Identifying Gene Function Research Articles

Heritable gene editing using FT mobile guide RNAs and DNA viruses

BackgroundThe virus-induced genome editing (VIGE) system can be used to quickly identify gene functions and generate knock-out libraries as an alternative to the virus-induced gene silencing (VIGS). Although plant virus-mediated VIGE has been shown to have great application prospects, edited genes cannot be transferred to the next generations using this system, as viruses cannot enter into shoot apical meristem (SAM) in plants.ResultsWe developed a novel cotton leaf crumple virus (CLCrV)-mediated VIGE system designed to target BRI1, GL2, PDS genes, and GUS transgene in A. thaliana by transforming Cas9 overexpression (Cas9-OE) A. thaliana. Given the deficiency of the VIGE system, ProYao::Cas9 and Pro35S::Cas9 A. thaliana were transformed by fusing 102 bp FT mRNAs with sgRNAs so as to explore the function of Flowering Locus T (FT) gene in delivering sgRNAs into SAM, thus avoiding tissue culture and stably acquiring heritable mutant offspring. Our results showed that sgRNAs fused with FT mRNA at the 5′ end (FT strategy) effectively enabled gene editing in infected plants and allowed the acquisition of mutations heritable by the next generation, with an efficiency of 4.35–8.79%. In addition, gene-edited offspring by FT-sgRNAs did not contain any components of the CLCrV genome.ConclusionsFT strategy can be used to acquire heritable mutant offspring avoiding tissue culture and stable transformation based on the CLCrV-mediated VIGE system in A. thaliana.

Genes adapt to outsmart gene-targeting strategies in mutant mouse strains by skipping exons to reinitiate transcription and translation

BackgroundGene disruption in mouse embryonic stem cells or zygotes is a conventional genetics approach to identify gene function in vivo. However, because different gene disruption strategies use different mechanisms to disrupt genes, the strategies can result in diverse phenotypes in the resulting mouse model. To determine whether different gene disruption strategies affect the phenotype of resulting mutant mice, we characterized Rhbdf1 mouse mutant strains generated by three commonly used strategies—definitive-null, targeted knockout (KO)-first, and CRISPR/Cas9.ResultsWe find that Rhbdf1 responds differently to distinct KO strategies, for example, by skipping exons and reinitiating translation to potentially yield gain-of-function alleles rather than the expected null or severe hypomorphic alleles. Our analysis also revealed that at least 4% of mice generated using the KO-first strategy show conflicting phenotypes.ConclusionsExon skipping is a widespread phenomenon occurring across the genome. These findings have significant implications for the application of genome editing in both basic research and clinical practice.

LA EDICIÓN DE GENOMAS: PLANTAS A LA CARTA

The plants we eat are the outcome of a humans’ long history of domestication of wild species. The introduction of CRISPR/Cas gene-editing technology has provided a new approach to crop improvement and offers an interesting range of possibilities for obtaining varieties with new and healthier characteristics. The technology is based on two fundamental pillars: on the one hand, knowing complete genome sequences, and on the other, identifying gene functions. In less than a decade, the prospect of being able to design plants on demand is now no longer a dream, but a real possibility.

Gene-gene interaction: the curse of dimensionality.

Identified genetic variants from genome wide association studies frequently show only modest effects on the disease risk, leading to the "missing heritability" problem. An avenue, to account for a part of this "missingness" is to evaluate gene-gene interactions (epistasis) thereby elucidating their effect on complex diseases. This can potentially help with identifying gene functions, pathways, and drug targets. However, the exhaustive evaluation of all possible genetic interactions among millions of single nucleotide polymorphisms (SNPs) raises several issues, otherwise known as the "curse of dimensionality". The dimensionality involved in the epistatic analysis of such exponentially growing SNPs diminishes the usefulness of traditional, parametric statistical methods. With the immense popularity of multifactor dimensionality reduction (MDR), a non-parametric method, proposed in 2001, that classifies multi-dimensional genotypes into one- dimensional binary approaches, led to the emergence of a fast-growing collection of methods that were based on the MDR approach. Moreover, machine-learning (ML) methods such as random forests and neural networks (NNs), deep-learning (DL) approaches, and hybrid approaches have also been applied profusely, in the recent years, to tackle this dimensionality issue associated with whole genome gene-gene interaction studies. However, exhaustive searching in MDR based approaches or variable selection in ML methods, still pose the risk of missing out on relevant SNPs. Furthermore, interpretability issues are a major hindrance for DL methods. To minimize this loss of information, Python based tools such as PySpark can potentially take advantage of distributed computing resources in the cloud, to bring back smaller subsets of data for further local analysis. Parallel computing can be a powerful resource that stands to fight this "curse". PySpark supports all standard Python libraries and C extensions thus making it convenient to write codes to deliver dramatic improvements in processing speed for extraordinarily large sets of data.

