www.nature.com/scientificreports OPEN Further dissection of QTLs for salt- induced stroke and identifcation of candidate genes in the stroke-prone Received: 2 February 2018 Accepted: 5 June 2018 spontaneously hypertensive rat Published: xx xx xxxx Kaoru Niiya1, Hiroki Ohara1, Masato Isono 3, Abdullah Md. Sheikh2, Hiroyuki Matsuo1, Koichi Fujikawa1, Minoru Isomura4, Norihiro Kato3 & Toru Nabika1 We previously revealed that two major quantitative trait loci (QTLs) for stroke latency of the stroke- prone spontaneously hypertensive rat (SHRSP) under salt-loading were located on chromosome (Chr) 1 and 18. Here, we attempted further dissection of the stroke-QTLs using multiple congenic strains between SHRSP and a stroke-resistant hypertensive rat (SHR). Cox hazard model among subcongenic strains harboring a chromosomal fragment of Chr-1 QTL region showed that the most promising region was a 2.1 Mbp fragment between D1Rat177 and D1Rat97. The QTL region on Chr 18 could not be narrowed down by the analysis, which may be due to multiple QTLs in this region. Nonsynonymous sequence variations were found in four genes (Cblc, Cxcl17, Cic, and Ceacam 19) on the 2.1 Mbp fragment of Chr-1 QTL by whole-genome sequence analysis of SHRSP/Izm and SHR/Izm. Signifcant changes in protein structure were predicted in CBL-C and CXCL17 using I-TASSER. Comprehensive gene expression analysis in the kidney with a cDNA microarray identifed three candidate genes (LOC102548695 (Zinc fnger protein 45-like, Zfp45L), Ethe1, and Cxcl17). In conclusion, we successfully narrowed down the QTL region on Chr 1, and identifed six candidate genes in this region. Cerebral stroke is a major health problem in Japan as well as in the world not only because it is a major cause of death but also because it is a major cause of severe disability in the elderly1. Because the stroke-prone spontane- ously hypertensive rat (SHRSP) is thought to be a good model for cerebral hemorrhage and lacunar infarction, genetic analysis of this model may provide new insights about the genetic risks of these disorders, which may be useful for the prevention of the disease in humans2–5. We performed a quantitative trait locus (QTL) analysis on stroke susceptibility in F2 progenies between SHR and SHRSP and identifed two major QTLs for stroke latency under salt-loading on chromosome (Chr) 1 and 186. Analysis of the double congenic strains for these two QTLs showed that they had an additive efect on stroke latency, which explained a major part of the stroke susceptibility in SHRSP6. Because the QTL regions identifed on Chr 1 and 18 were too large for further analysis (about 36 and 37 Mbp, respectively), we attempted to reduce the QTL regions using multiple subcongenic strains in this study. Furthermore, we identifed six candidate genes in the Chr-1 QTL region through comprehensive analysis of whole-genome sequence and gene expression. Results The double subcongenic strain SHRSPrch1.1_18.0. In the previous study6, we showed that a 18 Mbp fragment on Chr1 and a 29 Mbp fragment on Chr18, covered by SHRSP-based congenic strain SHRSPrch1.1 and SHRSPrch18.0 respectively, harbored major genes responsible for the stroke susceptibility under salt-loading in SHRSP. In the present study, we frst constructed a new double subcongenic strain, SHRSPrch1.1_18.0, by a cross between SHRSPrch1.1 and SHRSPrch18.0 to confrm whether stroke susceptibility of this strain is comparable 1Department of Functional Pathology, Shimane University Faculty of Medicine, Izumo, Japan. 2Department of Laboratory Medicine, Shimane University Faculty of Medicine, Izumo, Japan. 3Department of Gene Diagnostics and Therapeutics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan. 4Shimane University Faculty of Human Sciences, Matsue, Japan. Correspondence and requests for materials should be addressed to H.O. (email: [email protected]) SCIENTIFIC REPORTS | (2018) 8:9403 | DOI:10.1038/s41598-018-27539-2 1 www.nature.com/scientificreports/ Figure 1. Te double subcongenic strain SHRSPrch1.1_18.0. (a) Stroke latency under salt-loading. Te Cox hazard model was used to calculate relative risks (RR) in the table below. To compare with the latency of SHRSPrch1.1 and 1_18, the data obtained in the previous study were used for these two strains (see ref.6). Note that the data newly obtained in this study is shown for SHRSPrch18.0 (see also ref.6). 