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Oil produced by castor (Ricinus communis) has broad industrial applications. However, knowledge on the genetic diversity, especially genetic alterations that occurred during domestication and subsequent traits selection, of this oil crop is limited. Here, our population genomics analyses show that the Chinese castors have developed a geographic pattern, classified into the southern-, the middle-, and the northern-China groups. We detect a number of candidate genomic loci that are associated with the selection signals during the geographical differentiation and domestication. Using genome-wide association analysis, we identify candidate genes associated with nine agronomically important traits. One of the candidate genes encoding a glycosyltransferase related to cellulose and lignin biosynthesis is associated with both capsule dehiscence and endocarp thickness. We hypothesize that the abundance of cellulose or lignin in endocarp is an important factor for capsule dehiscence. Our results provide foundation for castor breeding and genetic study., Castor is an important industrial oil crop, but knowledge on its genetic diversity is limited. Here, Fan et al. show geographic pattern of Chinese castors that have developed during domestication by population genetic analyses, and reveal candidate genes associated with agronomically important traits.

Additional file 9: Table S9. Classification of FLNC sequences with genome alignment.

Additional file 7: Table S7. Gene structure annotation

Additional file 2: Table S2. Effect of drought stress (SAWS=10%) on drought tolerant related traits in Z141 and NY-17

Additional file 5: Table S5. Sequence summary of PacBio subreads.

Additional file 6: Table S6. Full length evaluation

Additional file 4: Table S4. Sequence summary of PacBio SMRT Cells.

Additional file 8: Table S8. Illumina RNA-seq data of each stress.

Additional file 3: Table S3. Effect of drought stress on ALWC and RLWC in Z141 and NY-17.

Additional file 1: Table S1. Methodology for measuring the drought-tolerant related traits.

Summary Flax has been cultivated for its oil and fiber for thousands of years. However, it remains unclear how the modifications of agronomic traits occurred on the genetic level during flax cultivation. In this study, we conducted genome-wide variation analyses on multiple accessions of oil-use, fiber-use, landraces, and pale flax to identify the genomic variations during flax cultivation. Our findings indicate that, during flax domestication, genes relevant to flowering, dehiscence, oil production, and plant architecture were preferentially selected. Furthermore, regardless of origins, the improvement of the modern oil-use flax preceded that of the fiber-use flax, although the dual selection on oil-use and fiber-use characteristics might have occurred in the early flax domestication. We also found that the expansion of MYB46/MYB83 genes may have contributed to the unique secondary cell wall biosynthesis in flax and the directional selections on MYB46/MYB83 may have shaped the morphological profile of the current oil-use and fiber-use flax., Graphical Abstract, Highlights • Assemblies of genomes, including oil-use flax, fiber-use flax and pale flax • Comparative genomic analysis between pale flax and cultivated flax • Dual-selection mode on oil-use and fiber-use characteristics might be existing • Expansion and selection of MYB46/MYB83 may shape the morphological profile of flax, Biological Sciences; Evolutionary Biology; Genomics; Plant Evolution; Plant Genetics

Background Oil flax (linseed, Linum usitatissimum L.) is one of the most important oil crops., However, the increases in drought resulting from climate change have dramatically reduces linseed yield and quality, but very little is known about how linseed coordinates the expression of drought resistance gene in response to different level of drought stress (DS) on the genome-wide level. Results To explore the linseed transcriptional response of DS and repeated drought (RD) stress, we determined the drought tolerance of different linseed varieties. Then we performed full-length transcriptome sequencing of drought-resistant variety (Z141) and drought-sensitive variety (NY-17) under DS and RD stress at the seedling stage using single-molecule real-time sequencing and RNA-sequencing. Gene Ontology (GO) and reduce and visualize GO (REVIGO) enrichment analysis showed that upregulated genes of Z141 were enriched in more functional pathways related to plant drought tolerance than those of NY-17 were under DS. In addition, 4436 linseed transcription factors were identified, and 1190 were responsive to stress treatments. Moreover, protein-protein interaction (PPI) network analysis showed that the proline biosynthesis pathway interacts with stress response genes through RAD50 (DNA repair protein 50) interacting protein 1 (RIN-1). Finally, proline biosynthesis and DNA repair structural gene expression patterns were verified by RT- PCR. Conclusions The drought tolerance of Z141 may be related to its upregulation of drought tolerance genes under DS. Proline may play an important role in linseed drought tolerance by maintaining cell osmotic and protecting DNA from ROS damage. In summary, this study provides a new perspective to understand the drought adaptability of linseed.

