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ARS Home » Southeast Area » Stoneville, Mississippi » Crop Production Systems Research » Research » Publications at this Location » Publication #299436
Title: Genomic stability of Palmer amaranth plants derived by macro-vegetative propagation

Author
item Teaster, Neal
item Hoagland, Robert

Submitted to: American Journal of Plant Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/21/2014
Publication Date: 10/30/2014
Citation: Teaster, N.D., Hoagland, R.E. 2014. Genomic stability of Palmer amaranth plants derived by macro-vegetative propagation. American Journal of Plant Sciences. 5:3302-3310.

Interpretive Summary: Palmer amaranth, first reported resistant to the herbicide glyphosate in 2006, is now widespread in the southern U.S. and is the most troublesome weed in agronomic crops. Numerous laboratories have studied this weed to more completely understand the biochemistry, physiology and molecular biology parameters related to its aggressive growth habit and mechanism(s) of resistance to glyphosate. Recently, elevated copy number of the gene coding the enzyme EPSPS (target site of glyphosate) was described as the resistance mechanism. Scientists in the USDA-ARS Crop Production Systems Research Unit, Stoneville, MS used a cloning method to propagate Palmer amaranth asexually (macro-vegetative reproduction), and compared tissues from parent plants and plants cloned successively over 10 generations to assess genetic stability. Q-PCR analysis indicated variation of the EPSPS gene copy number in six out of eight clones and four out of the eight clones differed in the RAPD analysis when profiles of the two generations were compared. Findings show that the trait of elevated copy number is retained but some alteration occurred. The process causing copy number elevation is poorly understood, hence this cloning technique may be useful in its elucidation. Slight changes in DNA profiles occurred in some clones over an extended time, but resistance to glyphosate was not affected. These results are important in the characterization of herbicide resistance mechanisms in this weed.

Technical Abstract: Q-PCR (quantitative polymerase chain reaction) and random amplified polymorphic DNA (RAPD) were utilized to investigate genetic stability of Palmer amaranth cloned plants over 10 generations. Q-PCR analysis of DNA from parent Palmer amaranth plants was repeated and confidence levels for determining Ct (threshold crossing) values established. ANOVA was used to determine variation (margin of error) parameters of Ct values. This margin of error was applied to Q-PCR analysis of DNA from eight individual parent plants and their descendants (10th generation) so that possible differences in EPSPS gene copy number could be ascertained. This method (and the associated error) indicated a lack of agreement in Ct values of DNA from plants of these two generations. Q-PCR analysis showed that in six out of eight clones, EPSPS gene copy number varied more than the calculated error (P = 0.05). A second technique to monitor genetic stability, RAPD was used to determine possible changes in genomic DNA due to extended cloning of these regenerated plants. RAPD analysis showed that four out of the eight clones differed when the profiles of the two generations were compared. Results show that qPCR and RAPD analysis generally agree that some Palmer amaranth clones are undergoing changes in genome structure during the 10 generations. Q-PCR analysis suggests EPSPS gene copy number changes are associated with the alterations detected by RAPD analysis. These results indicate that in cloning studies the genetic stability of the propagated lines should be monitored and that in these tests, high copy numbers (resistance to glyphosate) were retained.