Switchgrass Genomic Diversity, Ploidy, and Evolution: Novel Insights from a Network-Based SNP Discovery Protocol

Abstract

Switchgrass (Panicum virgatum L.) is a perennial grass that has been designated as an herbaceous model biofuel crop for the United States of America. To facilitate accelerated breeding programs of switchgrass, we developed both an association panel and linkage populations for genome-wide association study (GWAS) and genomic selection (GS). All of the 840 individuals were then genotyped using genotyping by sequencing (GBS), generating 350 GB of sequence in total. As a highly heterozygous polyploid (tetraploid and octoploid) species lacking a reference genome, switchgrass is highly intractable with earlier methodologies of single nucleotide polymorphism (SNP) discovery. To access the genetic diversity of species like switchgrass, we developed a SNP discovery pipeline based on a network approach called the Universal Network-Enabled Analysis Kit (UNEAK). Complexities that hinder single nucleotide polymorphism discovery, such as repeats, paralogs, and sequencing errors, are easily resolved with UNEAK. Here, 1.2 million putative SNPs were discovered in a diverse collection of primarily upland, northern-adapted switchgrass populations. Further analysis of this data set revealed the fundamentally diploid nature of tetraploid switchgrass. Taking advantage of the high conservation of genome structure between switchgrass and foxtail millet (Setaria italica (L.) P. Beauv.), two parent-specific, synteny-based, ultra high-density linkage maps containing a total of 88,217 SNPs were constructed. Also, our results showed clear patterns of isolation-by-distance and isolation-by-ploidy in natural populations of switchgrass. Phylogenetic analysis supported a general south-to-north migration path of switchgrass. In addition, this analysis suggested that upland tetraploid arose from upland octoploid. All together, this study provides unparalleled insights into the diversity, genomic complexity, population structure, phylogeny, phylogeography, ploidy, and evolutionary dynamics of switchgrass.

Geographic isolation and larval dispersal shape seascape genetic patterns differently according to spatial scale

“…For each sequenced library, the number of raw reads and filtered data are provided in Table S1. SNP calling per pool was performed using the Tassel 3.0 Universal Network‐Enabled Analysis Kit (UNEAK; Lu et al., 2013). We refiltered the individual raw sequences with Stacks software (Catchen, Amores, Hohenlohe, Cresko, & Postlethwait, 2011), which confirmed the low coverage and high rate of missing data for individual genotype calling.…”

The population genomic basis of geographic differentiation in North American common ragweed (Ambrosia artemisiifolia L.)

“…This pipeline enables variant locus identification and genotyping of GBS data lacking a reference genome via (1) reciprocal mapping of Illumina sequences for de novo discovery of likely allele pairs at the same loci, (2) employing network analysis and filtration (Lu et al. 2013), and ultimately (3) using a binomial likelihood ratio method (Glaubitz et al. 2014) for quantitative genotype calling at polymorphic sites.…”

Mapping resistance to the bird cherry-oat aphid and the greenbug in wheat using sequence-based genotyping

“…GBS in particular has proven to be very adequate for these tasks (Poland et al 2012;Saintenac et al 2013;Lu et al 2013). Here we constructed GBS libraries and employed QTL analyses in an F6 RIL population to map known and novel genomic regions associated to resistance to two aphid species in wheat.…”

“…We processed the GBS reads for SNP calling with the Universal Network Enabled Analysis Kit (UNEAK) implemented in TASSEL 3.0 standalone version (Lu et al 2013). The GBS raw data from the Illumina HiSeq2000 machine were first trimmed to a length of 64 bp to keep high quality sequences, then identical reads were grouped into tags; further these tags were pairwise aligned to identify single base pair mismatches, which represented candidate SNPs.…”