Identifying gene function and module connections by the integration of multispecies expression compendia.

The functions of many eukaryotic genes are still poorly understood. Here, we developed and validated a new method, termed GeneBridge, which is based on two linked approaches to impute gene function and bridge genes with biological processes. First, Gene-Module Association Determination (G-MAD) allows the annotation of gene function. Second, Module-Module Association Determination (M-MAD) allows predicting connectivity among modules. We applied the GeneBridge tools to large-scale multispecies expression compendia—1700 data sets with over 300,000 samples from human, mouse, rat, fly, worm, and yeast—collected in this study. G-MAD identifies novel functions of genes—for example, DDT in mitochondrial respiration and WDFY4 in T cell activation—and also suggests novel components for modules, such as for cholesterol biosynthesis. By applying G-MAD on data sets from respective tissues, tissue-specific functions of genes were identified—for instance, the roles of EHHADH in liver and kidney, as well as SLC6A1 in brain and liver. Using M-MAD, we identified a list of module-module associations, such as those between mitochondria and proteasome, mitochondria and histone demethylation, as well as ribosomes and lipid biosynthesis. The GeneBridge tools together with the expression compendia are available as an open resource, which will facilitate the identification of connections linking genes, modules, phenotypes, and diseases.

Comparative transcriptomics of Gymnosporangium spp. teliospores reveals a conserved genetic program at this specific stage of the rust fungal life cycle

BackgroundGymnosporangium spp. are fungal plant pathogens causing rust disease and most of them are known to infect two different host plants (heteroecious) with four spore stages (demicyclic). In the present study, we sequenced the transcriptome of G. japonicum teliospores on its host plant Juniperus chinensis and we performed comparison to the transcriptomes of G. yamadae and G. asiaticum at the same life stage, that happens in the same host but on different organs.ResultsFunctional annotation for the three Gymnosporangium species showed the expression of a conserved genetic program with the top abundant cellular categories corresponding to energy, translation and signal transduction processes, indicating that this life stage is particularly active. Moreover, the survey of predicted secretomes in the three Gymnosporangium transcriptomes revealed shared and specific genes encoding carbohydrate active enzymes and secreted proteins of unknown function that could represent candidate pathogenesis effectors. A transcript encoding a hemicellulase of the glycoside hydrolase 26 family, previously identified in other rust fungi, was particularly highly expressed suggesting a general role in rust fungi. The comparison between the transcriptomes of the three Gymnosporangium spp. and selected Pucciniales species in different taxonomical families allowed to identify lineage-specific protein families that may relate to the biology of teliospores in rust fungi. Among clustered gene families, 205, 200 and 152 proteins were specifically identified in G. japonicum, G. yamadae and G. asiaticum, respectively, including candidate effectors expressed in teliospores.ConclusionsThis comprehensive comparative transcriptomics study of three Gymnosporangium spp. identified gene functions and metabolic pathways particularly expressed in teliospores, a stage of the life cycle that is mostly overlooked in rust fungi. Secreted protein encoding transcripts expressed in teliospores may reveal new candidate effectors related to pathogenesis. Although this spore stage is not involved in host plant infection but in the production of basidiospores infecting plants in the Amygdaloideae, we speculate that candidate effectors may be expressed as early as the teliospore stage for preparing further infection by basidiospores.

