Molecular markers for low palmitic acid content in sunflower (helianthus annus), and methods of using the same

Abstract

This disclosure concerns methods and compositions for identifying sunflower plants that have a low palmitic acid content phenotype. Some embodiments concern molecular markers to identify, select, and/or construct low palmitic acid content plants and germplasm, or to identify and counter-select relatively high palmitic acid content plants. This disclosure also concerns sunflower plants comprising a low palmitic acid content phenotype that are generated by methods utilizing at least one marker described herein.

What may be claimed is: 
     
         1 . A method for identifying and producing a sunflower plant or germplasm that comprises low palmitic acid content, the method comprising:
 isolating a nucleic acid from a first sunflower plant or germplasm;   detecting whether a marker allele that positively correlates with low palmitic acid content is present in the isolated nucleic acid by amplifying the isolated nucleic acid with an amplification primer or primer pair that is complementary or partially complementary to at least a portion of the marker selected from the group consisting of HA0031B, HA0908, HA1665, HA0304A_H757B, HA0850_H757B, and HA0870, to generate at least one amplicon; and detecting the at least one marker amplicon;   identifying that the first sunflower plant or germplasm comprises low palmitic acid content when the at least one marker amplicon is detected; and   crossing the first sunflower plant or germplasm identified for low palmitic acid content with a second sunflower plant or germplasm, to produce a sunflower plant or germplasm progeny comprising low palmitic acid content.   
     
     
         2 . The method according to  claim 1 , wherein the isolated nucleic acid is a DNA molecule or RNA molecule. 
     
     
         3 . The method according to  claim 1 , wherein the amplifying comprises utilizing a polymerase chain reaction (PCR) or ligase chain reaction (LCR) using the nucleic acid isolated from the first sunflower plant or germplasm as a template in the PCR or LCR. 
     
     
         4 . The method according to  claim 1 , wherein detecting the at least one marker amplicon comprises using software selected from TASSEL™, GeneFlow™, and MapManager-QTX™. 
     
     
         5 . The method according to  claim 1 , wherein the method comprises selecting the first sunflower plant or germplasm. 
     
     
         6 . The method according to  claim 1 , wherein the method comprises selecting the sunflower plant or germplasm progeny. 
     
     
         7 . The method according to  claim 1 , wherein the second sunflower plant or germplasm is a plant or germplasm from an elite sunflower variety or an exotic sunflower variety. 
     
     
         8 . A method for identifying and producing a sunflower plant or germplasm that comprises low palmitic acid content, the method comprising:
 amplifying from genomic DNA of the sunflower plant or germplasm at least one marker linked to low palmitic acid content, wherein the at least one marker is selected from the group consisting of HA0031B, HA0908, HA1665, HA0304A_H757B, HA0850_H757B, and HA0870, to yield a marker amplicon, wherein the amplifying comprises:
 admixing an amplification primer or amplification primer pair with a nucleic acid isolated from the sunflower plant or germplasm, wherein the primer or primer pair is complementary or partially complementary to at least a portion of the marker, and is capable of initiating DNA polymerization by a DNA polymerase using the sunflower nucleic acid as a template, and 
 extending the primer or primer pair in a DNA polymerization reaction comprising a DNA polymerase and a template nucleic acid to generate at least one amplicon; 
   detecting the at least one marker amplicon; and   crossing the sunflower plant or germplasm with a different sunflower plant or germplasm.   
     
     
         9 . The method according to  claim 8 , wherein the different sunflower plant or germplasm is a plant or germplasm from an elite sunflower variety or an exotic sunflower variety. 
     
     
         10 . A method for producing an introgressed sunflower plant or germplasm, the method comprising:
 introgressing at least one marker allele that is positively correlated with low palmitic acid content from a first sunflower plant or germplasm into a second sunflower plant or germplasm, to produce an introgressed sunflower plant or germplasm,   
       wherein the at least one marker is selected from the group consisting of HA0031B, HA0908, HA1665, HA0304A, HA0850, HA0743, HA0870, HA0907, HA0612A, and a marker linked to at least one of HA0031B, HA0908, HA1665, HA0304A, HA0850, HA0743, HA0870, HA0907, and HA0612A. 
     
     
         11 . The method according to  claim 10 , wherein the second sunflower plant or germplasm displays a higher palmitic acid content as compared to the first sunflower plant or germplasm, and wherein the introgressed sunflower plant or germplasm displays an decreased palmitic acid content as compared to the second plant or germplasm. 
     
     
         12 . The introgressed sunflower plant or germplasm produced by the method according to  claim 10 . 
     
     
         13 . The introgressed sunflower plant or germplasm of  claim 12 , wherein the introgressed sunflower plant or germplasm comprises about 3.3% or less total combined palmitic acid (16:0) and stearic acid (18:0) content. 
     
     
         14 . The introgressed sunflower plant or germplasm of  claim 12 , wherein the introgressed sunflower plant or germplasm comprises less than about 2.5% total palmitic acid content. 
     
     
         15 . The introgressed sunflower plant or germplasm of  claim 14 , wherein the introgressed sunflower plant or germplasm comprises less than 2.5% total palmitic acid content. 
     
     
         16 . The introgressed sunflower plant or germplasm of  claim 15 , wherein the introgressed sunflower plant or germplasm comprises less than 2.2% total palmitic acid content. 
     
     
         17 . The introgressed sunflower plant or germplasm of  claim 16 , wherein the introgressed sunflower plant or germplasm comprises less than 2.1% total palmitic acid content. 
     
     
         18 . The introgressed sunflower plant or germplasm of  claim 17 , wherein the introgressed sunflower plant or germplasm comprises less than 2.0% total palmitic acid content. 
     
     
         19 . The method according to  claim 10 , wherein the second sunflower plant or germplasm is a plant or germplasm from an elite sunflower variety or an exotic sunflower variety. 
     
     
         20 . A system for identifying a sunflower plant predicted to have a low palmitic acid content phenotype, the system comprising:
 a set of marker probes or primers configured to detect at least one marker linked to low palmitic acid content, wherein the marker is selected from the group consisting of HA0031B, HA0908, HA1665, HA0304A, HA0850, HA0743, HA0870, HA0907, HA0612A, and a marker linked to at least one of HA0031B, HA0908, HA1665, HA0304A, HA0850, HA0743, HA0870, HA0907, and HA0612A;   a detector that is configured to detect one or more signal outputs from the set of marker probes or primers, or an amplicon thereof, thereby identifying the presence or absence of the marker; and   system instructions that correlate the presence or absence of the marker with the low palmitic acid content phenotype.