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.
Highlights
Driven by the need for greater energy security and a reduced impact of fuel consumption on the environment, there has been a growing interest in recent years to produce biofuels from cellulosic biomass
Fifty RFLP loci originated from Missaoui et al [4], 599 simple sequence repeat (SSR) loci were from Okada et al [5], 778 loci including 336 Diversity Array Technology (DArT) loci, 439 SSR loci, and 3 sequenced-tagsites markers developed from expressed sequenced tags (ESTSTSs) were from Serba et al [6], and 32 loci were newly mapped in the AP13×VS16 mapping population
Switchgrass consensus maps were developed as a tool for the switchgrass community to facilitate trait analyses and to provide the marker density needed to conduct comparative analyses between switchgrass and its genomic model, foxtail millet
Summary
Driven by the need for greater energy security and a reduced impact of fuel consumption on the environment, there has been a growing interest in recent years to produce biofuels from cellulosic biomass. (2015) 8:137–151 one of the crops that was identified in the 1990s as a potential feedstock for the production of cellulosic biofuels because of its high biomass yield, low nutrient and water requirements, and adaptation to marginal lands [1,2,3]. Switchgrass belongs to the family Poaceae, subfamily Panicoideae, tribe Paniceae and comprises two ecotypes, upland and lowland, that largely vary in their ploidy level, zone of adaptation, and plant architecture. Switchgrass has extensive genetic diversity and a large potential for genetic improvement [1]. The improvement of switchgrass for traits important for bioenergy production, including total biomass yield and biomass composition, is key to making switchgrass an integral part of a successful cellulosic biofuel production program
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