Comparative proteomic and transcriptomic analyses provide new insight into the formation of seed size in castor bean

QTL mapping and candidate gene mining of seed size and seed weight in castor plant (Ricinus communis L.)

BACKGROUND

Castor (Ricinus communis L., 2n = 2x = 20) is an important industrial crop, due to its oil is very important to the global special chemical industry. Seed size and seed weight are fundamentally important in determining castor yield, while little is known about it. In this study, QTL analysis and candidate gene mining of castor seed size and seed weight were conducted with composite interval mapping (CIM), inclusive composite interval mapping (ICIM) and marker enrichment strategy in 4 populations, i.e., populations F2, BC1, S1-1 and S1-2, derived from 2 accessions with significant phenotypic differences.

RESULTS

In the QTL primary mapping, 2 novel QTL clusters were detected in marker intervals RCM520-RCM76 and RCM915-RCM950. In order to verify their accuracy and to narrow their intervals, QTL remapping was carried out in populations F2 and BC1. Among them, 44 and 30 QTLs underlying seed size and seed weight were detected in F2 population using methods CIM and ICIM-ADD respectively, including 4-9 and 3-5 ones conferring each trait were identified with a phenotypic variation explained ranged from 37.92 to 115.81% and 32.86-45.98% respectively. The remapping results in BC1 population were consistent with those in F2 population. Importantly, 3 QTL clusters (i.e. QTL-cluster1, QTL-cluster2 and QTL-cluster3) were found in marker intervals RCM74-RCM76 (37.1 kb), RCM930-RCM950 (259.8 kb) and RCM918-RCM920 (172.9 kb) respectively; in addition, all of them were detected again, the former one was found in the S1-2 population, and the latter two were found simultaneously in the populations S1-1 and S1-2. Finally, 6 candidate genes (i.e. LOC8266555, LOC8281168, LOC8281151, LOC8259066, LOC8258591 and LOC8270077) were screened in the above QTL clusters, they were differentially expressed in multiple seed tissues of both parents, signifying the potential role in regulating seed size and seed weight.

CONCLUSION

The above results not only provide new insights into the genetic structure of seed size and seed weight in castor, but also lay the foundation for the functional identification of these candidate genes.

Modern day breeding approaches for improvement of castor

Castor (Ricinus communis L.) is an industrially important oil producing crop belongs to Euphorbiaceae family. Castor oil has unique chemical properties make it industrially important crop. It is a member of monotypic genus even though it has ample amount of variability. Using this variability, conventionally many varieties and hybrids have been developed. But, like other crops, the modern and unconventional methods of crop improvement has not fully explored in castor. This article discusses the use of polyploidy induction, distant/wide hybridization and mutation breeding as tools for generating variety. Modern approaches accelerate the speed of crop breeding as an alternative tool. To achieve this goal, molecular markers are employed in breeding to capture the genetic variability through molecular analysis and population structuring. Allele mining is used to trace the evolution of alleles, identify new haplotypes and produce allele specific markers for use in marker aided selection using Genome wide association studies (GWAS) and quantitative trait loci (QTL) mapping. Plant genetic transformation is a rapid and effective mode of castor improvement is also discussed here. The efforts towards developing stable regeneration protocol provide a wide range of utility like embryo rescue in distant crosses, development of somaclonal variation, haploid development using anther culture and callus development for stable genetic transformation has reviewed in this article. Omics has provided intuitions to the molecular mechanisms of (a)biotic stress management in castor along with dissected out the possible genes for improving the yield. Relating genes to traits offers additional scientific inevitability leading to enhancement and sympathetic mechanisms of yield improvement and several stress tolerance.

Functional Genome Analyses Reveal the Molecular Basis of Oil Accumulation in Developing Seeds of Castor Beans

Castor (Ricinus communis L.) seeds produce abundant ricinoleic acid during seed maturation, which is important for plant development and human demands. Ricinoleic acid, as a unique hydroxy fatty acid (HFA), possesses a distinct bond structure that could be used as a substitute for fossil fuels. Here, we identified all homologous genes related to glycolysis, hydroxy fatty acid biosynthesis, and triacylglycerol (TAG) accumulation in castor seeds. Furthermore, we investigated their expression patterns globally during five seed development stages. We characterized a total of 66 genes involved in the glycolysis pathway, with the majority exhibiting higher expression levels during the early stage of castor bean seed development. This metabolic process provided abundant acetyl-CoA for fatty acid (FA) biosynthesis. Subsequently, we identified 82 genes involved in the processes of de novo FA biosynthesis and TAG assembly, with the majority exhibiting high expression levels during the middle or late stages. In addition, we examined the expression patterns of the transcription factors involved in carbohydrate and oil metabolism. For instance, RcMYB73 and RcERF72 exhibited high expression levels during the early stage, whereas RcWRI1, RcABI3, and RcbZIP67 showed relatively higher expression levels during the middle and late stages, indicating their crucial roles in seed development and oil accumulation. Our study suggests that the high HFA production in castor seeds is attributed to the interaction of multiple genes from sugar transportation to lipid droplet packaging. Therefore, this research comprehensively characterizes all the genes related to glycolysis, fatty acid biosynthesis, and triacylglycerol (TAG) accumulation in the castor and provides novel insight into exploring the genetic mechanisms underlying seed oil accumulation in the endosperm of castor beans.

