High Resolution Genetic Mapping by Genome Sequencing Reveals Genome Duplication and Tetraploid Genetic Structure of the Diploid Miscanthus sinensis

Abstract

We have created a high-resolution linkage map of Miscanthus sinensis, using genotyping-by-sequencing (GBS), identifying all 19 linkage groups for the first time. The result is technically significant since Miscanthus has a very large and highly heterozygous genome, but has no or limited genomics information to date. The composite linkage map containing markers from both parental linkage maps is composed of 3,745 SNP markers spanning 2,396 cM on 19 linkage groups with a 0.64 cM average resolution. Comparative genomics analyses of the M. sinensis composite linkage map to the genomes of sorghum, maize, rice, and Brachypodium distachyon indicate that sorghum has the closest syntenic relationship to Miscanthus compared to other species. The comparative results revealed that each pair of the 19 M. sinensis linkages aligned to one sorghum chromosome, except for LG8, which mapped to two sorghum chromosomes (4 and 7), presumably due to a chromosome fusion event after genome duplication. The data also revealed several other chromosome rearrangements relative to sorghum, including two telomere-centromere inversions of the sorghum syntenic chromosome 7 in LG8 of M. sinensis and two paracentric inversions of sorghum syntenic chromosome 4 in LG7 and LG8 of M. sinensis. The results clearly demonstrate, for the first time, that the diploid M. sinensis is tetraploid origin consisting of two sub-genomes. This complete and high resolution composite linkage map will not only serve as a useful resource for novel QTL discoveries, but also enable informed deployment of the wealth of existing genomics resources of other species to the improvement of Miscanthus as a high biomass energy crop. In addition, it has utility as a reference for genome sequence assembly for the forthcoming whole genome sequencing of the Miscanthus genus.

Genome-wide SNP discovery and genetic linkage map construction in sunflower (Helianthus annuus L.) using a genotyping by sequencing (GBS) approach

“…To date, the GBS approach has been popular and applied to many plant species for SNP discovery and genotyping. These species include barley (Elshire et al 2011), Miscanthus sinensis (Ma et al 2012), Rubus idaeus (Ward et al 2013) and maize (Romay et al 2013). Also GBS was applied in an F 2 population of oil palm to identify 21,471 SNPs and to construct a linkage map containing 1085 SNPs (Pootakham et al 2015).…”

Molecular Regulation of Flowering Time in Grasses

“…Comparisons between the Sorghum genome and the genus Miscanthus reveal that whole genome duplication occurred in Miscanthus after its divergence from a common ancestor shared with sorghum. The base chromosome number of Miscanthus is approximately twice that of sorghum with nominally diploid and tetraploid species [46,68]. Analysis of natural variation in flowering in different ecotypes of grasses with economic value, such as Miscanthus spp.…”

“…The ability of SbPRR37 to inhibit their expression could be due to inhibition of SbEhd1 or SbCO, activators of SbCN8 and SbCN12 expression [14,16]. The PhyB regulation of SbCN15 expression may modify flowering time in a photoperiod-insensitive manner [46] ( Figure 1). In switchgrass, the flowering time regulatory network is similarly to maize (Zea mays L.) and is regulated by both photoperiod-dependent and autonomous pathways.…”

“…We also detected two loci in MsiGhd7. The current diploid M. sinensis evolved from genome duplication of its progenitor that was very close to a sorghum ancestor [46]. Gene duplication is a key mechanism in evolution because it can provide genes with new functions.…”

“…The plant circadian system consists of biochemical timing mechanisms that temporarily modulate the function of several signalling pathways to measures changes in day-length and promote suitable timing of flowering to maximize reproductive success [2,3,6,7,9,10,[13][14][15]21,24,26,28,29,31,36,38,41,42,46,48,49,[56][57][58][59][60][61][62][63][64][65][66]. The photoperiod response on flowering time varies among grasses.…”