DOI: 10.5061/dryad.9cnp5hqhv
title: Genetic loci associated with winter survivorship in diverse lowland switchgrass populations: SNP read count data

description: 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.
description: Twentynine lowland switchgrass populations were planted at
 Arlington, and West Madison, WI. The population were scored for winter
 survival.  Leaf samples from a maximum of 10% of the individuals (8 to 20)
 from all population at each location were bulked to survival and
 non-survival pools. DNA of the pooled samples were extracted and Exome
 capture sequence data was generated using the NimbleGen SeqCap EZ
 Switchgrass Exome probe. Sample libraries were pooled equally and
 sequenced at the University of Wisconsin Biotechnology Center DNA
 Sequencing Facility on a HiSeq 2500 generating 101nt single-end reads with
 a target sequencing coverage of 250x. The raw reads are available in the
 National Center for Biotechnology Sequence Read Archive under BioProject
 PRJNA529229.  The alignment of the sequence to the reference genome and
 generation of SNP matrix is mentioned in the manuscript
 (DOI 10.1002/tpg2.20159). Read data (allele counts) were extracted for
 5,596,351 bi-allelic loci.
description: The dataset WALS_BSA_ReadCount_SNP_Matrix.txt.gz is a 5,596,351 x
 84 matrix. The first four columns are Chromosome name, Position, Reference
 allele, and Alternate alternate allele. The rest 80 columns are the names
 of the samples. The description of the sample name can be found in the
 separate file named WALS_BSA_sample_name_description.xlsx.