Abstract
Background
Cotton (Gossypium spp.), as the
world’s most utilized textile fibre source, is an important, economically
valuable crop worldwide. Understanding the genomic variation of tetraploid
cotton species is important for exploitation of the excellent characteristics
of wild cotton and for improving the diversity of cotton in breeding. However,
the discovery of DNA polymorphisms in tetraploid cotton genomes has lagged
behind other important crops.
Results
A total of 111,795,823 reads, 467,735
specific length amplified fragment (SLAF) tags and 139,176 high-quality DNA
polymorphisms were identified using specific length amplified fragment
sequencing (SLAF-seq), including 132,880 SNPs and 6,296 InDels between the
reference genome (TM-1) and the five tetraploid cotton species. Intriguingly,
gene ontology (GO) enrichment analysis revealed that a number of significant
terms were related to reproduction in G. barbadense acc. 3–79. Based
on the new data sets, we reconstructed phylogenetic trees that showed a high
concordance to the phylogeny of diploid and polyploid cottons. A large amount
of interspecific genetic variations were identified, and some of them were
validated by the single-strand conformation polymorphism (SSCP) method, which
will be applied in introgression genetics and breeding with G.
hirsutum cv. Emian22 as the receptor and the other species as
donors.
DOI: 10.1186/s12864-017-3643-4 IF=3.82