Use of TRV-mediated VIGS for functional genomics research in citrus

Virus induced gene silencing (VIGS) is a powerful tool for identifying gene functions in plants. Tobacco rattle virus (TRV)-mediated VIGS has been reported for silencing of endogenous genes in many plants. In citrus, analysis of gene function is mainly relied on the table genetic transformation, even though this technique is low-efficiency and time-consuming. In this study, a TRV-mediated VIGS was successfully applied for verification of gene function in citrus. A reporter gene, Magnesium chelatase subunit I (ChlI) from C. grandis was constructed into TRV2 vector to induce gene silencing with visible photobleaching symptom. TRV VIGS induced photobleaching symptom was observed on the leaves of Nicotiana benthamiana and Citrus after infiltration. The susceptibility to VIGS vector was found to be genotype dependent. Mexican lemon is the most susceptible one. The chlorosis area per leaf was 65.5% of the whole leaf area. GXSTY pummelo exhibited less susceptible to VIGS with only tiny patches of chlorosis appeared on the leaves of treated plants. The parameters were optimized to improve the efficiency. The tiny young leaves and half expanded leaves were more susceptible to VIGS infection. Young seedlings were highly susceptible to vacuum infiltration. The expression of fluorescence from GFP reporter gene was observed in the young seedlings of GXSTY after infiltration with TRV. Close to 100% of infiltration efficiency was achieved by vacuum infiltration. The results indicated that TRV mediated VIGS with vacuum infiltration could be an ideal tool for gene function studies in citrus. A TRV mediated VIGS has been optimized to use in the citrus for verification of gene function. The sensitivity to VIGS vector was genotype dependent. Young seedling and young leaf were the suitable materials for VIGS infection. Vacuum infiltration was a high efficiency infiltration method.

Acquisition of seed dormancy breaking in rice (Oryza sativa L.) via CRISPR/Cas9-targeted mutagenesis of OsVP1 gene

Genome editing offers great advantages in identifying gene function and generating agronomical important mutations in crops. Here, we report the development of edited lines with reduced seed dormancy by knockout viviparous-1 (OsVP1) gene known as a transcription factor that regulates key aspects of plant seed development and ABA signaling in rice. Thirty-three genetic edited lines out of 55 T0 rice plants were generated using CRISPR/Cas9 system. Sequencing analysis showed that the plants had four different mutation types at the target site of OsVP1, the mutations were found to be transmitted to the succeeding generations. Stable transmission of CRISPR/Cas9-mediated mutant lines without the transferred DNA (T-DNA) was confirmed by segregation in the T1 generation. Regarding many investigated agronomic trait, there are no significant differences between homozygous mutants and wildtype plants under field’s growth conditions. Especially in RT-PCR analysis of ABA/GA signaling genes, the expression of OsNCED2, OsGA20ox1, OsGA20ox2, OsGA20ox3 genes in homozygous mutants was increased compared to wildtype plants. Results of this study exemplified the effectiveness of CRISPR/Cas9 as a gene editing tool in broke down the seed dormancy in rice.

CRISPR/Cas9-targeted mutagenesis of F3′H, DFR and LDOX, genes related to anthocyanin biosynthesis in black rice (Oryza sativa L.)

Altering a trait by CRISPR-Cas9-targeted mutagenesis offers great advantages in identifying gene function and crop improvement. In the present study, three genes (OsF3′H, OsDFR and OsLDOX) in the anthocyanin biosynthesis pathway were successfully edited on the Heugseonchal or Sinmyungheugchal variety using the CRISPR/Cas9 system. As a result, the ratio of the edited plants in the transformed early generation was 56.7%. These edited mutant lines were observed with the changes of seed color and anthocyanin content. All mutations were stably inherited to the T2 progeny. In addition, we could select edited homozygous mutant lines lacking the T-DNA already in the first offspring generation. Also the insertion of vector backbone sequences in f3′h-9, dfr-4 and ldox-16 lines was not detected in the whole genome resequencing. These results demonstrated that the CRISPR/Cas9 system can induce clearly gene-specific mutations with a high efficiency in rice and null plants selected from these mutants cannot be distinguished from non-GMO plants even under strict GMO regulation.

Application of virus-induced gene silencing for identification of FHB resistant genes

Virus-induced gene silencing (VIGS) showed several advantages to identify gene functions such as short experimental cycle, more broad hosts, etc. In this study, the feasibility and efficiency of employing Barley stripe mosaic virus (BSMV)-based VIGS system to evaluate Fusarium head blight (FHB) resistance were explored in wheat. With variable conditions tested, it showed that the maximal silencing efficiency 78% on spike was obtained when the recombinant BSMV was inoculated on flag leaf at flagging stage. However, the plant may reduce its own immunity to FHB when inoculated with BSMV. To induce this impact, different Fusarium graminearum strains were tested and SF06-1 strain was selected for FHB resistance evaluation. Using this system, TaAOC, TaAOS, and TaOPR3 involved in jasmonic acid (JA) signaling pathway were identified to positively regulate FHB resistance, which was underpinned by the results when silencing TaAOS in wheat by stable transgenic plants.

