The Genetic Basis of Upland/Lowland Ecotype Divergence in Switchgrass (Panicum virgatum)

Abstract

The evolution of locally adapted ecotypes is a common phenomenon that generates diversity within plant species. However, we know surprisingly little about the genetic mechanisms underlying the locally adapted traits involved in ecotype formation. The genetic architecture underlying locally adapted traits dictates how an organism will respond to environmental selection pressures, and has major implications for evolutionary ecology, conservation, and crop breeding. To understand the genetic architecture underlying the divergence of switchgrass (Panicum virgatum) ecotypes, we constructed a genetic mapping population through a four-way outbred cross between two northern upland and two southern lowland accessions. Trait segregation in this mapping population was largely consistent with multiple independent loci controlling the suite of traits that characterizes ecotype divergence. We assembled a joint linkage map using ddRADseq, and mapped quantitative trait loci (QTL) for traits that are divergent between ecotypes, including flowering time, plant size, physiological processes, and disease resistance. Overall, we found that most QTL had small to intermediate effects. While we identified colocalizing QTL for multiple traits, we did not find any large-effect QTL that clearly controlled multiple traits through pleiotropy or tight physical linkage. These results indicate that ecologically important traits in switchgrass have a complex genetic basis, and that similar loci may underlie divergence across the geographic range of the ecotypes.

Geographic variation in the genetic basis of resistance to leaf rust between locally adapted ecotypes of the biofuel crop switchgrass (Panicum virgatum)

“…To identify loci controlling variation in rust progression, we used a previously developed four-way phase-known (pseudo-testcross) mapping population derived from both upland and lowland genotypes (conceptual map in Figure 1). For full details of the development of the mapping population see (Milano et al, 2016). We clonally divided the outbred populations by manually splitting rhizomes at the Brackenridge Field Laboratory in Austin, TX.…”

“…Over three years, this resulted in more than 149,000 rust ratings, which we used for the QTL analyses. In addition, we measured other morphological and physiological traits at all sites, including the number of tillers, plant height at end of season, date of first flowering, and end-of-season aboveground biomass (see Milano et al, 2016 andLowry et al, 2019 for details of this phenotyping effort). Figure S4)…”

“…Switchgrass has also become an important study system for understanding the causes of ecological specialization (Casler, 2012;Lowry et al, 2014). Switchgrass is split into two locally adapted ecotypes, upland and lowland (Morris et al, 2011;Lowry et al, 2014;Milano et al, 2016). The upland ecotype is more common in northern North America, has a small stature (up to 190 cm), and has limited resistance to multiple pathogens, including rust and other fungal pathogens as well as viruses (Casler, 2012;Uppalapati et al, 2013;Milano et al, 2016;Lovell et al, 2016;Alexander et al, 2017).…”

“…Switchgrass is split into two locally adapted ecotypes, upland and lowland (Morris et al, 2011;Lowry et al, 2014;Milano et al, 2016). The upland ecotype is more common in northern North America, has a small stature (up to 190 cm), and has limited resistance to multiple pathogens, including rust and other fungal pathogens as well as viruses (Casler, 2012;Uppalapati et al, 2013;Milano et al, 2016;Lovell et al, 2016;Alexander et al, 2017). In contrast, the southern lowland ecotype is large (up to 285 cm) and is more resistant to fungal pathogens (Casler, 2012;Uppalapati et al, 2013;Milano et al, 2016;Lovell et al, 2016).…”

Sensitivity Analysis of the APEX Model for Assessing Sustainability of Switchgrass Grown for Biofuel Production in Central Texas

“…'Kanlow' was originally from Wetumka, OK, and was selected for use in low wetland areas and land areas subject to excessive moisture. WBC (West Bee Cave) is a clone of an individual plant collected in West Bee Cave, TX (30.32 N, 97.98 W), and is presumably locally adapted to central Texas [2,42]. Similar to other lowland genotypes, WBC exhibits delayed flowering, higher tiller number and higher tiller mass than upland genotypes [42].…”