Castor bean (Ricinus communis L.) is an important industrial oilseed crop with diverse sex patterns. Understanding the genetics and genomics of castor bean sexual reproduction is valuable for both its breeding and sex-determination researches. Here, we described the biology of flowering habit, sex forms, and sex variations in castor bean. Castor plant grows to raceme–cyme inflorescence and has the potential to be an ever-flowering perennial, it is normally monoecious raceme, but other inflorescence patterns such as pistillate, male, and intersperse also can be observed. A simplified overview on wide variation of sex tendency and variegation phenomenon in sex expression was given, and the factors affected sex expression were also summarized. Moreover, sex inheritance was also generalized, and the genes underlying or involved in the monocism, female, interspersed staminate flowers, and terminal hermaphroditism were mentioned. We reviewed the genetic variation of the replication for pistillate plant by the combination of tissue culture, molecular markers, and conventional breeding. It was showed that pistillate somaclones with high percentage of pistillate plants were obtained, and allelic differences were discovered among individuals of somaclonal populations with instable sex expression. Some genes associated with sex expression and reproduction, hormone response, transcription regulation and signal transduction, have also been identified by digital gene expression (DGE) analysis. This overview provided some information and valuable hints for insights into the molecular mechanism of sex determination.

Ricinus communis is a versatile industrial oil crop that is cultivated worldwide. Genetic improvement and marker-assisted breeding of castor bean have been slowed owing to the lack of abundant and efficient molecular markers. As co-dominant markers, simple sequence repeats (SSRs) are useful for genetic evaluation and molecular breeding. The recently released whole-genome sequence of castor bean provides useful genomic resources for developing markers on a genome-wide scale. In the present study, the distribution and frequency of microsatellites in the castor bean genome were characterised and numerous SSR markers were developed using genomic data mining. In total, 18,647 SSR loci at a density of one SSR per 18.89 Kb in the castor bean genome sequence (representing approximately 352.27 Mb) were identified. Dinucleotide repeats were the most frequently observed microsatellites, although the AAT repeat motif was also prevalent. Using six cultivars as screening samples, 670 polymorphic SSR markers from 1,435 primer pairs (46.7 %) were developed. Trinucleotide motif loci contained a higher proportion of polymorphisms (48.5 %) than dinucleotide motif loci (39.2 %). The polymorphism level in the SSR loci was positively correlated with the increasing number of repeat units in the microsatellites. The phylogenetic relationship among 32 varieties was evaluated using the developed SSR markers. Cultivars developed at the same institute clustered together, suggesting that these cultivars have a narrow genetic background. The large number of SSR markers developed in this study will be useful for genetic mapping and for breeding improved castor-oil plants. These markers will also facilitate genetic and genomic studies of Euphorbiaceae.

The castor (Ricinus communis L.) pistillate lines are important for hybrid seed production and research on sex traits. This study aimed to replicate the pistillate line of castor plants and detect somaclonal variation. Pistillate plants were successfully propagated and pistillate plant stability and somaclonal variation were tested. For propagation, 66 axillary buds with 96.97% survival were cultured on three different media: initial culture medium, proliferation medium, and rooting medium. At the end of this procedure, 108 plantlets were obtained and successfully transplanted into the field with 50–70% survival. Sex expression of the somaclones and their F1/F2 progenies indicated that pistillate was stable in the somaclones of three genotypes, and male flowers could be induced in other genotypes by tissue culture. The percentage of pistillate plants in the F1 progeny obtained from female somaclones was higher (30.00–100.00%) than that in the progeny of its pistillate donors (26.67–50.00%) and the monoecious regenerations (0–5.00%). Two pistillate somaclones with a reverted monoecious plant were grown together in isolation, and yielded 91.11% and 100.00% females in the F1 progeny, and 76.10% and 75.00% females in the F2 progeny from their sibling crosses. The detection of somaclonal variation suggested that the somaclones derived from the same donor and with a stable pistillate trait showed no allelic variation at simple sequence repeat loci, whereas allelic variation was detected among individuals of somaclonal populations with instable sex expression. These results provide a useful approach for pistillate plant propagation and heterosis utilization in castor via a combination of tissue culture and conventional breeding.

