Methods and compositions to select cotton plants resistant to cotton root knot nematode

Abstract

The present invention is in the field of plant breeding and disease resistance. More specifically, the invention provides a method for breeding cotton plants containing one or more quantitative trait loci that are associated with resistance to Root Knot Nematode(RKN), a disease associated with Meloidogyne incognita. The invention further provides germplasm and the use of germplasm containing quantitative trait loci (QTL) conferring disease resistance for introgression into elite germplasm in a breeding program, thus producing novel elite germplasm comprising one or more RKN resistance QTL.

1 . A cotton plant comprising in its genome the root knot nematode resistance loci RKN-1 and RKN-2, produced by a method comprising the steps of:
 a. crossing at least one root knot nematode resistant cotton plant with at least one other cotton plant in order to form a population segregating for resistance to root knot nematode;   b. genotyping at least one cotton plant from said population using at least one SNP marker selected from Table 3 and at least one SNP marker selected from Table 3A; and   c. identifying a cotton plant comprising a desirable genotype at each of RKN-1 locus and RKN-2 locus, wherein said desirable genotype is capable of conferring resistance to root knot nematode in said identified cotton plant.   
     
     
         2 . The cotton plant of  claim 1 , wherein said at least one SNP marker selected from Table 3 is NG0204877. 
     
     
         3 . The cotton plant of  claim 1 , wherein said at least one SNP marker selected from Table 3A are NG0206957, NG0207837, and NG0207518. 
     
     
         4 . The cotton plant of  claim 1 , wherein the cotton plant exhibits a transgenic trait. 
     
     
         5 . The cotton plant of  claim 4 , wherein the transgenic trait is selected from the group consisting of herbicide tolerance, increased yield, insect control, fungal disease resistance, virus resistance, nematode resistance, bacterial disease resistance, mycoplasma diseaseresistance, modified oils production, high oil production, high protein production, germination and/or seedling growth control, enhanced animal and human nutrition, low raffinose, environmental stress resistance, increased digestibility, improved processing traits, improved flavor, nitrogen fixation, hybrid seed production, and reduced allergenicity. 
     
     
         6 . A method of breeding a cotton plant capable of resisting root knot nematode, comprising the steps of:
 a. providing a population of cotton plants;   b. genotyping at least one cotton plant from said population with respect to the RKN-1 locus using at least one SNP marker selected from Table 3; and   c. identifying at least one cotton plant comprising a desirable genotype at the RKN-1 locus wherein said desirable genotype is capable of conferring resistance to root knot nematode in said identified cotton plants.   
     
     
         7 . The method of  claim 6 , wherein the population of cotton plants is derived by crossing at least one root knot nematode resistant cotton plant with at least one other cotton plant to form a population. 
     
     
         8 . The method of  claim 6 , further comprising exposing the identified at least one cotton plant to a root knot nematode inducing pathogen. 
     
     
         9 . The method of  claim 8 , wherein the identified at least one cotton plant exhibits a root knot nematode resistance reaction rating of no worse than about 2.0. 
     
     
         10 . The method of  claim 6 , wherein said at least one SNP marker selected from Table 3 is NG0204877. 
     
     
         11 . A method for selecting a cotton plant comprising in its genome the root knot nematode resistance loci RKN-1 and RKN-2, compromising the steps of:
 a. providing a population of cotton plants;   b. genotyping at least one cotton plant from said population using at least one SNP marker selected from Table 3 and at least one SNP marker selected from Table 3A; and   c. selecting a cotton plant comprising a desirable genotype at each of RKN-1 locus and RKN-2 locus, wherein said desirable genotype is capable of conferring resistance to root knot nematode in said identified cotton plant.   
     
     
         12 . The method of  claim 11 , wherein the population is derived by crossing at least one root knot nematode resistant cotton plant with at least one other cotton plant to form a population. 
     
     
         13 . The method of  claim 11 , further comprising exposing the selected cotton plant to a root knot nematode inducing pathogen. 
     
     
         14 . The method of  claim 13 , wherein the selected cotton plant exhibits a root knot nematode resistance reaction rating of no worse than about 2.0. 
     
     
         15 . The method of  claim 11 , wherein said at least one SNP marker selected from Table 3 is NG0204877. 
     
     
         16 . The method of  claim 11 , wherein said at least one SNP marker selected from Table 3A are NG0206957, NG0207837, and NG0207518. 
     
     
         17 . A substantially purified nucleic acid molecule for the detection of loci related to root knot nematode resistance comprising a nucleic acid molecule selected from the group consisting of SEQ ID NOs: 6, 8, 9, 12, 13, 15-17, 22, 25, 28-32, 34-36, 64-66, 69, 71, 72, 76-78, 80-83, 85, 89.