Abstract
The quantitative trait loci (QTL) for porcine ear size was previously reported to mainly focus on SSC5 and SSC7. Recently, a missense mutation, G32E, in PPARD in the QTL interval on SSC7 was identified as the causative mutation for ear size. However, on account of the large interval of QTL, the responsible gene on SSC5 has not been identified. In this study, an intercross population was constructed from the large-eared Minzhu, an indigenous Chinese pig breed, and the Western commercial Large White pig to examine the genetic basis of ear size diversity. A GWAS was performed to detect SNPs significantly associated with ear size. Thirty-five significant SNPs defined a 10.78-Mb (30.14–40.92 Mb) region on SSC5. Further, combining linkage disequilibrium and haplotype sharing analysis, a reduced region of 3.07-Mb was obtained. Finally, by using a selective sweep analysis, a critical region of about 450-kb interval containing two annotated genes LEMD3 and WIF1 was refined in this work. Functional analysis indicated that both represent biological candidates for porcine ear size, with potential application in breeding programs. The two genes could also be used as novel references for further study of the mechanism underlying human microtia.
Highlights
The large-ear feature of pigs (e.g., Erhualian) have historically been favored by owners in many areas of China, and as a result, most Chinese pig breeds have medium to large sized ears [1]
Diversity in external ear size is apparent in humans, but diseases resulting from abnormal external ears have been the focus of more research than has diversity of ear size
The quantitative trait loci (QTL) for ear size were mapped on Sus Scrofa Chromosome (SSC) 1, 4, 5, 6, 7, 8, 9, 11, 12, 16, and X [4,5], and in which the two most significant QTL were on SSC5 and SSC7, respectively
Summary
The large-ear feature of pigs (e.g., Erhualian) have historically been favored by owners in many areas of China, and as a result, most Chinese pig breeds have medium to large sized ears [1]. Ear size has been regarded as an important characteristic distinguishing pig breeds [2]. Diversity in external ear size is apparent in humans, but diseases resulting from abnormal external ears have been the focus of more research than has diversity of ear size. There are large differences in the mechanisms determining ear-size diversity and ear disease (e.g., microtia), genetic research on porcine ear size can contribute to the understanding of human ear development and abnormalities. A missense mutation, G32E, in PPARD in the QTL interval on SSC7 was identified as the causative mutation for ear size [6]. In 2012, Li et al refined the QTL (11-cM interval) on SSC5 to an 8.7-cM interval and identified HMGA2 as the closest gene with a potential functional effect on the phenotype [7]. The causal mutation on SSC5 has still not been identified and need to study further
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