Genetic diversity and origin of North American green foxtail [Setaria viridis (L.) Beauv.] accessions

Abstract

Setaria viridis (L.) P. Beauv. and its domesticated form, S. italica (L.) P. Beauv., have been developed over the past few years as model systems for C 4 photosynthesis and for the analysis of bioenergy traits. S. viridis is native to Eurasia, but is now a ubiquitous weed. An analysis of the population structure of a set of 232 S. viridis lines, mostly from North America but also comprising some accessions from around the world, using 11 SSR markers, showed that S. viridis populations in the US largely separate by latitude and/or climatic zone. S. viridis populations from the Northern US and Canada (north of 44°N) group with accessions from Western Europe, while populations in the Mid and Southern US predominantly group with accessions from Turkey and Iran. We hypothesize that S. viridis in the US was most likely introduced from Europe, and that introductions were competitive only in regions that had climatic conditions that were similar to those in the regions of origins. This hypothesis is supported by the fact that Canadian S. viridis lines were fast cycling and undersized when grown in the Mid-Western and Southern US compared to their morphology in their native environment. A comparison of the population structure obtained with 11 SSR markers and *40,000 single nucleotide polymorphisms (SNPs) in a common set of S. viridis germplasm showed that both methods essentially yielded the same groupings, although admixture was identified at a higher frequency in the SNP analysis. Small numbers of SSR markers can thus 123Genet Resour Crop Evol (2017) 64:367-378 DOI 10.1007 be used effectively to discern the population structure in this inbreeding species.

Domestication and Improvement in the Model C4 Grass, Setaria

“…Therefore, studies on the full diversity of the crop, foxtail millet, are limited to Chinese researchers at this time. Fortunately, studies on North American green foxtail wild diversity reveal that much of the species diversity is found there ( Huang et al, 2014 ; Huang and Feldman, 2017 ; Schroder et al, 2017 ), a finding that will be important for future researchers. Another important aspect of the Setaria system is the promise of easy transformability, although there is as yet no published reports of transformation being used to confirm gene function.…”

“…Green foxtail accessions in China show a strong relationship to Chinese foxtail millet accessions, indicative of continued gene flow after domestication. The Chinese green foxtail accessions are distinct from populations in North America, some of which apparently arrived there prior to European settlement ( Huang et al, 2014 ; Huang and Feldman, 2017 ; Schroder et al, 2017 ).…”

“…More recent studies, on Chinese and on two sets of North American collections, have provided new insights into the relationships and diversity of foxtail and green foxtail. The large degree of overlap found by Wang et al (2010) in Chinese foxtail millet and green foxtail accessions may be due to their long shared history, as recent analyses of green foxtail accessions from North America, China, and other regions, found two main groups in North America, and a third group that was more foxtail millet-like, and to which all of the Chinese accessions belonged ( Huang et al, 2014 ; Schroder et al, 2017 ). A recent sequence study of multiple varieties of foxtail millet identified selective sweeps between landrace and improved varieties indicative of selection after domestication, as well as regions of low diversity in all varieties, indicative of a domestication bottleneck ( Jia et al, 2013c ).…”

QTL Mapping Combined With Comparative Analyses Identified Candidate Genes for Reduced Shattering in Setaria italica

“…Most of the resequencing data was for S. viridis accessions collected in the United States that belong to two major genetic subpopulations. Asian S. viridis germplasm largely forms a third subpopulation ( Huang et al, 2014 ; Schröder et al, 2016 )…”

Optimization of Phenotyping Assays for the Model Monocot Setaria viridis

“…The Setaria genome has been sequenced and Agrobacterium -mediated Setaria callus transformation and spike–dip transformation methods have been established ( Bennetzen et al, 2012 ; Martins et al, 2015 ; Saha and Blumwald, 2016 ). There is large extant genetic diversity in this species and mapping populations and large-scale mutant populations are being developed ( Huang et al, 2014 , 2017 ; Layton and Kellogg, 2014 ; Schroder et al, 2017 ). Together with its close relative S. italica , with which it is interfertile, S. viridis also serves as a good model system to study crop domestication ( Li and Brutnell, 2011 ).…”