Introduction

Bioresources represent a fundamental component of the research infrastructure that supports the life sciences. The development of bioresources is a lengthy and meticulous process, and they serve as the foundation for discoveries and future research endeavors. The sharing of these resources among researchers is crucial for the advancement of research and development. In response to this need, the Ministry of Education, Culture, Sports, Science and Technology (MEXT) established the National BioResource Project (NBRP) in FY2002. This initiative aims to create a systematic framework for the collection, preservation, and distribution of bioresources, with a particular emphasis on those requiring strategic development at the national level. This review synthesizes information on bioresources that have proven valuable for mammalian genome research. These resources include mice, rats, other animal resources, DNA-related materials, and human/animal cells and microbes. This review draws upon data extracted from a comprehensive database of publications related to NBRP bioresources, offering insights into the current landscape and potential future directions of bioresource utilization in genomic research.

Mice

The Core Center of NBRP-Mice is the Experimental Animal Division of the RIKEN BioResource Research Center (RIKEN BRC) (Mizuno-Iijima et al. 2022), which has collected mouse strains developed mainly in Japan that have been reported in academic publications (Fig. 1) in order to preserve unique and cutting-edge mouse models (Table 1). NBRP-Mice performs rigorous quality control, including microbial and genetic testing to ensure the reproducibility of animal experiments. As one of the international hubs for mouse resources, we continuously participate in global mouse resource networks such as International Mouse Strain Resource (IMSR), International Mouse Phenotyping Consortium (IMPC), Asian Mouse Mutagenesis & Resource Association (AMMRA) and Asian Network of Research Resource Centers (ANRRC). NBRP-Mice has archived approximately 10,000 mouse strains, most of which are genetically modified mice, as tools for gene functional analysis tools, including Cre/Flp drivers, fluorescent and luminescent reporters, and human disease models such as the third-generation Alzheimer’s disease model with genetic mutations of Alzheimer’s disease patients (Sasaguri et al. 2018; Sato et al. 2021) as well as a novel Down syndrome mouse model using a mouse artificial chromosome-based chromosome engineering technique (Kazuki et al. 2020). Information on the available mouse strains is disseminated through the NBRP-Mice website (https://mus.brc.riken.jp/) and the IMSR (https://www.findmice.org/), an all-encompassing database of the major international mouse repositories. NBRP-Mice receives requests from research communities worldwide (Fig. 2) and distributes live mice, frozen embryos/sperm, recovered litters from frozen embryos/sperm, and organ/tissue/genomic DNA. To date, NBRP-Mice has distributed mouse resources to researchers at 712 domestic and 1003 overseas academic and industry organizations in 44 countries. Outstanding research results from studies using NBRP-Mice have been published in 1300 papers so far (Fig. 3) and registered in our database.

Fig. 1
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Breakdown of collected mouse strains in NBRP-Mice (FY2017-FY2023)

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Table 1 Representative mouse resources for mammalian genomic research
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Fig. 2
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Breakdown of distributed mouse strains from NBRP-Mice (FY2017-FY2023)

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Fig. 3
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Number of publications using NBRP-Mice mouse resources

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In addition to genetically modified strains, NBRP-Mice also preserves wild-derived inbred strains such as the Japanese subspecies MSM/MsRbrc (MSM, RBRC00209) and JF1/MsRbrc (JF1, RBRC00639). The enormous number of genomic polymorphisms present between these subspecies and classical inbred strains is useful for understanding the genomic function and diverse biological phenotypes in mice and other mammals including humans as well. MoG+ (https://molossinus.brc.riken.jp/mogplus/) (Takada et al. 2022) is a mouse genome database designed to support research using Mus musculus subspecies, with a focus on comparisons between mouse subspecies and classical inbred strains. MoG+ provides access to more than 40 million polymorphisms found by comparative genomic analysis of 10 Asian wild-derived strains, including Mus musculus molossinus-derived MSM and JF1; Mus musculus musculus-derived KJR/Ms (RBRC00655), SWN/Ms (RBRC00654), CHD/Ms (RBRC00738), NJL/Ms (RBRC00207), and BLG2/Ms (RBRC00653); Mus musculus domesticus-derived BFM/2Ms (RBRC00659) and PGN2/Ms (RBRC00667); and Mus musculus castaneus-derived HMI/Ms (RBRC00657), all of which are available from NBRP-Mice, while linking to mouse resource catalog information, human genome variations, and so on. In addition, public genome polymorphism information on 36 classical inbred strains is stored. MoG+ has been utilized for disease and phenotypic analysis (Takeishi et al. 2022; Yasuda et al. 2020). Reproductive engineering techniques are being developed to support research involving subspecies mouse strains (Hasegawa et al. 2021; Hirose et al. 2017; Mochida et al. 2014). An example of the use of subspecies strains is gene expression analysis based on single nucleotide polymorphisms (SNPs) in F1 hybrid mice (Saito et al. 2024; Yagi et al. 2017, 2020). Genomic DNA derived from these multiple subspecies strains has also been used (Bamunusinghe et al. 2013, 2016, 2018).