Virus-induced gene silencing for phenylalanine ammonia-lyase affects pepper adaption to low temperature

Reverse genetics approaches in plants rely on post-transcriptional gene silencing to study the function of genes. In particular, virus-induced gene silencing (VIGS) has been successfully applied to identify gene function in some crops. To date, it is unclear whether phenylalanine ammonia-lyase (PAL) is involved in low temperature tolerance in the pepper. Here, we used an agroinfiltration protocol with tobacco rattle virus (TRV) constructs containing partial sequences from CaPAL for VIGS to test its role in anthocyanin biosynthesis and response to low temperature in the pepper (Capsicum annuum). We found that accumulation of anthocyanins in the leaves of pepper plants transformed with the TRV2:CaPAL vector was significantly reduced compared with peppers transformed with the empty TRV2 vector (TRV2:00). A significant reduction in expression of genes related to anthocyanins synthesis was also detected in peppers transformed with TRV2:CaPAL. When silenced pepper plants were exposed to a low temperature, we found decreased antioxidant system, PAL activity, and photosynthesis in plants transformed with TRV2:CaPAL compared with peppers transformed with TRV2:00. Low transcriptions of cold stress-response genes demonstrated that pepper tolerance to low temperature decreased. Future studies focused on the interaction between CaPAL and other abiotic and biotic stressors will shed further light into the role of CaPAL in stress response.

Efficient BoPDS Gene Editing in Cabbage by the CRISPR/Cas9 System

Genome editing offers great advantages in identifying gene function and generating agronomically important mutations in crops. Here, we report that the genome of cabbage (Brassica oleracea var. capitata), an important cruciferous vegetable, can also be precisely edited by a CRISPR/Cas9 system stacked with multiple single-guide RNA-expressing cassettes. When the phytoene desaturase BoPDS gene was used as the target gene, an albino-phenotype transgenic shoot in T0 Basta-resistant lines was observed, and 37.5% of the transgenic cabbage shoots carried BoPDS gene mutations as a result of nucleotide deletions at the expected position. Moreover, mutations were detected in sites with the same target sequence in gene Bol016089 which is paralogous to the BoPDS gene. Our results show that the CRISPR/ Cas9 system is a powerful tool for cabbage variety improvement by genome editing.

Genome-Wide Association Analyses in the Model Rhizobium Ensifer meliloti.

Genome-wide association studies (GWAS) can identify genetic variants responsible for naturally occurring and quantitative phenotypic variation. Association studies therefore provide a powerful complement to approaches that rely on de novo mutations for characterizing gene function. Although bacteria should be amenable to GWAS, few GWAS have been conducted on bacteria, and the extent to which nonindependence among genomic variants (e.g., linkage disequilibrium [LD]) and the genetic architecture of phenotypic traits will affect GWAS performance is unclear. We apply association analyses to identify candidate genes underlying variation in 20 biochemical, growth, and symbiotic phenotypes among 153 strains of Ensifer meliloti For 11 traits, we find genotype-phenotype associations that are stronger than expected by chance, with the candidates in relatively small linkage groups, indicating that LD does not preclude resolving association candidates to relatively small genomic regions. The significant candidates show an enrichment for nucleotide polymorphisms (SNPs) over gene presence-absence variation (PAV), and for five traits, candidates are enriched in large linkage groups, a possible signature of epistasis. Many of the variants most strongly associated with symbiosis phenotypes were in genes previously identified as being involved in nitrogen fixation or nodulation. For other traits, apparently strong associations were not stronger than the range of associations detected in permuted data. In sum, our data show that GWAS in bacteria may be a powerful tool for characterizing genetic architecture and identifying genes responsible for phenotypic variation. However, careful evaluation of candidates is necessary to avoid false signals of association.IMPORTANCE Genome-wide association analyses are a powerful approach for identifying gene function. These analyses are becoming commonplace in studies of humans, domesticated animals, and crop plants but have rarely been conducted in bacteria. We applied association analyses to 20 traits measured in Ensifer meliloti, an agriculturally and ecologically important bacterium because it fixes nitrogen when in symbiosis with leguminous plants. We identified candidate alleles and gene presence-absence variants underlying variation in symbiosis traits, antibiotic resistance, and use of various carbon sources; some of these candidates are in genes previously known to affect these traits whereas others were in genes that have not been well characterized. Our results point to the potential power of association analyses in bacteria, but also to the need to carefully evaluate the potential for false associations.

