Markers linked to reniform nematode resistance

Abstract

This disclosure concerns methods and compositions for identifying cotton plants that have a reniform nematode resistance trait. Some embodiments concern molecular markers to identify, select, and/or construct reniform nematode resistant plants and germplasm, or to identify and counter-select relatively susceptible plants. This disclosure also concerns cotton plants comprising a reniform nematode resistance trait that are generated by methods utilizing at least one marker described herein.

What is claimed is: 
     
         1 . A method for producing a reniform nematode (RN) resistant cotton plant comprising the steps of:
 a) isolating nucleic acids from a cotton plant selected from population of cotton plants;   b) detecting in the nucleic acids of (a) at least one allele of a SNP marker locus that is associated with RN resistance in a cotton plant,
 i) wherein said SNP marker locus is located within an 18 cM chromosomal interval on  Gossypium barbadense  chromosome 21 defined by and including SNP markers DCTE1_232591_126 (SEQ ID NO:8) and DASCTP_10515_556 (SEQ ID NO:21) or 
 ii) wherein said SNP marker locus is located within an 9 cM chromosomal interval on  Gossypium barbadense  chromosome 21 defined by and including SNP markers DASCTP_39375_356 (SEQ ID NO:10) and DASCTP_8602_418 (SEQ ID NO:20), 
 and wherein the SNP marker comprises an allele that is indicative of RN resistance; 
   c) selecting a first cotton plant from the population of (a) based on the presence of the marker locus of (b);   d) crossing the first cotton plant of (c) with a second cotton plant not comprising in its genome the marker detected in (b);   e) collecting seed from the cross of (d); and   f) growing a F1 progeny cotton plant from the seed of (e), wherein said F1 progeny cotton plant comprises in its genome said marker locus associated with RN resistance, thereby producing a RN resistant cotton plant.   
     
     
         2 . The method of  claim 1 , wherein the at least one allele of a SNP marker locus that is associated with RN resistance in a cotton plant is selected from the group consisting of DCTE1_232591_126 (SEQ ID NO:8), DCTE1_365870_69 (SEQ ID NO:9), DASCTP_39375_356 (SEQ ID NO:10), DCTE1_240643_347 (SEQ ID NO: 11), DCTE1_208529_965 (SEQ ID NO:12), DCTE1_271930_223 (SEQ ID NO:13), DASCTP_59246_191 (SEQ ID NO:14), DASCTP_28910_164 (SEQ ID NO:15), DASCTP_1656_527 (SEQ ID NO:16), DASCTP_51689_504 (SEQ ID NO:17), DCTE1_214869_124 (SEQ ID NO:18), DASCTP_8602_496 (SEQ ID NO: 19), DASCTP_8602_418 (SEQ ID NO:20), and DASCTP_10515_556 (SEQ ID NO:21). 
     
     
         3 . The method of  claim 1  or  2 , wherein the method comprises detecting at least one allele of a SNP marker locus located within a 9 cM  G. barbadense  chromosome 21 interval flanked by and including SNP markers DASCTP_39375_356 (SEQ ID NO:10) and DASCTP_8602_418 (SEQ ID NO:20), wherein the SNP marker comprises an allele that is indicative of RN resistance. 
     
     
         4 . The method of  claim 3 , wherein the at least one allele of a SNP marker locus that is associated with RN resistance in a cotton plant is selected from the group consisting of DASCTP_39375_356 (SEQ ID NO:10), DCTE1_240643_347 (SEQ ID NO:11), DCTE1_208529_965 (SEQ ID NO:12), DCTE1_271930_223 (SEQ ID NO: 13), DASCTP_59246_191 (SEQ ID NO:14), DASCTP_28910_164 (SEQ ID NO: 15), DASCTP_1656_527 (SEQ ID NO:16), DASCTP_51689_504 (SEQ ID NO: 17), DCTE1_214869_124 (SEQ ID NO:18), DASCTP_8602_496 (SEQ ID NO:19), and DASCTP_8602_418 (SEQ ID NO:20). 
     
     
         5 . The method according to any one of  claims 1 - 4 , wherein the cotton plant comprises one or more RN resistant SNP marker allele (i) from variety IncaGB713 or its lineage, or (ii) DASCTP_1656_527 (SEQ ID NO:16). 
     
     
         6 . The method according to any one of  claims 1 - 5 , wherein detecting the one or more RN resistant marker alleles comprises allele-specific polymerase chain reaction (PCR) amplification or nucleic acid sequencing. 
     
     
         7 . The method according to  claim 1 , wherein the first cotton plant is a plant from an elite cotton variety. 
     
     
         8 . The method according to  claim 1 , wherein the first cotton plant is Upland cotton. 
     
     
         9 . A cotton plant identified by the method of any one of  claims 1 - 5 . 
     
     
         10 . Seed from a cotton plant according to  claim 9 . 
     
     
         11 . The method according to  claim 1 , wherein the first cotton plant comprises root knot nematode (RKN) resistance. 
     
     
         12 . The method according to  claim 11 , wherein the selected F1 progeny plant comprises increased RN resistance as compared to a selected F1 progeny plant that does not comprise RKN resistance. 
     
     
         13 . The method according to  claim 1 , wherein the method further comprises
 a) selecting one or more F1 progeny plants that have the at least one SNP marker allele associated with RN resistance to produce selected F1 progeny plants;   b) crossing the selected F1 progeny plants with a second cotton plant to produce F2 progeny plants; and,   c) selecting one or more F2 progeny plants that have the at least one SNP marker allele to produce selected F2 progeny plants.   
     
     
         14 . The method according to  claim 13 , wherein the method further comprises repeating the crossing and selection step three or more times, to produce selected fourth or higher progeny plants that have the at least one SNP marker allele. 
     
     
         15 . The method according to  claim 13 , wherein the second cotton plant is a plant from an elite cotton variety.