Dynamics of imprinted genes and their epigenetic mechanisms in castor bean seed with persistent endosperm

Genomic imprinting refers to parent-of-origin-dependent gene expression and primarily occurs in the endosperm of flowering plants, but its functions and epigenetic mechanisms remain to be elucidated in eudicots. Castor bean, a eudicot with large and persistent endosperm, provides an excellent system for studying the imprinting. Here, we identified 131 imprinted genes in developing endosperms and endosperm at seed germination phase of castor bean, involving into the endosperm development, accumulation of storage compounds and specially seed germination. Our results showed that the transcriptional repression of maternal allele of DNA METHYLTRANSFERASE 1 (MET1) may be required for maternal genome demethylation in the endosperm. DNA methylation analysis showed that only a small fraction of imprinted genes was associated with allele-specific DNA methylation, and most of them were closely associated with constitutively unmethylated regions (UMRs), suggesting a limited role for DNA methylation in controlling genomic imprinting. Instead, histone modifications can be asymmetrically deposited in maternal and paternal genomes in a DNA methylation-independent manner to control expression of most imprinted genes. These results expanded our understanding of the occurrence and biological functions of imprinted genes and showed the evolutionary flexibility of the imprinting machinery and mechanisms in plants.

Proteome Landscape during Ripening of Solid Endosperm from Two Different Coconut Cultivars Reveals Contrasting Carbohydrate and Fatty Acid Metabolic Pathway Modulation

Cocos nucifera L. is a crop grown in the humid tropics. It is grouped into two classes of varieties: dwarf and tall; regardless of the variety, the endosperm of the coconut accumulates carbohydrates in the early stages of maturation and fatty acids in the later stages, although the biochemical factors that determine such behavior remain unknown. We used tandem mass tagging with synchronous precursor selection (TMT-SPS-MS3) to analyze the proteomes of solid endosperms from Yucatan green dwarf (YGD) and Mexican pacific tall (MPT) coconut cultivars. The analysis was conducted at immature, intermediate, and mature development stages to better understand the regulation of carbohydrate and lipid metabolisms. Proteomic analyses showed 244 proteins in YGD and 347 in MPT; from these, 155 proteins were shared between both cultivars. Furthermore, the proteomes related to glycolysis, photosynthesis, and gluconeogenesis, and those associated with the biosynthesis and elongation of fatty acids, were up-accumulated in the solid endosperm of MPT, while in YGD, they were down-accumulated. These results support that carbohydrate and fatty acid metabolisms differ among the developmental stages of the solid endosperm and between the dwarf and tall cultivars. This is the first proteomics study comparing different stages of maturity in two contrasting coconut cultivars and may help in understanding the maturity process in other palms.

Analysis of the mechanism of Ricinus communis L. tolerance to Cd metal based on proteomics and metabolomics

The pollution of soil with heavy metals is an increasingly serious worldwide problem, and cadmium (Cd) has attracted attention because of its high toxicity to almost all plants. Since castor tolerates the accumulation of heavy metals, it has the potential for heavy metal soil remediation. We studied the mechanism of the tolerance of castor to Cd stress treatments at three doses: 300 mg/L, 700 mg/L, and 1,000 mg/L. This research provides new ideas for revealing the defense and detoxification mechanisms of Cd-stressed castor. By combining the results of physiology, differential proteomics and comparative metabolomics, we conducted a comprehensive analysis of the networks that regulate the response of castor to Cd stress. The physiological results mainly emphasize the super-sensitive responses of castor plant roots to Cd stress and the effects of Cd stress on plants' antioxidant system, ATP synthesis and ion homeostasis. We confirmed these results at the protein and metabolite levels. In addition, proteomics and metabolomics indicated that under Cd stress, the expressions of proteins involved in defense and detoxification, energy metabolism and other metabolites such as organic acids and flavonoids were significantly up-regulated. At the same time, proteomics and metabolomics also show that castor plants mainly block the root system's absorption of Cd2+ by enhancing the strength of the cell wall, and inducing programmed cell death in response to the three different doses of Cd stress. In addition, the plasma membrane ATPase encoding gene (RcHA4), which was significantly upregulated in our differential proteomics and RT-qPCR studies, was transgenically overexpressed in wild type Arabidopsis thaliana for functional verification. The results indicated that this gene plays an important role in improving plant Cd tolerance.

Integration of the Physiology, Transcriptome and Proteome Reveals the Molecular Mechanism of Drought Tolerance in Cupressus gigantea

Drought stress can dramatically impair woody plant growth and restrict the geographical distribution of many tree species. To better understand the dynamics between the response and mechanism of Cupressus gigantea to drought and post-drought recovery, a comparative analysis was performed, relying on physiological measurements, RNA sequencing (RNA-Seq) and two-dimensional gel electrophoresis (2-DE) proteins. In this study, the analyses revealed that photosynthesis was seriously inhibited, while osmolyte contents, antioxidant enzyme activity and non-enzymatic antioxidant contents were all increased under drought stress in seedlings. Re-watering led to a recovery in most of the parameters analyzed, mainly the photosynthetic parameters and osmolyte contents. Transcriptomic and proteomic profiling suggested that most of the differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) were specifically altered, and a few were consistently altered. Drought induced a common reduction in the level of DEGs and DEPs associated with photosynthesis. Notably, DEGs and DEPs involved in reactive oxygen species (ROS) scavenging, such as ascorbate oxidase and superoxide dismutase (SOD), showed an inverse pattern under desiccation. This study may improve our understanding of the underlying molecular mechanisms of drought resistance in C. gigantea and paves the way for more detailed molecular analysis of the candidate genes.