Rats

The Core Center of NBRP-Rats is the Institute of Laboratory Animals, Graduate School of Medicine, Kyoto University. Scientists conducting research involving rats have conventionally accumulated physiological and pharmacological data. Compared with mice, rats have typically been used for experiments involving drug administration and surgery because of their larger body size and for behavioral studies because of their higher intelligence. NBRP-Rats collects rat strains that have been maintained by individual scientists or laboratories in Japan and overseas, making over 800 strains available, including inbred and genetically modified strains, and has provided about 1500 strains so far (Table 2). NBRP-Rats has common inbred strains, spontaneous mutants, congenic strains, recombinant inbred strains, transgenic and newly genetically modified strains, and so on. Recently, genome-edited rats have also been collected. Available strains can be accessed via the NBRP-Rats website (https://www.anim.med.kyoto-u.ac.jp/nbr/Default.aspx). NBRP-Rats provides reference information for strain selection, including the results of approximately 200 strains on 109 phenotypic measurements for physiological and behavioral parameters such as body weight at various ages, blood pressure, spontaneous locomotor activity, and the passive avoidance test (https://www.anim.med.kyoto-u.ac.jp/nbr/phenome.aspx); the phylogenetic tree of 132 rat strains based on genomic profile data (https://www.anim.med.kyoto-u.ac.jp/nbr/phylo.aspx); and a pedigree-like charting tool showing 357 simple sequence length polymorphism (SSLP) marker differences for 179 genotyped rat strains (https://www.anim.med.kyoto-u.ac.jp/nbr/pedigree/sb.aspx). NBRP-Rats has also worked to develop reproductive technology and has established optimal freezing and thawing methods for sperm, stable in vitro fertilization (IVF) technology (Honda et al. 2019; Mochida et al. 2024; Morita et al. 2023) and is making progress in the cryopreservation of rat strains.

Table 2 Representative rat resources for mammalian genomic research
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At the Institute of Medical Science, The University of Tokyo, which is an NBRP-Rats Sub-Core Center, the development of novel genome-edited rat models is underway. Three severely immunodeficient (SCID) rat strains generated using the CRISPR/Cas9 system [F344-Il2rgem1Iexas (NBRP Rat No: 0883), F344-Rag2em1Iexas (NBRP Rat No: 0894), and F344-Il2rg/Rag2em1Iexas (NBRP Rat No: 0895)] (Mashimo et al. 2010) have already been made available to researchers (https://www.ims.u-tokyo.ac.jp/animal-genetics/scid/index_en.html). SCID rats can be transplanted with human induced pluripotent stem cells (iPS cells), cancer cells, liver cells, and so on. Therefore, SCID rats are useful for analyzing human physiological functions in vivo (Eguchi et al. 2022; Lahr et al. 2021; Miyasaka et al. 2022). In fact, the demand from translational research and regenerative medicine is increasing every year. In addition, NBRP-Rats has been collecting and developing new Cre driver rats, and 22 Cre driver strains are available for conditional studies. In the near future, a database of Cre driver rats will be made available on the website, and the results of comprehensive expression analysis, local expression analysis using adeno-associated virus (AAV), behavioral analysis, and magnetic resonance imaging (MRI) analysis will be published as phenotype information.