The castor plant (Ricinus communis L.) is a versatile industrial oilseed crop with a diversity of sex patterns, its hybrid breeding for improving yield and high purity is still hampered by genetic instability of female and poor knowledge of sex expression mechanisms. To obtain some hints involved in sex expression and provide the basis for further insight into the molecular mechanisms of castor plant sex determination, we performed DGE analysis to investigate differences between the transcriptomes of apices and racemes derived from female (JXBM0705P) and monoecious (JXBM0705M) lines. A total of 18 DGE libraries were constructed from the apices and racemes of a wild monoecious line and its isogenic female derivative at three stages of apex development, in triplicate. Approximately 5.7 million clean tags per library were generated and mapped to the reference castor genome. Transcriptomic analysis showed that identical dynamic changes of gene expression were indicated in monoecious and female apical bud during its development from vegetation to reproduction, with more genes expressed at the raceme formation and infant raceme stages compare to the early leaf bud stage. More than 3 thousands of differentially expressed genes (DEGs) were detected in Ricinus apices at three developmental stages between two different sex types. A number of DEGs involved in hormone response and biosynthesis, especially auxin response and transport, transcription factors, signal transduction, histone demethylation/methylation, programmed cell death, and pollination, putatively associated with sex expression and reproduction were discovered, and the selected DEGs showed consistent expression between qRT-PCR validation and the DGE patterns. Most of those DEGs were suppressed at the early leaf stage in buds of the mutant, but then activated at the following transition stage (5-7-leaf stage) of buds in the mutant, and ultimately, the number of up-regulated DEGs was equal to that of down-regulation in the small raceme of the mutant. In this study, a large number of DEGs and some suggestions involved in sex expression and reproduction were discovered using DGE analysis, which provides large information and valuable hints for next insights into the molecular mechanism of sex determination. It is useful for other further studies in Ricinus.

Castor bean (Ricinus communis L.), an important non-edible oilseed crop, is originated in tropical regions, but is now cultivated in many subtropical areas around the world. Although it has a high economic value and is broadly used in industry, castor bean is very sensitive to low temperature, especially at the germination stage. So far, the knowledge about the mechanisms underlying the environmental effects on seed germination was largely unknown. In this study, the transcriptional profile analysis was performed in germinating castor bean seeds in response to cold stress (20 °C), and a total of 2411 differentially expressed genes (DEGs) were indentified in the seeds germinating at 20 °C in comparison with those germinating at 30 °C (control). The pathway enrichment analysis of DEGs showed that most of over-represented pathways were mainly related to plant secondary metabolisms. Also, most of the DEGs in the enriched pathways, including the 20 phenylpropanoids-related genes, were coordinately up-regulated in the seeds germinating at 20 °C, indicating that they might be key candidate genes or regulators involved in seed germination under chilling conditions. Thus, these results would give us a guide to promote the germination of crop seeds sowed in spring under low temperature.

Cadmium (Cd) and dichlorodiphenyltrichloroethane (DDT) or its metabolite residues are frequently detected in agricultural soils and food, posing a threat to human health. The objective of this study was to compare the ability of 23 genotypes of Ricinus communis in mobilizing and uptake of Cd and DDTs (p,p'-DDT, o,p'-DDT, p,p'-DDD and p,p'-DDE) in the co-contaminated soil. The plant genotypes varied largely in the uptake and accumulation of DDTs and Cd, with mean concentrations of 0.37, 0.43 and 70.51 for DDTs, and 1.22, 2.27 and 37.63 mg kg(-1) dw for Cd in leaf, stem and root, respectively. The total uptake of DDTs and Cd varied from 83.1 to 267.8 and 66.0 to 155.1 μg per pot, respectively. These results indicate that R. communis has great potential for removing DDTs and Cd from contaminated soils attributed to its fast growth, high biomass, strong absorption and accumulation for both DDTs and Cd.