SSR-based genetic maps of Miscanthus sinensis and M. sacchariflorus, and their comparison to sorghum

Abstract

We present SSR-based genetic maps from a cross between Miscanthus sacchariflorus Robustus and M. sinensis, the progenitors of the promising cellulosic biofuel feedstock Miscanthus × giganteus. cDNA-derived SSR markers were mapped by the two-way pseudo-testcross model due to the high heterozygosity of each parental species. A total of 261 loci were mapped in M. sacchariflorus, spanning 40 linkage groups and 1,998.8 cM, covering an estimated 72.7% of the genome. For M. sinensis, a total of 303 loci were mapped, forming 23 linkage groups and 2,238.3 cM, covering 84.9% of the genome. The use of cDNA-derived SSR loci permitted alignment of the Miscanthus linkage groups to the sorghum chromosomes, revealing a whole genome duplication affecting the Miscanthus lineage after the divergence of subtribes Sorghinae and Saccharinae, as well as traces of the pan-cereal whole genome duplication. While the present maps provide for many early research needs in this emerging crop, additional markers are also needed to improve map density and to further characterize the structural changes of the Miscanthus genome since its divergence from sorghum and Saccharum.

Comparative Analysis of Miscanthus and Saccharum Reveals a Shared Whole-Genome Duplication but Different Evolutionary Fates

“…Based on the Burrows-Wheeler Aligner results, we determined sorghum exons to which only two different Miscanthus contigs aligned and extracted those sorghum exons as well as matching Miscanthus exons. Because the Miscanthus genome reportedly had an additional genome duplication since its divergence from sorghum (Kim et al, 2012;Ma et al, 2012), these pairs were putatively defined as paralogous sequences formed by the most recent genome duplication in Miscanthus. Saccharum ESTs obtained from the NCBI's dbEST (www.ncbi.nlm.nih.…”

“…A sister genus, Miscanthus, which is sufficiently closely related to occasionally be used in sugarcane breeding (Chen and Lo, 1989), shows a general 2:1 correspondence to sorghum in chromosome number (Kim et al, 2012;Ma et al, 2012;Swaminathan et al, 2012), consistent with a single genome duplication since Miscanthus-sorghum divergence. Miscanthus has less complex ploidy relationships than Saccharum, for example, with M. sacchariflorus (2n = 4x = 76) and M. sinensis (2n = 2x = 38) thought to be progenitors of the sterile and vegetatively propagating triploid (2n = 3x = 57) M. 3 giganteus (Hodkinson and Renvoize, 2001) of interest as a biomass crop in Europe and the US (Clifton-Brown et al, 2001).…”

Targets and tools for optimizing lignocellulosic biomass quality of miscanthus

“…Genetic maps form the basis for finding marker-trait associations, but their construction in miscanthus is complicated by its large genome size (varying from 4.5 -7 pg, depending on the species (Rayburn et al, 2009) and the high levels of heterozygosity that are the result of its obligate outcrossing nature . Nonetheless, several genetic maps are published to date (Atienza et al, 2002, Kim et al, 2012, Liu et al, 2015, Swaminathan et al, 2012, which provide valuable resources for genetic studies to find markers that are related to traits of interest that can be exploited for marker-assisted selection in the foreseeable future. …”

“…In miscanthus, ploidy levels vary amongst species in the genus, with the three species with the highest potential for biomass production, M. × giganteus being a triploid (2n = 3x = 57), M. sinensis a diploid (2n = 2x = 38) and M. sacchariflorus a tetraploid (2n = 4x = 76) . Recently, Kim et al (2012) reported M. sacchariflorus accession from Japan to be typically tetraploid, whereas accessions from China were reported to be typically diploid. M. × giganteus is a sterile hybrid, but the other two species are obligate outcrossers due to self-incompatibility .…”

“…Hence, the knowledge that will be acquired on the synthesis, deposition and recalcitrance of the cell wall in maize or sorghum can most likely be utilized to improve biomass quality of the other C4 grasses. Sorghum shares a high level of colinearity with the genomes of miscanthus (Kim et al, 2012;Swaminathan et al, 2012) and sugarcane (Wang et al, 2010), which makes the sorghum genome ideal as a template for comparative genomic studies with these species. In addition, the use of comparative genetics coupled with transcriptomic and proteomic analyses will be an important tool to expedite the genome assembly of closely related C4 grasses.…”