Identification of Novel lncRNAs Differentially Expressed in Placentas of Chinese Ningqiang Pony and Yili Horse Breeds

SIMPLE SUMMARY: The Ningqiang pony (NQ) is a famous breed with an average adult height at the withers (the ridge between horse’s shoulder blades) of less than 106 cm, but the genetic mechanism responsible for its small stature remains unclear. Research on Chinese pony breeds is a topic of theoretical and practical importance. Long non-coding RNA (lncRNA) has been shown to regulate many biological functions, including growth. Our study, for the first time, reports the lncRNAs transcribed in horse placentas. By comparing 3011 transcripts coding 1464 lncRNAs from NQ ponies and Yili horses (YL) with distinct body sizes, six (TBX3 (T-box3), CACNA1F (L-type voltage-dependent calcium channel a1F), EDN3 (endothelin-3), KAT5 (histone acetyltransferase KAT5), ZNF281 (zinc finger protein 281), TMED2 (transmembrane emp24 domain), and TGFB1 (transforming growth factor beta 1)) out of the 233 genes targeted by differentially expressed lncRNAs were identified as being involved in limb development, skeletal myoblast differentiation, and embryo development. These results provide new insights into the genetic architecture of horse body size. ABSTRACT: As a nutrient sensor, the placenta plays a key role in regulating fetus growth and development. Long non-coding RNAs (lncRNAs) have been shown to regulate growth-related traits. However, the biological function of lncRNAs in horse placentas remains unclear. To compare the expression patterns of lncRNAs in the placentas of the Chinese Ningqiang (NQ) and Yili (YL) breeds, we performed a transcriptome analysis using RNA sequencing (RNA-seq) technology. NQ is a pony breed with an average adult height at the withers of less than 106 cm, whereas that of YL is around 148 cm. Based on 813 million high-quality reads and stringent quality control procedures, 3011 transcripts coding for 1464 placental lncRNAs were identified and mapped to the horse reference genome. We found 107 differentially expressed lncRNAs (DELs) between NQ and YL, including 68 up-regulated and 39 down-regulated DELs in YL. Six (TBX3, CACNA1F, EDN3, KAT5, ZNF281, TMED2, and TGFB1) out of the 233 genes targeted by DELs were identified as being involved in limb development, skeletal myoblast differentiation, and embryo development. Two DELs were predicted to target the TBX3 gene, which was found to be under strong selection and associated with small body size in the Chinese Debao pony breed. This finding suggests the potential functional significance of placental lncRNAs in regulating horse body size.