The HSRA rat is a unique polygenic model of congenital abnormalities of the kidney and urogenital tract, with 50–75% of offspring developing a single kidney. The model also exhibits nephron deficiency (~20% less nephrons) in the remaining kidney, glomerular and kidney hypertrophy, and elevated single nephron GFR, which leads to progressive kidney injury and decline in kidney function with age. A number of animal studies have provided an understanding of the physiological mechanism of injury, but it remains unknown the specific genetic factors that cause failure of one kidney to develop, as well as the mechanism of nephron deficiency in the remaining kidney. A recent genome‐wide association study (GWAS) performed by others using the heterogeneous stock rat (progenitor of the HSRA model), identified genomic loci on chromosomes (RNO) 4, 10, and 14 associated with the solitary kidney trait. The confidence interval for the RNO4 locus is ~4.2 Mb containing 14 genes, the RNO10 interval is ~1.5Mb containing 15 genes, and the RNO14 locus is consistent with locus linked to solitary kidney in the ACI rat. The whole genome was sequenced to a depth of 18X coverage using the Illumina NextSeq500 platform. Sequence alignment and annotation [BN reference genome (UCSC Rn5)], identified 1,776,635 SNP, 314,786 INDEL, and 25,346 structural variants. RNA sequencing of embryonic kidney isolated at key stages of nephrogenesis (E14.5, 15.5, and 16.5) between single kidney and two‐kidney control identified dysregulation of genes linked to cellular movement (p‐value= 2.36E‐06 ‐ 1.49E‐02 n=78/451), cell morphology (p‐value= 1.86E‐05 ‐ 1.49E‐02 n=82/451) and cell‐to‐cell signaling and interaction (p‐value= 8.38E‐05 ‐1.49E‐02 n=68/451). The top canonical pathway was associated with Wnt/b‐catenin (p‐value= 4.89E‐05) which includes Wnt2/Nlk candidates genes and is highly relevant to kidney development. Based on the GWAS, whole genome sequencing, and RNA sequencing, the causative genomic loci were refined to specific genes [c‐Kit (RNO14), Fam58b and Nlk (RNO10), and Met and Wnt2 (RNO4)] that could play a role in the solitary kidney trait and nephron deficiency in the HSRA model. In summary, the identification of the specific gene defect, 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 InformationSupported by HL094446 (Garrett), UMMC, and Robert Hearin Foundation. Genomics Core [P20 GM103476 [MS‐INBRE‐(Elarsi)], P30GM103328 (CPN‐COBRE) and P20GM104357 (Obesity‐COBRE)