Comparative Relationships and Chromosome Evolution in Switchgrass (Panicum virgatum) and Its Genomic Model, Foxtail Millet (Setaria italica)

Abstract

A switchgrass (Panicum virgatum L.) consensus map was developed that combined data from two mapping populations and integrated recombination data from both parents of this largely obligate outcrossing species. The consensus map consisted of 1,321 loci and spanned 2,122 cM. An analysis of the distribution of genic and genomic markers across the length of a linkage group showed that genic markers were relatively overrepresented in distal regions, while genomic markers were relatively overrepresented in pericentromeric regions. Furthermore, genic markers located in distal and pericentromeric regions identified orthologs in the genome of the closely related species foxtail millet (Setaria italica (L.) P. Beauv.) at a similar rate, but fewer orthologs were found for genomic markers that mapped to pericentromeric regions compared to distal regions. Because cross-species sequence conservation is largely limited to genes, our data suggest that genomic markers that map to distal regions are more likely to be derived from genic regions than those that map to pericentromeric regions. A comparative analysis between loci on the switchgrass consensus map and their orthologs in the foxtail millet genome showed that the two species varied by at least nine inversions and one reciprocal translocation. Extending the comparative analysis to sorghum demonstrated that the majority of the rearrangements occurred in the foxtail millet genome in the past 13 million years. The reduction in chromosome number from 10 in the Andropogoneae to 9 in the Paniceae was achieved through a complex set of rearrangements involving three ancestral chromosomes orthologous to sorghum chromosomes 6, 8, and 9 and chromosomes III and VII in the lineage leading to switchgrass and foxtail millet. Upon insertion of ancestral chromosome 9 into ancestral chromosome 8, the centromere of the recipient chromosome was lost, and this was accompanied by a loss of repetitive DNA. The switchgrass-foxtail millet comparative map provides a guide of the rearrangements that need to be taken into account when using foxtail millet as a surrogate for switchgrass in genetic analyses.

High-Resolution Linkage Map With Allele Dosage Allows the Identification of Regions Governing Complex Traits and Apospory in Guinea Grass (Megathyrsus maximus)

“…This genetic proximity was confirmed based on the consistent distribution of the markers in the genetic map ( Figure 3 and Supplementary Table 4). In addition, considering our tetraploid mapping population, the use of a tetraploid genome as reference might be more informative than the use of diploid genomes because there is a greater possibility of similar chromosomal rearrangements between these species (Daverdin et al, 2015). However, the possibility of using the genome of P. virgatum as reference does not preclude the need for a sequenced genome of M. maximus, mainly due to the possibility of identifying exclusive markers of the species, and our linkage map can contribute to the assembly of this reference genome.…”

Analysis of Segregation Ratio Distortion and Linkage Mapping in Two Switchgrass F1 Populations: Lowland-lowland and Lowland-upland Using Genotyping by Sequencing Data

“…A possible pericentromeric region for each linkage group is suggested based on the highest marker density found within 20 cM bin sliding window. The high frequency of markers in the likely pericentromeric region of the genetic map may have lower recombination resulting in lower amount of recombination events observed (26,27,29).…”

“…For the construction of linkage maps, the two-way pseudo-testcross mapping strategy is adopted whereby recombinations that occur at each parental side; during egg and pollen formation, are used to construct two linkage maps per chromosome (28,29). This paper describes the genotyping-bysequencing methodology and construction of two genetic maps for each population.…”

High-resolution Linkage Map with Allele Dosage Allows the Identification of an Apomixis Region and Complex Traits in Guinea Grass (Megathyrsus maximus)

“…This genetic proximity was confirmed based on the consistent distribution of the markers in the genetic map (Figure 3 and Supplementary Table 4). In addition, the use of a tetraploid genome, such as that of P. virgatum, may be more informative than the use of diploid genomes, considering our tetraploid mapping population, as there is a greater possibility of similar chromosomal rearrangements between these species (Daverdin et al, 2015). It is common to find a smaller number of SNPs in linkage maps of forage grass species without an assembled genome, as observed for common millet (Panicum miliaceum) (Rajput et al, 2016) and signalgrass (Urochloa decumbens) (Ferreira et al, 2019), than in those of species with a reference genome, such as foxtail millet (Setaria italica) (Jia et al, 2017) and pearl millet (Pennisetum glaucum) (Punnuri et al, 2016).…”