The other animal resources

In addition to laboratory mice and rats, the NBRP provides Aged mice and Japanese macaques as mammalian resources for researchers in Japan. NBRP-Aged mice provides three standard mouse strains [C57BL/6J, C57BL/6N (B6N), BALB/cA] that are bred for about 2 years in a uniform environment under strict microbiological control. Aged mice are expected to be used for various aging research, such as elucidating the mechanisms of the aging process, aging control, and aging-related diseases. The Japanese macaque is a species of macaque monkey. Due to their close relationship with humans, Japanese macaques are used mainly in the field of neuroscience but also in the fields of infectious diseases, immunology, and regenerative medicine. Compared with other Southeast Asian macaque species such as rhesus and cynomolgus macaques, Japanese macaques have a curious and calm temperament as well as highly developed cognitive and learning abilities, making them suitable for research on higher brain functions and fine motor functions that require complex task acquisition (Kubota et al. 2024; Kumano and Uka 2024; Sasaki et al. 2024). In fact, Japanese macaques have contributed to the elucidation of the pathogenesis and pathology of neurological disorders such as dementia and Parkinson's disease as well as to the development of treatments to restore neurological functions (Chiken et al. 2021; Darbin et al. 2022; Oyama et al. 2023).

The NBRP supports life science research by providing a total of 12 animal bioresources for which whole-genome sequencing has been performed, which is necessary for analyzing orthologs of human genes (Table 3). For example, chickens and quails have been used in a variety of fields, particularly in embryology. In vitro culture of primordial germ cells (PGCs) is now possible in 20 chicken strains, and gene transfer and genome editing of chickens using such cells are under development. To meet the demand for fluorescent live imaging of developmental processes, NBRP-Chickens & Quails provides a transgenic chicken strain (pLSi/ΔAeGFP-TG) that expresses enhanced green fluorescent protein (eGFP) almost systemically under the control of the chicken β-actin promoter (Motono et al. 2010; Tsujino et al. 2019) and a PRDM14-eGFP knock-in chicken strain that express eGFP under the control of the chicken endogenous PRDM14 promoter (Hagihara et al. 2020). As a tool for generating new models, Cas9-T2A-mCherry transgenic chickens that expresses Cas9 under the control of the homeostatic human EF1α promoter are also available. NBRP-Chickens & Quails releases the results of quail genome analysis as the Quail Genome Browser (http://viewer.shigen.info/uzura/index.php). A PGK:H2B-chFP-TG quail strain that expresses mCherry throughout the body (Huss et al. 2015) is used for live imaging of developmental processes, with the advantage of easy microsurgery in embryos (Haneda et al. 2024; Yoshihi et al. 2020).

Table 3 Animal resources available from the NBRP
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Zebrafish are transparent throughout embryogenesis, are easy to breed, have a short life cycle, and are amenable to mutation and genetic modification. NBRP-Zebrafish has about 400 mutant lines and about 1800 transgenic lines. The neuronal composition and neural mechanisms of the zebrafish brain are highly conserved with those of humans, making zebrafish particularly useful in the field of neuroscience. Tg(CM-isl1:GFP), which expresses green fluorescent protein (GFP) in hindbrain motor neurons (Higashijima et al. 2020), is useful for imaging neural circuit networks (Derrick et al. 2024; Zhao et al. 2024). Tg(vglut2a:loxP-DsRed-loxP-GFP), which expresses DsRed in glutamatergic neurons prior to Cre recombinase exposure and GFP in the Cre-recombined cells (Satou et al. 2012), has been used to elucidate the mechanisms of neural circuit construction processes (Itoh et al. 2024; Schmidt et al. 2024) and the relationship between behavior/movement and neuronal activity (Berg et al. 2023; Carbo-Tano et al. 2023).

Drosophila is used to study life phenomena and in disease research because of its many similarities to humans, including gene homology and basic biological mechanisms. The NBRP-Drosophila conserves many useful mutants for life science research, including about 14,000 RNAi strains and about 30 FlyCas9 strains. CAS-001 (Kondo and Ueda 2013), a transgenic line expressing the Cas9 protein, can be crossed with various guide RNA strains to generate gene knock-out mutant flies with high efficiency. The generation of mutant strains with CAS-001 is versatile and has been reported in the development of novel models for metabolic disease research (Martelli et al. 2024) and biochemical research (Banreti et al. 2022). GAL4 enhancer trap insertion strains (Hayashi et al. 2002) are useful for tissue-specific expression and knock-down using the GAL4/UAS system, and approximately 4200 such lines have been conserved. A traffic jam-GAL4 driver strain (DGRC#104055), which is expressed in all stages of ovarian follicle cells at every developmental stage, has been used by many scientists in various fields as well as for the elucidation of reproductive mechanisms (Mallart et al. 2024; Taniguchi and Igaki 2023).

