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ARS Home » Midwest Area » Urbana, Illinois » Global Change and Photosynthesis Research » Research » Publications at this Location » Publication #234657

Title: Development of microsatellite markers for waterhemp population genetics

item Thinglum, Kate
item Liu, Jianyang
item Lee, Ryan
item Tranel, Patrick
item Davis, Adam

Submitted to: North Central Weed Science Society US Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 11/27/2008
Publication Date: 6/15/2009
Citation: Thinglum, K., Liu, J., Lee, R., Tranel, P.J., Davis, A.S. 2009. Development of Microsatellite Markers for Waterhemp Population Genetics. North Central Weed Science Society US Proceedings. 63:70.

Interpretive Summary:

Technical Abstract: Waterhemp is a major weed in IL and throughout the Midwest, and has evolved resistance to several widely used herbicides. As a dioecious species, with wind-pollinated flowers and prolific seed production, waterhemp tends to evolve resistance rapidly and widely. To evaluate how herbicide resistance spreads within and among populations, it is important to understand waterhemp genetic diversity and population structure. To this end, research is in progress to develop microsatellite markers for waterhemp. Microsatellite markers, based on simple sequence repeats (SSRs) commonly found throughout genomes, are robust, informative DNA markers commonly used in genetic diversity studies. Microsatellites (or SSRs) were identified from partial genome sequencing of a waterhemp plant derived from an Adams County, Illinois population (ACR). Based on these sequence data, 382 primer pairs were identified using SSR Finder Software. A subset of these primer pairs was tested on waterhemp samples from four locations, including two from IL (ACR and WCS) and one each from Missouri and Kansas. Of 136 primer pairs tested, 54 amplified consistently in all four samples under the same reaction conditions, and were kept for further analysis. The PCR products from about half of these 54 primer pairs were sequenced, and results confirmed that the expected fragment was amplified in all cases and an SSR was present. Gel analysis of the PCR products showed that 13 primer pairs generated polymorphic fragments among the four populations. Sequence data from two of these confirmed that the polymorphic fragments were due to the presence of differing numbers of SSR repeats. The primer pairs producing polymorphic band sizes will be useful for population genetics studies of waterhemp.