1.1_18.0: SHRSPrch1.1_18.0. (b) SBP measured by telemetry during salt-loading. No signifcant increase was observed (n = 3). (c) Genomic construction of SHRSPrch1.1_18.0 in comparison with the original double congenic strain SHRSPrch1_18. Note that the congenic region on Chr 1 was much shorter in SHRSPrch1.1_18.0. to that of the original double congenic strain, SHRSPrch1_18 (Fig. 1c, see also ref.6). SHRSPrch1.1_18.0 has the largest chromosomal fragments from the QTL region among the series of subcongenic strains evaluated in this study (see Fig. 1c and Fig. 2). Note that the telomeric side marker on Chr18, D18Rat11 (see ref.6), was replaced with D18Rat82 in the present study because of an additional genotyping for this simple sequence repeat marker (Fig. 1c). As shown in Fig. 1a, the stroke latency in SHRSPrch1.1_18.0 did not signifcantly difer from that in the original double congenic strain SHRSPrch1_18, but did signifcantly difer from that in the single congenic strains, SHRSPrch1.1 and SHRSPrch18.0, as well as that in SHRSP. Furthermore, telemetry analysis indicated that no signifcant systolic blood pressure (SBP) increase was observed under salt-loading in this strain (Fig. 1b), which was similar to that of SHRSPrch1_186. Tese observations strongly suggested that the regions covered by SHRSPrch1.1_18.0 included the gene(s) for stroke latency as well as salt-induced BP increase that the original double congenic strains harbored. Accordingly, we focused on these regions for further dissection using subcon- genic strains. Blood pressure and body weight of subcongenic strains. SBP and body weight (BW) for the sub- congenic strains are shown in Table S1. No signifcant diferences were observed in SBP in Chr-18 subcongenic strains. In contrast, among Chr-1 subcongenic strains, SHRSPrch1.6 and 1.31 had signifcantly higher and lower SBP than that of SHRSP, respectively. Figure 2 shows genomic composition of the subcongenic strains with their SBP (see also Table S1) and relative risk of stroke (see also Fig. 3). All of them were established by a backcross of SHRSPrch1.1 or 18.0 to SHRSP, i.e., each subcongenic strain has a dissected Chr-1 or −18 QTL fragment from SHRSPrch1.1 or 18.0 (see also Methods). Stroke latency of subcongenic strains. Figure 3 summarizes the results of the evaluation of stroke latency in the subcongenic strains. Using the Cox hazard model, we compared stroke latency of the subcongenic strains with that of SHRSP and of SHRSPrch1.1 or 18.0, which had the largest fragment from the QTL region and showed the longest stroke latency among the subcongenic strains examined. As for the QTL on Chr 1, the analysis on the subcongenic strains indicated that the latency in SHRSPrch1.8, 1.31, and 1.10 did not signifcantly difer from that in SHRSPrch1.1. When compared with SHRSP, the two subcongenic strains, SHRSPrch1.6 and 1.9, showed stroke latency that was not diferent from that in SHRSP, indicating that the region harbored by these two subcongenic strains could be excluded from the target region. SBP had a marginally signifcant efect on stroke SCIENTIFIC REPORTS | (2018) 8:9403 | DOI:10.1038/s41598-018-27539-2 2 www.nature.com/scientificreports/ Figure 2. Genomic composition of the subcongenic strains. Congenic regions (homozygous for SHR alleles) of subcongenic strains are shown as closed columns. Vertical bars indicate regions including a recombination. Light grey boxes indicate the haplotype blocks that difered between SHRSP and SHR (see ref.6). A dark grey box indicates the region narrowed down through the current analysis of subcongenic strains (see Results). Note that ‘SHRSPrch’ was omitted from the names of the subcongenic lines. ‘SHRSPrch1.’ and ‘SHRSPrch18.’ mean Chr-1 and −18 subcongenic strains, respectively. Te numbers following period, e.g., 31 in the SHRSPrch1.31, are the identifcation number for each subconogenic strain. Averages of systolic blood pressure (SBP) and relative risk of stroke are shown under the columns representing the subcongenic strains (see Table S1 and Fig. 3 for the details). *P < 0.05 vs. SHRSP by Dunnet’s post-hoc test. #P < 0.05 by the Cox hazard model. latency (P = 0.03). Tese observations implied that the most promising region was the 2.1 Mbp fragment between D1Rat177 and D1Rat97 (see Fig. 2). Te data from SHRSPrch1.3 may need more careful interpretation. Te relative risk to SHRSPrch1.1 was marginally signifcant in this congenic strain even though it harbored the target region above. Tis suggests that SHRSPrch1.3 has an additional genetic locus (or loci) with an adverse impact on the stroke latency. In contrast to the Chr-1 QTL, it was difcult to narrow down the QTL region on Chr 18 by analysis of the subcongenic strains – stroke latency in most of the subcongenic strains difered signifcantly from both SHRSP and SHRSPrch18.0, which may be a result of multiple QTLs in this region (see Discussion). SBP did not show a signifcant efect on the stroke latency among the subcongenic strains for the Chr-18 QTL (P = 0.10). Similar reasons to SHRSPrch1.3 may apply to the data for SHRSPrch18.3, 18.4, and 18.7. Tese strains had marginal levels of signifcance in risk relative to the reference strains. Te genomic fragments harbored by these congenic strains may need careful evaluation.