Resequencing of 301 ramie accessions identifies genetic loci and breeding selection for fibre yield traits.

Ramie is an important fibre-producing crop in China; however, the genetic basis of its agronomic traits remains poorly understood. We produced a comprehensive map of genomic variation in ramie based on resequencing of 301 landraces and cultivars. Genetic analysis produced 129 signals significantly associated with six fibre yield-related traits, and several genes were identified as candidate genes for respective traits. Furthermore, we found that natural variations in the promoter region of Bnt14G019616 were associated with extremely low fibre abundance, providing the first evidence for the role of pectin methylesterase in fibre growth of plants. Additionally, nucleotide diversity analysis revealed that breeding selection has been markedly focussed on chromosome 9 in which ~ 39.6% sequence underwent selection, where one gibberellin-signalling-repressed DELLA gene showed distinct selection signatures in the cultivars. This study provides insights into the genetic architecture and breeding history of fibre yield traits in ramie. Moreover, the identification of fibre yield-related genetic loci and large-scale genomic variation represent valuable resources for genomics-assisted breeding of this crop.

Genomic analyses provide comprehensive insights into the domestication of bast fiber crop ramie (Boehmeria nivea).

Ramie (Boehmeria nivea) is an economically important natural fiber-producing crop that has been cultivated for thousands of years in China; however, the evolution of this crop remains largely unknown. Here, we report a ramie domestication analysis based on genome assembly and resequencing of cultivated and wild accessions. Two chromosome-level genomes representing wild and cultivated ramie were assembled de novo. Numerous structural variations between two assemblies, together with the genetic variations from population resequencing, constituted a comprehensive genomic variation map for ramie. Domestication analysis identified 71 high-confidence selective sweeps comprising 320 predicted genes, and 29 genes from sweeps were associated with fiber growth in the expression. In addition, we identified seven genetic loci associated with the fiber yield trait in the segregated population derived from the crossing of two assembled accessions, and two of which showed an overlap with the selective sweeps. These findings indicated that bast fiber traits were focused on during the domestication history of ramie. This study sheds light on the domestication of ramie and provides a valuable resource for biological and breeding studies of this important crop.

Linkage mapping of quantitative trait loci for fiber yield and its related traits in the population derived from cultivated ramie and wild B. nivea var. tenacissima.

Ramie is an important natural fiber crop, and the fiber yield and its related traits are the most valuable traits in ramie production. However, the genetic basis for these traits is still poorly understood, which has dramatically hindered the breeding of high yield in this fiber crop. Herein, a high-density genetic map with 6,433 markers spanning 2476.5 cM was constructed using a population derived from two parents, cultivated ramie Zhongsizhu 1 (ZSZ1) and its wild progenitor B. nivea var. tenacissima (BNT). The fiber yield (FY) and its four related traits-stem diameter (SD) and length (SL), stem bark weight (BW) and thickness (BT)-were performed for quantitative trait locus (QTL) analysis, resulting in a total of 47 QTLs identified. Forty QTLs were mapped into 12 genomic regions, thus forming 12 QTL clusters. Among 47 QTLs, there were 14 QTLs whose wild allele from BNT was beneficial. Interestingly, all QTLs in Cluster 10 displayed overdominance, indicating that the region of this cluster was likely heterotic loci. In addition, four fiber yield-related genes underwent positive selection were found either to fall into the FY-related QTL regions or to be near to the identified QTLs. The dissection of FY and FY-related traits not only improved our understanding to the genetic basis of these traits, but also provided new insights into the domestication of FY in ramie. The identification of many QTLs and the discovery of beneficial alleles from wild species provided a basis for the improvement of yield traits in ramie breeding.

A genomic resource derived from the integration of genome sequences, expressed transcripts and genetic markers in ramie.

BACKGROUND: The redundancy of genomic resources, including transcript and molecular markers, and their uncertain position in the genome have dramatically hindered the study of traits in ramie, an important natural fiber crop. RESULTS: We obtained a high-quality transcriptome consisting of 30,591 non-redundant transcripts using single-molecule long-read sequencing and proposed it as a universal ramie transcriptome. Additionally, 55,882 single nucleotide polymorphisms (SNPs) were identified and a high-density genetic map was developed. Based on this genetic map, 181.7 Mb ramie genome sequences were assembled into 14 chromosomes. For the convenient use of these resources, 29,286 (~ 95.7%) of the transcripts and all 55,882 SNPs, along with 1827 previously reported sequence repeat markers (SSRs), were mapped into the ramie genome, and 22,343 (~ 73.0%) transcripts, 50,154 (~ 89.7%) SNPs, and 1466 (~ 80.3%) SSRs were assigned to a specific location in the corresponding chromosome. CONCLUSION: This is the first study to characterize the ramie transcriptome by long-read sequencing, and the substantial number of transcripts of significant length obtained will accelerate our understanding of ramie growth and development. This integration of genome sequences, expressed transcripts, and genetic markers will provide an extremely useful resource for genetic, molecular, and breeding studies of ramie.

A Comparative Analysis of the Venom Gland Transcriptomes of the Fishing Spiders Dolomedes mizhoanus and Dolomedes sulfurous.

Dolomedes sulfurous and Dolomedes mizhoanus are predaceous arthropods catching and feeding on small fish. They live in the same area and have similar habits. Their venoms exhibit some similarities and differences in biochemical and electrophysiological properties. In the present work, we first performed a transcriptomic analysis by constructing the venom gland cDNA library of D. sulfurous and 127 novel putative toxin sequences were consequently identified, which were classified into eight families. This venom gland transcriptome was then compared with that of D. mizhoanus, which revealed that the putative toxins from both spider venoms might have originated from the same gene ancestors although novel toxins were evolved independently in the two spiders. The putative toxins from both spiders contain 6-12 cysteine residues forming seven cysteine patterns. As revealed by blast search, the two venoms are rich in neurotoxins targeting ion channels with pharmacological and therapeutic significance. This study provides insight into the venoms of two closely related species of spider, which will be of use for future investigations into the structure and function of their toxins.

