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Population Genetics/Genomics

Lopez, Alexander Joseph [1], Shrestha, Anil [2], Sosnoskie, Lynn [3], Waselkov, Katherine [4].

Origins of Amaranthus tuberculatus (Waterhemp) in Central Valley Agroecosystems: A Population Genetics Approach Using Genotyping-By-Sequencing.

Native to wetland environments of the Mississippi valley, Amaranthus tuberculatus (waterhemp) began invading agricultural cropping systems in the 1950’s and has since become a widespread troublesome weed throughout the Midwestern United States. This species of Amaranthus was not historically a common weed in the agriculturally intensive Central Valley of California; however, in the last decade waterhemp has been increasingly observed invading agroecosystems within Merced County. The aim of this study is to (1) document and map the distribution of these recent waterhemp infestations in the Central Valley, (2) genetically characterize and determine the geographic origin of the source(s) of this invasion, and (3) evaluate likely evolutionary route(s) that may have facilitated this invasion. Between 2019-2020, we conducted multiple surveys to identify the extent of the distribution of waterhemp within the Central Valley; 7 populations of waterhemp were identified invading various agricultural fields (almond, corn, hay, rice) in Merced County between Highways 140 & 152. At each location, we collected leaf samples (20 individuals/population) and subsequently isolated high molecular weight DNA from each individual for genetic characterization. 100-bp DNA libraries for these samples were prepared using the robust method of genotyping-by-sequencing with the restriction enzyme ApeKI and subsequently sequenced to 10x coverage on the massively parallel Illumina HiSeq 4000 next-generation sequencing platform. We also sequenced 4-10 individuals from 16 wild and invasive populations from across the species’ native range in the Midwestern U.S. and Canada for genetic comparison. Raw single end reads from the Illumina platform in FastQ format were de-multiplexed, filtered, and genotyped for SNP discovery using the STACKS 1.44 pipeline, resulting in 15,316 variant sites. To determine the origin of these infestations, we will assess and compare allelic variation within Merced infestations to Midwestern populations using both the model-based genetic clustering method STRUCTURE 2.3.4, and the non-model-based clustering method of PCA. Evolutionary history and routes of this invasion will be evaluated through demographic modeling using the method of approximate Bayesian computation with DIY ABC 1.0 software. Many Midwestern waterhemp populations have previously been genetically characterized; therefore, by determining the source and evolutionary routes of this invasion, we can infer the potential invasiveness and incidence of herbicide resistances in these recent introductions. Furthermore, we hope to shed some light on the relative importance of preadaptation and evolutionary change in overcoming selection pressures in agroecosystem invasions, as well as the role and importance of multiple introductions.

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1 - California State University Fresno, Biology, 5241 N Maple Ave, Fresno, CA, 93740, USA
2 - California State University Fresno, Plant Science, 2415 E. San Ramon Ave, M/S AS72, Fresno, CA, 93740, USA
3 - Cornell University, School of Integrative Plant Science, 635 W North St., 221 Hedrick Hall, Geneva, NY, 14456, USA
4 - California State University, Fresno, Biology Department, M/S SB73, 2555 E. San Ramon Ave., Science 1, Fresno, CA, 93740, United States

Population Genetics.

Presentation Type: Oral Paper
Session: PGG3, Population Genetics and Genomics III
Location: /
Date: Wednesday, July 21st, 2021
Time: 1:00 PM(EDT)
Number: PGG3003
Abstract ID:470
Candidate for Awards:Margaret Menzel Award

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