Genomic Variation Shaped by Environmental and Geographical Factors in Prairie Cordgrass Natural Populations Collected across Its Native Range in the USA.

Jia Guo,Carolyn J Butts-Wilmsmeyer,Patrick J Brown,Dokyoung Lee,Arvid Boe,Albert L Rayburn

doi:10.3390/genes12081240

Abstract

Prairie cordgrass (Spartina pectinata Link) is a native perennial warm-season (C4) grass common in North American prairies. With its high biomass yield and abiotic stress tolerance, there is a high potential of developing prairie cordgrass for conservation practices and as a dedicated bioenergy crop for sustainable cellulosic biofuel production. However, as with many other undomesticated grass species, little information is known about the genetic diversity or population structure of prairie cordgrass natural populations as compared to their ecotypic and geographic adaptation in North America. In this study, we sampled and characterized a total of 96 prairie cordgrass natural populations with 9315 high quality SNPs from a genotyping-by-sequencing (GBS) approach. The natural populations were collected from putative remnant prairie sites throughout the Midwest and Eastern USA, which are the major habitats for prairie cordgrass. Partitioning of genetic variance using SNP marker data revealed significant variance among and within populations. Two potential gene pools were identified as being associated with ploidy levels, geographical separation, and climatic separation. Geographical factors such as longitude and altitude, and environmental factors such as annual temperature, annual precipitation, temperature of the warmest month, precipitation of the wettest month, precipitation of Spring, and precipitation of the wettest month are important in affecting the intraspecific distribution of prairie cordgrass. The divergence of prairie cordgrass natural populations also provides opportunities to increase breeding value of prairie cordgrass as a bioenergy and conservation crop.

Highlights

Prairie grass species native to North America, such as switchgrass (Panicum virgatum L.), big bluestem (Andropogon gerardii Vitman), indiangrass (Sorghastrum nutans L.), and prairie cordgrass have shown potential use for conservation practices and potential bioenergy production [1,2,3,4]
We evaluated the likelihood provided by fastSTRUCTURE and the Bayesian information criterion (BIC) score provided by DAPC to infer the best number of demes supported by the data Figure A2
As chloroplast DNA is mediated through a uni-parental inheritance pattern, the populations from the first chloroplast haplotype group may represent one large ancestral ecotype with a wide distribution that later subdivided into two ecotypes as indicated by the single nucleotide polymorphisms (SNPs) data from this study

Summary

Introduction

Prairie grass species native to North America, such as switchgrass (Panicum virgatum L.), big bluestem (Andropogon gerardii Vitman), indiangrass (Sorghastrum nutans L.), and prairie cordgrass have shown potential use for conservation practices and potential bioenergy production [1,2,3,4]. Prairie cordgrass is a native, perennial, warm-season (C4) grass that once dominated North American tallgrass prairies. Common nursery evaluation of prairie cordgrass in Europe [11], eastern South Dakota [12,13], and central Illinois [1], has shown high biomass yield potential, comparable to that of switchgrass and other warm-season grasses. Compared to other perennial grasses, such as switchgrass and big bluestem, prairie cordgrass has a limited breeding history, with only five cultivars released as sourceidentified genetic material [14,15]. The information of genetic background of other prairie cordgrass natural populations is limited

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