Allotetraploid cotton species (Gossypium hirsutum and Gossypium barbadense) have long been cultivated worldwide for natural renewable textile fibers. The draft genome sequences of both species are available but they are highly fragmented and incomplete 1-4. Here we report referencegrade genome assemblies and annotations for G. hirsutum accession Texas Marker-1 (TM-1) and G. barbadense accession 3-79 by integrating single-molecule real-time sequencing, BioNano optical mapping and high-throughput chromosome conformation capture techniques. Compared with previous assembled draft genomes 1,3 , these genome sequences show considerable improvements in contiguity and completeness for regions with high content of repeats such as centromeres. Comparative genomics analyses identify extensive structural variations that probably occurred after polyploidization, highlighted by large paracentric/pericentric inversions in 14 chromosomes. We constructed an introgression line population to introduce favorable chromosome segments from G. barbadense to G. hirsutum, allowing us to identify 13 quantitative trait loci associated with superior fiber quality. These resources will accelerate evolutionary and functional genomic studies in cotton and inform future breeding programs for fiber improvement. Cotton represents the largest source of natural textile fibers in the world. Over 90% of annual fiber production comes from allotetraploid cotton (G. hirsutum and G. barbadense), which originated from an allopolyplodization event approximately 1-2 million year ago, followed by millennia of asymmetric subgenome selection 5,6. G. hirsutum is cultivated all over the world because of its high yield and G. barbadense is prized for its superior fiber quality. To cultivate G. hirsutum that produces longer, finer and stronger fibers, one approach is to introduce the superior fiber traits from G. barbadense into G. hirsutum. A genomics-enabled breeding strategy requires a detailed and robust understanding of genomic organization. Genomic feature G. hirsutum G. barbadense

SummaryBrown fibre cotton is an environmental‐friendly resource that plays a key role in the textile industry. However, the fibre quality and yield of natural brown cotton are poor, and fundamental research on brown cotton is relatively scarce. To understand the genetic basis of brown fibre cotton, we constructed linkage and association populations to systematically examine brown fibre accessions. We fine‐mapped the brown fibre region, Lc 1, and dissected it into 2 loci, qBF‐A07‐1 and qBF‐A07‐2. The qBF‐A07‐1 locus mediates the initiation of brown fibre production, whereas the shade of the brown fibre is affected by the interaction between qBF‐A07‐1 and qBF‐A07‐2. Gh_A07G2341 and Gh_A07G0100 were identified as candidate genes for qBF‐A07‐1 and qBF‐A07‐2, respectively. Haploid analysis of the signals significantly associated with these two loci showed that most tetraploid modern brown cotton accessions exhibit the introgression signature of Gossypium barbadense. We identified 10 quantitative trait loci (QTLs) for fibre yield and 19 QTLs for fibre quality through a genome‐wide association study (GWAS) and found that qBF‐A07‐2 negatively affects fibre yield and quality through an epistatic interaction with qBF‐A07‐1. This study sheds light on the genetics of fibre colour and lint‐related traits in brown fibre cotton, which will guide the elite cultivars breeding of brown fibre cotton.

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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3643-4) contains supplementary material, which is available to authorized users.

Summary To enrich our knowledge about gene network of fatty acid biosynthesis in cottonseed, we conducted comparative transcriptome to reveal the differences in gene expression between Gossypium hirsutum and Gossypium barbadense during cottonseed development. The prolonged expression period and increased expression abundance of oil‐related genes are the main reasons for producing high seed oil content (SOC) in G. barbadense, which manifested as the bias of homeologous gene expression in Dt‐subgenome after 25 day postanthesis (DPA). The dynamic expression profile showed that SAD6 and FATA are more important for oil biosynthesis in G. barbadense than that in G. hirsutum. Three key transcription factors, WRI1, NF‐YB6 and DPBF2, showed their elite roles in regulating seed oil in cotton. We observed that sequence variations in the promoter region of BCCP2 genes might contribute to its divergence in expression level between the two species. Based on the quantitative trait loci (QTL) information of the seed oil content and utilizing additional G. barbadense introgression lines (ILs), we propose 21 candidate genes on the basis of their differential expression level, of which the GbSWEET and the GbACBP6 showed the potential functional to improve the oil content. Taken together, studying the different expression of oil‐related genes and their genetic regulation mechanisms between G. hirsutum and G. barbadense provide new insights to understanding the mechanism of fatty acid biosynthesis network and fatty acid genetic improving breeding in cotton.

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