
         26 . The method of  claim 24  wherein cut flesh of the fruit of the selected watermelon plant loses less than about four percent water after three days storage at 4° centigrade. 
     
     
         27 . The method of  claim 24  wherein the polymorphic nucleic acid is located in a genomic region flanked by:
 a) loci NW0251464 (SEQ ID NO: 1) and NW0251011 (SEQ ID NO: 12); 
 b) loci NW0251464 (SEQ ID NO: 1) and NW0252274 (SEQ ID NO: 10); 
 c) loci NW0248953 (SEQ ID NO: 2) and NW0250266 (SEQ ID NO: 18); 
 d) loci NW0248953 (SEQ ID NO: 2) and NW0251011 (SEQ ID NO: 12); 
 e) loci NW0248953 (SEQ ID NO: 2) and NW0252274 (SEQ ID NO: 10); 
 f) loci NW0250301 (SEQ ID NO: 3) and NW0250266 (SEQ ID NO: 18); 
 g) loci NW0250301 (SEQ ID NO: 3) and NW0251011 (SEQ ID NO: 12); or 
 h) loci NW0250301 (SEQ ID NO: 3) and NW0252274 (SEQ ID NO: 10). 
 
     
     
         28 . The method of  claim 24  wherein at least one of said polymorphic nucleic acid is selected from the group consisting of NW0248953 (SEQ ID NO: 2), NW0250301 (SEQ ID NO: 3), NW0248949 (SEQ ID NO: 4), NW0248646 (SEQ ID NO: 5), NW0249077 (SEQ ID NO: 6), NW0249132 (SEQ ID NO: 7), NW0252494 (SEQ ID NO: 8), NW0248163 (SEQ ID NO: 9), NW0252274 (SEQ ID NO: 10), NW0248905 (SEQ ID NO: 11), NW0251011 (SEQ ID NO: 12), NW0248869 (SEQ ID NO: 13), NW0251470 (SEQ ID NO: 14), NW0251308 (SEQ ID NO: 15), NW0250718 (SEQ ID NO: 16), and NW0248059 (SEQ ID NO: 17). 
     
     
         29 . The method of  claim 24 , wherein at least one of said polymorphic nucleic acid is selected from the group consisting of NW0250301 (SEQ ID NO: 3), NW0248646 (SEQ ID NO: 5), and NW0252274 (SEQ ID NO: 10). 
     
     
         30 . A watermelon plant or part of said watermelon plant obtained by the method of  claim 24 .