A survey of the venom of the spider Lycosa vittata by biochemical, pharmacological and transcriptomic analyses.

Lycosa vittata, mainly distributed in the southwest of China, is a medium-sized and venomous spider, whose venom remains unexplored so far. This study aims to present an overview of the venom. It mainly consisted of diverse peptides and exhibited inhibitory effects on voltage-gated ion channels in rat dorsal root ganglia neurons, with a strongest inhibition on tetrodotoxin-sensitive and tetrodotoxin-resistant voltage-gated Na(+) channels. Interestingly, it exerted cytotoxicity to cancer cells, with approximately 10-fold selectivity on PC-3 over others, implying the existence of selective anti-PC-3 agents in the venom. Moreover, 51 toxin-like peptides were deduced from the venom gland transcriptome. Bioinformatic analyses suggested their structures might have some distinguished properties and their predicted functions were consistent with the venom activities. This study suggests that the venom is an attractive source of neurotoxins with therapeutic significance, and provides references for the structure and function investigation of specific toxins in the future.

A comparative study of the molecular composition and electrophysiological activity of the venoms from two fishing spiders Dolomedes mizhoanus and Dolomedes sulfurous.

Dolomedes mizhoanus and Dolomedes sulfurous are two venomous spiders found in the same area in southern China and are characterized by living in water plants and feeding on fish. In this study, the chemical compositions and activities of these venoms were compared. Both venoms contain hundreds of peptides as shown by off-line RP-HPLC/MALDI-TOF-MS analysis, but have a different peptide distribution, with D. mizhoanus venom containing fewer high molecular mass (7000-9000 Da) peptides (3%) than D. sulfurous venom (25.6%). Patch-clamp analyses showed that both venoms inhibited voltage-activated Na(+), K(+) and Ca(2+) channels in rat DRG neurons, however, differences in their inhibitory effects were observed. In general, D. mizhoanus venom had lower inhibitory activity than D. sulfurous venom and both venoms had a different inhibitory spectrum against these ion channels, showing that both venoms are useful for identifying antagonists to them. In addition, intrathoracic injection of both venoms caused severe neurotoxic effects in zebrafish and death at higher concentrations, respectively. Considering that both spiders belong to the same genus, live in the same area and have similar habits, elucidation of the differences between the peptide toxins from both venoms would provide new molecular insights into the evolution of spider peptides.

Beneficial effects of trypsin inhibitors derived from a spider venom peptide in L-arginine-induced severe acute pancreatitis in mice.

HWTI is a 55-residue protein isolated from the venom of the spider Ornithoctonus huwena. It is a potent trypsin inhibitor and a moderate voltage-gated potassium channel blocker. Here, we designed and expressed two HWTI mutants, HWTI-mut1 and HWTI-mut2, in which the potassium channel inhibitory activity was reduced while the trypsin inhibitory activity of the wild type form (approximately 5 EPU/mg) was retained. Animal studies showed that these mutants were less toxic than HWTI. The effects of HWTI and HWTI-mut1 were examined in a mouse model of acute pancreatitis induced by intraperitoneal injection of a large dose of L-arginine (4 mg/kg, twice). Serum amylase and serum lipase activities were assessed, and pathological sections of the pancreas were examined. Treatment with HWTI and HWTI-mut1 significantly reduced serum amylase and lipase levels in a dose dependent manner. Compared with the control group, at 4 mg/kg, HWTI significantly reduced serum amylase level by 47% and serum lipase level by 73%, while HWTI-mut1 significantly reduced serum amylase level by 59% and serum lipase level by 72%. Moreover, HWTI and HWTI-mut1 effectively protected the pancreas from acinar cell damage and inflammatory cell infiltration. The trypsin inhibitory potency and lower neurotoxicity of HWTI-mut1 suggest that it could potentially be developed as a drug for the treatment of acute pancreatitis with few side effects.

The venom of the fishing spider Dolomedes sulfurous contains various neurotoxins acting on voltage-activated ion channels in rat dorsal root ganglion neurons.

Dolomedes sulfurous is a venomous spider distributed in the south of China and characterized with feeding on fish. The venom exhibits great diversity and contains hundreds of peptides as revealed by off-line RP-HPLC/MALDI-TOF-MS analysis. The venom peptides followed a triple-modal distribution, with 40.7% of peptides falling in the mass range of 1000-3000 Da, 25.6% peptides in the 7000-9000 Da range and 23.5% peptides in the 3000-5000 Da range. This distribution modal is rather different from these of peptides from other spider venoms analyzed. The venom could inhibit voltage-activated Na(+), K(+) and Ca(2+) channels in rat DRG neurons as revealed by voltage-clamp analysis. Significantly, the venom exhibited inhibitory effects on TTX-R Na(+) and T-type Ca(2+) currents, suggesting that there exist both channel antagonists which might be valuable tools for investigation of both channels and drug development. Additionally, intrathoracically injection of venom could cause serve neurotoxic effects on zebrafish and death at higher concentrations. The LD50 value was calculated to be 28.8 µg/g body weight. Our results indicated that the venom of D. sulfurous contain diverse neurotoxins which serve to capture prey. Intensive studies will be necessary to investigate the structures and functions of specific peptides of the venom in the future.