Genetic loci associated with winter survivorship in diverse lowland switchgrass populations: SNP read count data

High winter mortality is the most important factor limiting biomass yield
of lowland switchgrass planted in the northern latitudes of North America.
Due to the perennial growth habit and strong dependence on weather
conditions to generate sufficient selection pressure to identify
winter-hardy individuals, breeding of cold tolerant switchgrass cultivars
requires many years. Identification of causal genetic variants for winter
survivorship would accelerate the improvement of switchgrass biomass
production. The objective of this study was to identify allelic variation
associated with winter survivorship in lowland switchgrass populations
using bulk segregant analysis (BSA). Twenty-nine lowland switchgrass
populations were evaluated for winter survival at two locations in
southern Wisconsin and 21 population with differential winter survivorship
was used for BSA. A maximum of 10% of the individuals per population
(8-20) was bulked to create survivor and non-survivor DNA pools. The DNA
pools were evaluated using exome capture sequencing and allele frequencies
were used to conduct statistical tests. The BSA tests revealed nine QTL
from tetraploid populations and seven QTL from octoploid populations. Some
markers were identified in multiple populations that originated across a
broad geographic landscape, while other markers were site-specific. QTL at
positions 88 Mb on chromosome 2N, 115 Mb on chromosome 5K, and 1 and 100
Mb on chromosome 9N were potentially the most useful QTL. Markers
associated with winter survivorship in this study can be used to
accelerate breeding cycles of lowland switchgrass populations and should
lead to improvements in adaptation within USDA hardiness zones 4 and 5.