Investigation of Genetic Relationships within Miscanthus Using Snp Markers Identified Using Slaf-Seq

Abstract

Miscanthus, which is a leading dedicated-energy grass in Europe as well as in parts of Asia, is expected to play a key role in the development of the future bioeconomy. However, due to its complex genetic background, it is difficult to investigate phylogenetic relationships and the evolution of gene function in this genus. Here, we investigated 50 Miscanthus germplasms: 1 female parent ( M. lutarioriparius ), 30 candidate male parents ( M. lutarioriparius, M. sinensis, and M. sacchariflorus ), and 19 hybrids. We used high-throughput Specific-Locus Amplified Fragment sequencing (SLAF-seq) to identify informative single nucleotide polymorphisms (SNPs) in all germplasms. We identified 800,081 SLAF tags, of which 160,368 were polymorphic. Each tag was 264–364 bp long. From these tags, we derived 469,509 SNP markers. The obtained SNPs were used to investigate genetic relationships within Miscanthus. We constructed a phylogenetic tree of the 50 germplasms using the obtained SNPs, and found that the germplasms fell into two clades: one clade of M. sinensis only and one clade that included the hybrids, M. lutarioriparius and M. sacchariflorus . Genetic cluster analysis indicated that a M. lutarioriparius germplasm was the most likely male parent of the hybrid progeny. The ability to identify the parental material of the hybrid progeny will be useful for future Miscanthus genetics and breeding programs.