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

By Fei Lu, A. Lipka, Jeffrey Glaubitz, Robert Elshire, Jerry H. Cherney, Michael D. Casler, Edward S. Buckler, D. Costich. PLoS Genetics, 2013

644 citations recorded by the source corpus.

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.

Subfields: Agronomy and Crop Science, Genetics, Plant Science

View Paper: https://www.semanticscholar.org/paper/b67a251628bd25aaaecedd41997bcabfa9149497

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Citations in the corpus

TASSEL-GBS: A High Capacity Genotyping by Sequencing Analysis Pipeline (2014, positive): “approach, appropriate for small to medium scale studies, has already been implemented in TASSEL [22].”
vcfr: a package to manipulate and visualize variant call format data in R (2017, background): “For example, projects may be based on draft de novo genomes consisting of many short contigs or sometimes no reference genome at all (Lu et al. 2013).”
High-Throughput SNP Genotyping to Accelerate Crop Improvement (2014, methodology): “For GBS calling in species without a reference genome, the Universal NetworkEnabled Analysis Kit (UNEAK) software can sort through networks of repeats, paralogs and error tags to identify reciprocal tag pairs that can be used for SNP calling (Lu et al. 2013).”
Genotyping-By-Sequencing for Plant Genetic Diversity Analysis: A Lab Guide for SNP Genotyping (2014, methodology): “[34] developed an SNP calling routine called UNEAK to analyze HiSeq GBS data for polyploid species, but its reliability in SNP calling remains to be determined.”