Abstract
BackgroundCotton (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.ResultsA 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.ConclusionsUsing SLAF-seq, a large number of DNA polymorphisms were identified. The comprehensive analysis of DNA polymorphisms provided invaluable insights into the different tetraploid cotton species. More importantly, the identification of numerous interspecific genetic variations provides the basis and is very practical for future introgression breeding. The results presented herein provide a valuable genomic resource for new insights into the genetics and breeding of cotton.
Highlights
Cotton (Gossypium spp.), as the world’s most utilized textile fibre source, is an important, economically valuable crop worldwide
80% of the high-quality reads were mapped to the cotton reference genome, which covered approximately 6.4% of the total genome for each material (Table 1)
specific length amplified fragment (SLAF) tags were compared, polymorphic SLAF tags were identified (Additional file 1: Table S1), and it was observed that the number of polymorphic SLAF tags were unevenly distributed between the A subgenome (At) and D subgenome (Dt)
Summary
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. Upland cotton is the primary source for cotton production, representing over 95% of the cotton fibre produced in the world [4]; its genetic diversity. G. barbadense has been used to improve fibre quality in upland cotton, as the second domesticated tetraploid cotton. It has some limitations, such as low yield and limited adaption. Wild cotton germplasms harbour extensive genetic diversity and potential practicability, and they have rich sources of novel traits and are currently being mined to improve many beneficial agronomic traits. With the rapid development of next-generation sequencing (NGS) technologies, the recent publications on the genome sequence of the tetraploid AD1-genome [6, 7] and AD2-genome [8] and the diploid A-genome [9] and D-genome [10, 11] have improved the development of new analyses and comparative approaches for the genomics of both diploid and polyploid cottons
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