Whole Genome Sequencing of a Rat Model of Congenital Abnormalities of Kidney and Urinary Tract
Authors: Showmaker Kurt C , Cobb Meredith , Johnson Ashley C , Garrett Michael R 
Published: June 2021

The HSRA rat is a model of congenital abnormalities of the kidney and urogenital tract (CAKUT), with offspring exhibiting renal agenesis and other urogenital abnormalities. Our laboratory has used this model to investigate the role of nephron number in susceptibility to develop chronic kidney disease as offspring are born with a single kidney (HSRA‐S; 50%–75%) or with two‐kidneys (HSRA‐C, 25–50%). The model provides a unique advantage by allowing to directly compare congenital one‐kidney animals (~20,400 nephrons, less than comparable kidney), nephrectomized two‐kidney animals (HSRA‐UNX, ~25,100 nephrons) and two‐kidney littermates (~50,000 nephrons) in the same model, a comparison not possible in models that utilize nephrectomy. HSRA‐S rats are highly susceptible to the hypertension induced kidney injury (DOCA/1% NaCl) compared to HSRA‐UNX, suggesting that even slight nephron differences can be an important driver of elevated blood pressure, hastening kidney injury and accelerating decline in kidney function. The HSRA rat was selected and inbred (>20 generation) from a single pair of outbred heterogeneous stock (HS) rats that exhibited a high incidence of CAKUT (~50% versus 1% in HS population). The HS model was originally developed from 8 inbred strains (ACI, BN, BUF, F344, M520, MR, WKY, and WN). Thus, the genetic make‐up of the HSRA model is a mosaic of these 8 inbred strains. Interestingly, the ACI progenitor of the HS model exhibits CAKUT in 10–15% of offspring with the genetic cause being attributed to presence of a long‐term repeat (LTR) within exon 1 of c‐Kit gene. Our hypothesis is that the HSRA and ACI share this common genetic cause, but other genes in the HSRA genome contribute to increase penetrance of CAKUT (75% vs 15% in ACI). To facilitate genetic studies and better characterize the model, the whole genome of the HSRA was sequenced to a depth of 50X using the Illumina NextSeq500 platform. Sequence alignment and annotation [BN reference genome (UCSC Rn5)] identified 4,692,623 SNPs and 1,438,131 INDELs. Sequence analysis of fifteen recessive and 25 dominant genes linked to CAKUT in humans identified three genes (Frem2, Hnf1b, and Six5) predicted to have high‐impact variation that could play a role in the observed CAKUT. Future studies will involve performing a linkage analysis using a segregating population [F2(HSRA x ACI)] to map the QTL/location of modifier genes, which in combination with genome sequence and annotation data will include/exclude known genes as well as identify additional candidate genes linked to CAKUT. In summary, the identification of specific gene defects, modifier genes, and signaling pathways that lead to loss of one kidney and nephron deficiency will provide a mechanistic link between the solitary kidney genotype and the development of kidney dysfunction exhibited by the HSRA rat.Support or Funding InformationThe whole genome sequencing performed through the UMMC Molecular and Genomics Facility is supported, in part, by funds from the NIGMS, including P20GM103476, P20GM104357, and P20GM121334.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.