Stepping Forward in Molecular Breeding of Cellulosic Feedstocks by Using SNP Markers

One of the barriers using cellulosic feedstocks including various grasses is to retain biomass production sufficiently and efficiently. Recent increase in food price is partly attributed to appropriation of the agricultural food products for bioenergy. In such a sense, non-food cellulosic biomass crop is essential option and Miscanthus has many advantages to meet the criteria. In our lab, EST sequences from four libraries prepared in two distinctive species, diploid M. sinensis and tetraploid M. sacchariflorus are valuable resources for molecular marker development. The EST sequences covered the Miscanthus genome 15.5 and 14.3 times for the diploid and tetraploid, respectively. After going through QC and trimming processes, the obtained contig numbers from 4 libraries (diploid leaf and rhizome, and tetraploid leaf and rhizome) were 12166, 13170, 8732, and 8104, respectively. Because some of the contigs are expected to be redundant, about 21K and 14K contigs from diploid and tetraploid Miscanthuse species, respectively, were used to identify SNP loci, resulting in 10,729 and 10,773 homo-type loci. We designed primers for the SNP candidates fitting to HRM analysis where the melting temperature and expected allele size enabled to set PCR conditions and allele verification. The developed SNP markers will be applied to explore allelic variations in the Miscanthus and other grass collections, to identify individuals with superior traits of interest, to tag QTL and genes in the genome, and to select progenies with target traits in marker-assisted cultivar development.