| Summary: | Two <i>FGF4</i> retrogenes (<i>FGF4L1</i> on chromosome 18 and <i>FGF4L2</i> on chromosome 12) have been identified to cause dwarfism across many dog breeds. Some breeds are nearly homozygous for both retrogenes (e.g., Dachshunds) and others are homozygous for just one (e.g., Beagles and Scottish Terriers). Since most breeds do not segregate both of these retrogenes, it is challenging to evaluate their individual effects on long bone length and body size. We identified two dog breeds selected for hunting ability, the Alpine Dachsbracke and the Schweizer Niederlaufhund, that segregate both of these retrogenes. Using individual measurements of height at the shoulder, back length, head width, thorax depth and width, and thoracic limb measurements, we evaluated the combined effects of <i>FGF4</i> retrogenes within these breeds. We applied multivariable linear regression analysis to determine the effects of retrogene copy numbers on the measurements. Copy numbers of both retrogenes had significant effects reducing height at the shoulders and antebrachial length, with <i>FGF4L1</i> having a much greater effect than <i>FGF4L2</i>. <i>FGF4L1</i> alone influenced the degree of carpal valgus and <i>FGF4L2</i> alone increased head width. Neither retrogene had an effect on thorax width or depth. Selectively breeding dogs with <i>FGF4L1</i> and without <i>FGF4L2</i> would likely lead to a reduction in the <i>FGF4L2</i>-related risk of intervertebral disc herniation while maintaining the reduction in leg length resulting from <i>FGF4L1.</i>
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