Field experiment and phenotyping
The details of the creation of this population were described in Milano
et al. (2016). Briefly, the grandparents of the mapping population were
derived from highly divergent southern lowland and northern upland
ecotypes. The population was developed by initial crosses between AP13
(A) x DAC6 (B) and WBC3 (C) x VS16 (D). AP13 and WBC3 are genotypes
clonally derived from an individual selected from the lowland cultivar
‘Alamo’ (southern Texas accession) and an individual from naturally
occurring population ‘West Bee Cave’ (central Texas accession),
respectively. DAC6 and VS16 are genotypes clonally derived from
individuals selected from the upland cultivars ‘Dacotah’ and ‘Summer’
(both northern upland accessions), respectively. The F1hybrids of each of those crosses were then intercrossed reciprocally to
produce the four-way outbred mapping population.
The grandparents, F1 hybrid parents, and the
F2 progeny were propagated by dividing plants manually
to produce 10 clones, each of which was maintained in a 3.8-L pot at the
Brackenridge Field Laboratory, Austin, TX in 2013-2015. One replicate of
each of the mapping progeny genotypes, along with multiple replicates of
grandparents and F1 parents, were transplanted from May
to July of 2015 at 10 field sites. In three of the 10 sites, 370 extra
genotypes were planted. The 10 field sites cover 17 degrees of latitude
from South Texas to South Dakota (Figure 1A). Detailed information of
the 10 field sites, including latitude, longitude and soil type is
provided in Table 1. The annual mean temperature at the 10 sites in 2016
ranged from 10.4 °C in the north to 20.7 °C in the south, and the total
rainfall varied from 574 mm to 1440 mm (Figure 1B, data are from local
weather station or from NOAA if local weather data are not available;
the weather station or NOAA link is included in Table 1). To control
weeds, each field site was covered with one layer of weed barrier cloth
(Dewitt, Sikeston, MO). Holes were cut into the weed cloth in a
honeycomb fashion. Plants were randomized into the holes, with each
plant having four nearest neighbors each located 1.56m away from each
other. A row of border plants was planted at every edge position of the
field to minimize edge effects. The border plants were derived from
rhizome plugs obtained from an approximately 10-year-old stand of Alamo
switchgrass. Plants were well watered in the field during the summer of
2015 to facilitate establishment and all phenotypes were collected in
2016.
Three panicles were cut from each plant at full maturity. Panicle length
(PL in mm), primary branching number (PBN), and secondary branching
number (SBN) were assessed at the end of the growing season. A diagram
depicting these phenotypes is presented in Figure 2, with representative
images of panicles from the four grandparents. PL was measured on the
primary panicle from the base of the first primary branch to the top of
the panicle. PBN was counted as the total number of branches along the
primary rachis. Due to the numerous secondary branches in switchgrass,
SBN in our study referred to the total number of secondary branches on
the lowest primary branch of the panicle (Figure 2). In total, over
10,000 separate panicle morphology measurements were collected in our
study. The phenotypic data (i.e., average values) for each genotype at
each field site are provided in Supplemental Table S1.