Caenorhabditis elegans is useful for understanding gene function because C.elegans has only about 1000 somatic cells, the cell lineage of which has been extensively described, and detailed descriptions of its morphology have been made through serial electron microscopy images. NBRP-C. elegans has about half the number of deletion mutants as there are genes in wild-type C. elegans. The drp-1 deletion mutant (tm1108), an ortholog of the human DMNL1 gene that functions in mitochondrial division, has been used to study mitochondria-related diseases (Chen et al. 2024) and aging (Sharifi et al. 2024). The brc-1 deletion mutant (tm1145), an ortholog of the human BRCA1 gene that is involved in DNA repair and has been reported to be associated with several diseases including cancer, is used to elucidate DNA repair mechanisms (Bujarrabal-Dueso et al. 2023; Wang et al. 2023).

DNA-related materials

The Gene Engineering Division, RIKEN BRC provides genetic materials such as plasmids, expression and reporter vectors, and comprehensive clone sets of cDNAs and genomic DNAs. To date, NBRP-DNA-related materials have conserved about 3.8 million resources including about 3400 research tools for imaging and genome editing, about 600,000 human cDNA/genomic DNA clones, about 350,000 mouse cDNA/genomic DNA clones, and 1.3 million animal cDNA/genomic DNA clones (Table 4). Mammalian expression vectors for protein production and gene expression, mouse and rat BAC clones, and fluorescent and luminescent protein expression vectors for imaging are used to generate genetically modified mice, rats, and mammalian cells. BAC clones can be searched with the BAC browser, using gene symbols as keywords, and the physical location of BAC clones on the genome can be confirmed. The BAC browsers for B6N and MSM mouse strains (http://analysis2.nig.ac.jp/mouseBrowser/cgi-bin/index.cgi?org=mm), for F344/Stm and LE/Stm rat strains (http://analysis2.nig.ac.jp/ratBrowser/cgi-bin/index.cgi?org=rn), and for Japanese macaque (http://analysis2.nig.ac.jp/jmonkeyBrowser/cgi-bin/index.cgi?org=jm) are published on the website. The B6N BAC library consists of 128,000 clones representing 90.2% of the actual coverage of the haploid genome. The MSM BAC library consists of 200,000 BAC clones.

Table 4 Representative DNA materials for mammalian genomic research
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NBRP-DNA-related materials collects useful tools that are expected to be requested by researchers in the future using artificial intelligence technology. Regarding genome-editing tools, Cas9-poly(A) expressing improved plasmid [T7-NLS hCas9-pA (RDB13130)] (Yoshimi et al. 2016) and the expression vector of sgRNA with hSpCas9-Cdt1(mouse) fusion protein [px330-mC (RDB14406)] (Mizuno-Iijima et al. 2021) are available. In addition to conventionally used fluorescent and luminescent proteins, NBRP-DNA-related materials also provides the highly photostable and bright GFP StayGold [e.g., (n1)StayGold/pRSET (RDB19605) (Hirano et al. 2022) and pRSETB/mStayGold (RDB20214) (Ando et al. 2023)], and the novel yellow fluorescent protein Achilles [Achilles/pRSETB (RDB15982)] (Yoshioka-Kobayashi et al. 2020) to meet the needs of researchers. The highly luminescent luciferases Akaluc [pcDNA3 Venus-Akaluc (RDB15781)] (Iwano et al. 2018) and oFluc [pPmat Luc1 (RDB14359)] (Ogoh et al. 2020) are also provided. Reporter mice expressing Akaluc or oFluc are available from NBRP-Mice [C57BL/6J-Gt(ROSA)26Sorem13(CAG-luc)Rbrc/#77 (RBRC10451), C57BL/6J-Gt(ROSA)26Sorem14(CAG-Venus/Akaluc)Rbrc/#87 (RBRC10858), C57BL/6J-Gt(ROSA)26Sorem13.1(CAG-luc)Rbrc/#77 (RBRC10919), and C57BL/6J-Gt(ROSA)26Sorem17.1(CAG-Venus/Akaluc)Rbrc/#11 (RBRC10921)] (Nakashiba et al. 2023).