Protein Barcodes Enable High-Dimensional Single-Cell CRISPR Screens

CRISPR pools are being widely employed to identify gene functions. However, current technology, which utilizes DNA as barcodes, permits limited phenotyping and bulk-cell resolution. To enable novel screening capabilities, we developed a barcoding system operating at the protein level. We synthesized modules encoding triplet combinations of linear epitopes to generate >100 unique protein barcodes (Pro-Codes). Pro-Code-expressing vectors were introduced into cells and analyzed by CyTOF mass cytometry. Using just 14 antibodies, we detected 364 Pro-Code populations; establishing the largest set of protein-based reporters. By pairing each Pro-Code with a different CRISPR, we simultaneously analyzed multiple phenotypic markers, including phospho-signaling, on dozens of knockouts. Pro-Code/CRISPR screens found two interferon-stimulated genes, the immunoproteasome component Psmb8 and a chaperone Rtp4, are important for antigen-dependent immune editing of cancer cells and identified Socs1 as a negative regulator of Pd-l1. The Pro-Code technologyenables simultaneous high-dimensional protein-level phenotyping of 100s of genes with single-cell resolution.

A co-silencing system for functional analysis of genes without visible phenotype in tomato plant development and fruit ripening using tobacco rattle virus

Abstract Virus-induced gene silencing (VIGS) is known as a powerful tool for identifying gene functions during plant growth and development. Tobacco rattle virus (TRV) based VIGS has been successfully employed in many plants. However, there have been few reports that VIGS can be used to study the function of gene at fruit level, especially the genes without visible silencing phenotype. Here we used miniature tomato cultivar Micro-Tom (Solanum lycopersicum L.) as material to silence phytoene desaturase (SlPDS) and SlARG2, an important gene encoding arginase in arginine metabolism, separately or simultaneously with TRV agroinoculated by sprout vacuum-infiltration to test the utility of concurrently silencing two genes. When SlPDS and SlARG2 were co-silenced in the same tissue at the same time, there are no compromises in silencing efficiency and silencing efficacy compared with SlPDS or SlARG2 silenced separately. Moreover, the silence of SlPDS and SlARG2 with TRV agroinoculated by sprout vacuum-infiltration occurred at the early stage of tomato plant, and the silence can extend to full red stage of fruit. Therefore, our results provide a means for functional analysis of genes, particularly the genes with no obvious visible phenotype after silencing, involved in all of the metabolic networks during fruit development and ripening.

Virus-induced gene silencing database for phenomics and functional genomics in Nicotiana benthamiana.

Virus‐induced gene silencing (VIGS) is an important forward and reverse genetics method for the study of gene function in many plant species, especially Nicotiana benthamiana. However, despite the widespread use of VIGS, a searchable database compiling the phenotypes observed with this method is lacking. Such a database would allow researchers to know the phenotype associated with the silencing of a large number of individual genes without experimentation. We have developed a VIGS phenomics and functional genomics database (VPGD) that has DNA sequence information derived from over 4,000 N. benthamiana VIGS clones along with the associated silencing phenotype for approximately 1,300 genes. The VPGD has a built‐in BLAST search feature that provides silencing phenotype information of specific genes. In addition, a keyword‐based search function could be used to find a specific phenotype of interest with the corresponding gene, including its Gene Ontology descriptions. Query gene sequences from other plant species that have not been used for VIGS can also be searched for their homologs and silencing phenotype in N. benthamiana. VPGD is useful for identifying gene function not only in N. benthamiana but also in related Solanaceae plants such as tomato and potato. The database is accessible at http://vigs.noble.org.

