Genetic diversity and population genetic structure of saltmarsh Spartina alterniflora from four coastal Louisiana basins Herry S. Utomo a, *, Ida Wenefrida a , Michael D. Materne b , Stephen A. Harrison b a Rice Research Station, Louisiana Agricultural Experiment Station, Louisiana State University, Agricultural Center, 1373 Caffey Road, Rayne, LA 70578, USA b School of Plant, Soil, and Environmental Sciences, Louisiana State University Agricultural Center, 104 Sturgis Hall, Baton Rouge, LA 70803, USA 1. Introduction Smooth cordgrass (Spartina alterniflora Loisel.) is a low- intertidal plant species native to the Atlantic and Gulf Coast saltmarshes (Bruno, 2000). As a perennial warm-season grass, it grows vigorously at seawater salinity. It possesses an extensive root system and can tolerate fluctuating water levels and has a great adaptation to many soil types. It provides an effective buffer that reduces shoreline scouring and entraps floating sediments and other solids. Because it is the predominant plant species in coastal marshes, a current practice in coastal erosion control and habitat restoration involves the use of S. alterniflora. Vermilion is currently the only S. alterniflora cultivar released for use in the northern Gulf of Mexico basins. Even though it has a very low-seed set, it has demonstrated superior growth characteristics, has performed well on newly created, enhanced, or highly disturbed saltmarsh, and is often specified as the species of choice by many federal and state conservation agencies when issuing vegetative restoration con- tracts. If the trend continues, however, reclaiming a large area using a single cultivar possesses inherent risks over long-term persistence or survival. Even though inbreeding rates could vary, the use of a single S. alterniflora cultivar may cause genetic decline over time due to inbreeding depression (Daehler, 1999). Genetic variation affects population viability by providing the raw material for natural selection during periods of environmental change (Hamrick, 2004). Development of superior and widely diverse S. alterniflora through breeding becomes critically important to greatly enhance its ability to restore and reclaim degrading saltmarshes (Harrison et al., 2007; Utomo et al., 2007). Louisiana coastal marshes are being rapidly converted into open water at rates estimated at 65–91 km 2 of saltmarsh loss annually (Bourne, 2000). This coastal marsh disappearance represents 80% of the coastal wetland loss nationally and is due to a combination of natural and human causes, including subsidence, sea level rise, hydrologic modification, ditching, dredging, and herbivory (Day et al., 2001). If loss persists at the current rate, it will have devastating effects, since the coastal marshes play a pivotal role in the ecology and economic well being of Louisiana. Because S. alterniflora is the predominant coastal marsh plant that plays a major role in determining estuarine Aquatic Botany 90 (2009) 30–36 ARTICLE INFO Article history: Received 16 August 2007 Received in revised form 2 May 2008 Accepted 10 May 2008 Available online 23 May 2008 Keywords: Spartina alterniflora Smooth cordgrass Genetic diversity DNA marker Population structure Coastal erosion control Habitat restoration ABSTRACT Seventy-two Spartina alterniflora accessions originating from four coastal Louisiana basins (18 accessions per basin) were used to evaluate the genetic structure of this native perennial low-intertidal plant species. The objective of this study was to determine the population genetic structure and diversity of S. alterniflora accessions originating from these four basins using amplified fragment length polymorphism (AFLP) markers. A total of 250 unambiguous and highly repeatable AFLP markers, 186 of which (74.4%) were polymorphic, were obtained using four primer combinations. Overall, pairwise similarity estimates between accessions ranged from 0.70 to 0.93 (average = 0.80) with only a small portion of alleles (0.54– 1.08%) unique to each basin. The average H s (genetic diversity within coastal basins) was 0.20 with an H s values of 0.19, 0.20, 0.20, and 0.21 for Mermentau, Terrebonne, Calcasieu, and Barataria-Breton basin, respectively. AMOVA analysis showed no genetic structure among basins, with the majority of genetic variation, 96.6%, residing within the basins. There was no indication of isolation by distance. Our results suggest that maintaining high levels of genetic diversity can be accomplished through the use of an adequate number of S. alterniflora samples collected within any large basin. Choosing parental lines from several Louisiana coastal basins for breeding purposes may not significantly increase genetic variability among the progeny lines. ß 2008 Elsevier B.V. All rights reserved. * Corresponding author. Tel.: +1 337 7887531; fax: +1 337 7887553. E-mail address: hutomo@agcenter.lsu.edu (H.S. Utomo). Contents lists available at ScienceDirect Aquatic Botany journal homepage: www.elsevier.com/locate/aquabot 0304-3770/$ – see front matter ß 2008 Elsevier B.V. All rights reserved. doi:10.1016/j.aquabot.2008.05.003