Transcriptome Profile at Different Physiological Stages Reveals Potential Mode for Curly Fleece in Chinese Tan Sheep

<div><p>Tan sheep (<i>Ovis aries</i>), a Chinese indigenous breed, has special curly fleece after birth, especially at one month old. However, this unique phenotype disappears gradually with age and the underlying reasons of trait evolvement are still unknown. In this study, skin transcriptome data was used to study this issue. In total 51,215 transcripts including described transcripts and transfrags were identified. Pathway analysis of the top 100 most highly expressed transcripts, which included <i>TCHH</i> and keratin gene family members, such as <i>KRT25</i>, <i>KRT5</i>, <i>KRT71</i>, <i>KRT14</i> and others, showed pathways known to be relevant to hair/fleece development and function. Six hundred differentially expressed (DE) transcripts were detected at two different physiological ages (one-month-old with curly fleece and 48-month-old without curly fleece) and were categorized into three major functional groups: cellular component, molecular function, and biological process. The top six functional categories included cell, cell part, cellular process, binding, intracellular, metabolic process. The detected differentially expressed genes were particularly involved in signal, signal peptide, disulfide bond, glycoprotein and secreted terms, respectively. Further splicing isoform analysis showed that the metallothionein 3 isoform was up-regulated in Tan lamb skin, indicating that it may be related to the conformation of curly fleece in Chinese Tan lamb. The hair-related important differentially expressed genes (<i>SPINK4</i>, <i>FGF21</i>, <i>ESRα</i>, <i>EphA3</i>, <i>NTNG1</i> and <i>GPR110</i>) were confirmed by qPCR analysis. We deduced that the differences existed in expressed transcripts, splice isoforms and GO categories between the two different physiological stages, which might constitute the major reasons for explaining the trait evolvement of curly fleece in Chinese Tan sheep. This study provides some clues for elucidating the molecular mechanism of fleece change with age in Chinese Tan sheep, as well as supplying some potential values for understanding human hair disorder and texture changes.</p></div

Hair-related important DE genes between two groups.

<p>Hair-related important DE genes between two groups.</p

The Chinese Tan sheep and its fleece.

<p>A: The Chinese Tan lamb (L); B: The pelt of Tan lamb at one month old; C: The Chinese adult Tan sheep (A); D: The pelt of Tan adult sheep.</p

The genetic information and variation on chromosome based on the skin transcriptome in Tan sheep.

<p><b>Total No of splice variants: defined as more than one transcript for a ‘genic’ gene. Splice variants denote differences compared with annotated ovine genes.</b></p

Expression of the top 20 most highly expressed genes in sheep skin.

<p>The x-axis shows gene ID; y-axis shows gene expression level (FPKM).</p

Functional categorization of differentially expressed genes based on known genes in the Uniprot database.

<p>The x-axis shows the 2nd level term of Gene Ontology; y-axis shows percent of genes in DE genes.</p

Additional file 7: of Integrated miRNA-mRNA analysis reveals regulatory pathways underlying the curly fleece trait in Chinese tan sheep

Table S6. The signaling pathways analysis with target genes that form miRNA-mRNA pairs with differentially expressed miRNAs between the two stages of Tan sheep. (XLS 30 kb

Additional file 5: of Integrated miRNA-mRNA analysis reveals regulatory pathways underlying the curly fleece trait in Chinese tan sheep

Table S4. Detailed results of GO terms analysis for gene transcripts targeted by miRNAs (Table S4A showed the GO terms of target genes of the miRNAs that are more abundant in lambs than in adults; Table S4B showed the GO terms of target genes of the miRNAs that are less abundant in lambs than in adults). (XLS 922 kb

Additional file 8: of Integrated miRNA-mRNA analysis reveals regulatory pathways underlying the curly fleece trait in Chinese tan sheep

Table S7. Sequences of primer used for amplification of wild type or mutant KRT83 CDS region. (DOCX 48 kb

Additional file 1: of Integrated miRNA-mRNA analysis reveals regulatory pathways underlying the curly fleece trait in Chinese tan sheep

Table S1. Conserved and novel miRNAs detected in lambs and adults. (XLS 82 kb