Select and resequence reveals relative fitness of bacteria in symbiotic and free-living environments

Assays to accurately estimate relative fitness of bacteria growing in multistrain communities can advance our understanding of how selection shapes diversity within a lineage. Here, we present a variant of the "evolve and resequence" approach both to estimate relative fitness and to identify genetic variants responsible for fitness variation of symbiotic bacteria in free-living and host environments. We demonstrate the utility of this approach by characterizing selection by two plant hosts and in two free-living environments (sterilized soil and liquid media) acting on synthetic communities of the facultatively symbiotic bacterium Ensifer meliloti We find (i) selection that hosts exert on rhizobial communities depends on competition among strains, (ii) selection is stronger inside hosts than in either free-living environment, and (iii) a positive host-dependent relationship between relative strain fitness in multistrain communities and host benefits provided by strains in single-strain experiments. The greatest changes in allele frequencies in response to plant hosts are in genes associated with motility, regulation of nitrogen fixation, and host/rhizobia signaling. The approach we present provides a powerful complement to experimental evolution and forward genetic screens for characterizing selection in bacterial populations, identifying gene function, and surveying the functional importance of naturally occurring genomic variation.

Non-viral and viral delivery systems for CRISPR-Cas9 technology in the biomedical field.

The clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (CRISPR-Cas9) system provides a novel genome editing technology that can precisely target a genomic site to disrupt or repair a specific gene. Some CRISPR-Cas9 systems from different bacteria or artificial variants have been discovered or constructed by biologists, and Cas9 nucleases and single guide RNAs (sgRNA) are the major components of the CRISPR-Cas9 system. These Cas9 systems have been extensively applied for identifying therapeutic targets, identifying gene functions, generating animal models, and developing gene therapies. Moreover, CRISPR-Cas9 systems have been used to partially or completely alleviate disease symptoms by mutating or correcting related genes. However, the efficient transfer of CRISPR-Cas9 system into cells and target organs remains a challenge that affects the robust and precise genome editing activity. The current review focuses on delivery systems for Cas9 mRNA, Cas9 protein, or vectors encoding the Cas9 gene and corresponding sgRNA. Non-viral delivery of Cas9 appears to help Cas9 maintain its on-target effect and reduce off-target effects, and viral vectors for sgRNA and donor template can improve the efficacy of genome editing and homology-directed repair. Safe, efficient, and producible delivery systems will promote the application of CRISPR-Cas9 technology in human gene therapy.

A collection of enhancer trap insertional mutants for functional genomics in tomato.

SummaryWith the completion of genome sequencing projects, the next challenge is to close the gap between gene annotation and gene functional assignment. Genomic tools to identify gene functions are based on the analysis of phenotypic variations between a wild type and its mutant; hence, mutant collections are a valuable resource. In this sense, T‐DNA collections allow for an easy and straightforward identification of the tagged gene, serving as the basis of both forward and reverse genetic strategies. This study reports on the phenotypic and molecular characterization of an enhancer trap T‐DNA collection in tomato (Solanum lycopersicum L.), which has been produced by Agrobacterium‐mediated transformation using a binary vector bearing a minimal promoter fused to the uidA reporter gene. Two genes have been isolated from different T‐DNA mutants, one of these genes codes for a UTP‐glucose‐1‐phosphate uridylyltransferase involved in programmed cell death and leaf development, which means a novel gene function reported in tomato. Together, our results support that enhancer trapping is a powerful tool to identify novel genes and regulatory elements in tomato and that this T‐DNA mutant collection represents a highly valuable resource for functional analyses in this fleshy‐fruited model species.

Phenotype Analysis Method for Identification of Gene Functions Involved in Asymmetric Division of Caenorhabditis elegans

In gene function analysis, it is arduous to identify gene function individually, and the way to screen out all involved genes according to a particular phenotype or disease usually shows us little information for a specific problem. We present a data-driven analysis system based on wild type (WT) embryos to study the concrete function of each gene associated with certain category of abnormal phenotypes. It can be applied to genes with very few RNAi embryos. Instead of presupposing the particular function of a gene, its function is confirmed by the statistical testing of built models. The scheme includes the following five: first, verify the to be detected genes and determine related recognized features according to the given category; second, compute the value of each feature based on WT embryos and merge them by principal component analysis (PCA); third, for each of the selected components of PCA, build a normal distribution and verify its normality; fourth, project the RNAi embryos to each component and probe them; and finally, analyze the more detailed functions of each gene based on the physical or biological meaning of each component. Choosing the first-round asymmetric division process of Caenorhabditis elegans as the phenotype, experimental results show that on the different aspects of the asymmetric division process, par-2, par-3, and let-754 are related to scalar differences; dcn-1 and mcm-5 are associated with the divergences of scalar variation, which may reflect the disaccord in development; and dcn-1, par-2, and par-3 are involved with morphological discrepancies.