Human and animal cells

The Cell Engineering Division, RIKEN BRC has collected many cultured cell lines, including about 4600 human cell lines and about 3800 animal cell lines. Mouse embryonic stem (ES) cell lines with germline-transmission [e.g., B6J-S1UTR (AES0140), B6NJ-22UTR (AES0141) (Tanimoto et al. 2008), and EGR-G101 (AES0182) (Fujihara et al. 2013)] are used to generate genetically engineered mice, using both conventional gene targeting and genome-editing technologies (Hasan et al. 2021; Noda et al. 2017, 2019; Serizawa et al. 2019). As mentioned above, because SCID rat strains are transplantable with human cells, human iPS cells and cancer cells have been transplanted and used for in vivo functional analysis. Some users have reported research results in combination with human iPS cells derived from healthy volunteers provided by NBRP-Human and animal cells (Gima et al. 2024; Hayashi et al. 2024; Tada et al. 2022). NBRP-Human and animal cells also provides human iPS cell lines derived from patients with various diseases (Table 5). These disease-specific iPS cell lines are expected to be further used for research with a view toward clinical application.

Table 5 Disease-specific iPS cells available from the NBRP
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NBRP-Human and animal cells performs genetic analysis of some disease-specific iPS cells to promote their use. For example, for iPS cells derived from amyotrophic lateral sclerosis, commonly referred to as ALS, the results of target sequence analysis for the casual genes (SOD1/ TARDBP/ ALS10/ TDP-43 genes) have been published on the RIKEN BRC website (https://cell.brc.riken.jp/en/ga-als). As for iPS cells derived from spinocerebellar degeneration, the results of the number of repeated sequences in related 8-gene regions have been published (https://cell.brc.riken.jp/en/ga-scd). In addition to the cell material itself, human iPS cell lines (disease-specific iPS cells and healthy human iPS cells) provide clinical information such as sex, age and the names of diseases, and researchers can use these data upon appropriate application and review.

Microbes

The NBRP also manages general microbes (bacteria, archaea, yeast, and filamentous fungi), prokaryotes (Escherichia coli and Bacillus subtilis), pathogenic eukaryotic microbes, pathogenic bacteria, and human pathogenic viruses). The most popular paper among NBRP-Mice users’ results sorted by Citation Index is one that identified and isolated 11 gut bacterial strains that strongly induce IFNγ-producing CD8T cells and showed that administration of these strains inhibited infection and tumor growth in mouse strains (Tanoue et al. 2019). The influence of the gut microbiota and skin microbiota on phenotype is a topic of great interest, and more results are expected in the future.

Research Resource Circulation

All the article information discussed in this paper, which is based on studies using NBRP resources, is registered and accessible in the Research Resource Circulation (RRC) database (https://rrc.nbrp.jp/) (Fig. 4). RRC is an integrated database that connects published research outcomes to the specific bioresources used in those studies. Its primary objective is to aggregate and organize information on published papers and patents that have utilized these resources and to make this information publicly available along with statistical data, thereby enhancing the information content of each resource and promoting their utilization.

Fig. 4
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Research Resource Circulation (RRC) Database: a system for tracking and analyzing the utilization of NBRP bioresources and research outcomes

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A key feature of the RRC is assigning a unique RRC ID to each paper corresponding PubMed information, strain names, citation metrics, and other relevant data. Development of the RRC began in 2007, and it presently contains entries for approximately 55,000 papers and 1300 patents. Users can easily register papers using PubMed IDs or DOIs. Moreover, the RRC is linked with NCBI’s LinkOut service, enabling resource links to be added to corresponding papers in PubMed.

Conclusion

The NBRP provides useful biological resources, technologies, and information for mammalian genome research both in Japan and overseas, and many users’ research results have been reported. Not only the use of individual bioresources but also the combination of bioresources has been reported by many users. We encourage global scientists to conduct a comprehensive search with biological resources of high quality available from NBRP. In addition, we are constantly updating the information on each bioresource to meet the needs of increasingly sophisticated and complex research while reviewing the latest research trends and increasing the number of stored resources. We hope you will make effective use of the NBRP to advance mammalian genome research.