Prospects for the study of genetic variation among Moso bamboo wild-type and variants through genome resequencing

Abstract

A large number of genome regions exhibit high diversity among Moso bamboo species which can be used in marker-assisted selection programs to detect unique SNPs and Indels for variant fingerprinting to the bamboo development. Moso bamboo (Phyllostachys edulis (Carriere) J. Houz.) is one of the most important bamboo species worldwide. Since the sequencing of its reference genome, the interest in genome-wide structural variations (SV) of Moso bamboo cultivars and variants has grown. To investigate the genetic polymorphism of Moso bamboo, we selected one wild-type (WT) with normal colour internodes in green and two variants, one having yellow internodes with regularly interval green stripes (Ph. edulis (Carr.) Mitford cv. Viridisulcata) (PhV), and the other having green internodes with regularly interval yellow stripes (Ph. edulis (Carr.) Mitford cv. Luteosulcata) (PhL). We re-sequenced the genomes of three Moso bamboo species with an average genome coverage of at least 30x. A total of 4,700,803 unique single nucleotide polymorphisms (Uni-SNPs) and 268,150 unique InDels (Uni-Indels) were identified across the genome of three Moso bamboo species. Additionally, we detected 215,297 unique regions with SV and 65,935 unique regions with copy-number variations (CNVs) that could help to explain the divergence among the three accessions evaluated. A total of 24,303 new transposable elements (TEs) insertion sites were identified in three Moso bamboo species. Additionally, SNP mutations, InDel mutations and CNVs located in coding regions were enriched for gene ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathways analysis. The analysis confirmed that allelic variations in genes were linked with many pathways such as ribosome biogenesis, caffeine metabolism, anion binding, carbohydrate derivative binding and ribonucleotide binding. The results presented a large number of highly diverse genomic regions of Moso bamboo indicating clear evolutionary separation of internode colour variants. A large number of allelic and SV identified in this study can be of potential use in variant fingerprinting and in breeding programs.