Integrated analysis of lncRNAs and mRNAs by RNA-Seq in secondary hair follicle development and cycling (anagen, catagen and telogen) of Jiangnan cashmere goat (Capra hircus)

Whole-genome resequencing reveals diversity and selective signals in the Wuxue goat

Animal genetic resources are crucial for ensuring global food security. However, in recent years, a noticeable decline in the genetic diversity of livestock has occurred worldwide. This decline is pronounced in developing countries, where the management of these resources is insufficient. In the current study, we performed whole genome sequencing for 20 Wuxue (WX) and five Guizhou White (GW) goats. Additionally, we utilized the published genomes of 131 samples representing five different goat breeds from various regions in China. We investigated and compared the genetic diversity and selection signatures of WX goats. Whole genome sequencing analysis of the WX and GW populations yielded 120 425 063 SNPs, which resided primarily in intergenic and intron regions. Population genetic structure revealed that WX exhibited genetic resemblance to GW, Chengdu Brown, and Jintang Black and significant differentiation from the other goat breeds. In addition, three methods (nucleotide diversity, linkage disequilibrium decay, and runs of homozygosity) showed moderate genetic diversity in WX goats. We used nucleotide diversity and composite likelihood ratio methods to identify within-breed signatures of positive selection in WX goats. A total of 369 genes were identified using both detection methods, including genes related to reproduction (GRID2, ZNF276, TCF25, and SPIRE2), growth (HMGA2 and GJA3), and immunity (IRF3 and SRSF3). Overall, this study explored the adaptability of WX goats, shedding light on their genetic richness and potential to thrive in challenges posed by climatic changes and diseases. Further investigations are warranted to harness these insights to enhance more efficient and sustainable goat breeding initiatives.

Screening of hair follicle telogen-associated circRNAs in sheep and construction of their ceRNA network

Sheep breeds with hair-shedding traits have many advantages over non-shedding sheep breeds, not only because of reduced shearing labor and feeding management costs but also because it reduces in vitro parasites and improves adaptability to summer heat stress. The wool of Dorper sheep naturally sheds in spring due to the periodic growth of hair follicles. CircRNAs primarily regulate the morphogenesis of hair follicles through the ceRNA mechanism. In this study, five 2-year-old Dorper ewes with extreme hair-shedding phenotype (S) and three Dorper ewes with non-shedding (N) phenotype were selected for subsequent analyses. For RNA extraction, skin tissues were collected on 27th September 2019 (S1, N1), 3rd January 2020 (S2, N2), and 17th March 2020 (S3, N3), which were then subjected to RNA-seq. RNA-seq technology revealed 20,185 novel circRNAs in the hair follicles of Dorper sheep. Among them, 1450 circRNAs were differentially expressed (DE). Clustering heatmap and expression pattern analyses were performed on DE circRNAs, which indicated 78 circRNAs with T pattern (Telogen, highly expressed in telogen), and the source genes for candidate circRNAs were further screened by functional enrichment analysis, which identified 13 crucial genes enriched in pathways associated with hair follicle development. Additionally, a ceRNA regulatory network comprising 4 circRNAs, 11 miRNAs, and 13 target genes was constructed. Overall, this study screened circRNAs that may be associated with the telogen phase of hair follicles in sheep, providing a relevant theoretical basis for wool shedding in sheep and for breeding Dorper sheep with automatic wool shedding.

In ovo injection of AZD6244 suppresses feather follicle development by the inhibition of ERK and Wnt/β-catenin pathways in goose embryos (Anser cygnoides)

1. Feathers are an important product from poultry, and the state of feather growth and development plays an important role in their economic value.2. In total, 120 eggs were selected for immunoblotting and immunolocalisation experiments of ERK and β-catenin proteins in different developmental stages of goose embryos. The ERK protein was highly expressed in the early stage of goose embryo development, while β-catenin protein was highly expressed in the middle stage of embryo development.3. The 120 eggs were divided into four treatment groups, including an uninjected group (BLANK), a group injected with 100 µl of cosolvent (CK), a group injected with 100 µl of AZD6244 containing cosolvent in a dose of 5 mg/kg AZD6244 containing cosolvent (AZD5) and a group injected with 100 µl of AZD6244 containing cosolvent in a dose of 15 mg/kg AZD6244 containing cosolvent (AZD15). The eggs were injected on the ninth day of embryonic development (E9). Samples were collected at E21.5 to observe feather width, feather follicle diameter, ERK and Wnt/β-catenin pathway protein expression.4. The AZD5 and AZD15 doses were within the embryonic safety range compared to the BLANK and CK groups and had no significant effect on the survival rate and weight at the inflection point, but significantly reduced the feather width and feather follicle diameter (p < 0.05). The AZD6244 treatment inhibited ERK protein phosphorylation levels and blocked the Wnt/β-catenin pathway, which in turn significantly down-regulated the expression levels of FZD4, β-catenin, TCF4 and LEF1 (p < 0.05), with an inhibitory effect in the AZD15 group being more significant. The immunohistochemical results of β-catenin and p-ERK were consistent with Western blot results.5. The small molecule inhibitor AZD6244 regulated the growth and development of feather follicles in goose embryos by the ERK and Wnt/β-catenin pathways.

Effect of Fasted Live-Weight Gain during the Cashmere Non-Growing Period on Cashmere Production Performance and Secondary Hair Follicle Activity of Cashmere Goats

The objective of this study was to investigate the effects of fasted live-weight gain during the cashmere non-growing period on cashmere production performance and secondary hair follicle activity, to provide a theoretical basis for appropriate supplementary feeding of cashmere goats. Fifty Inner Mongolian cashmere goats aged 2-4 years old were randomly selected and weighed in May and September 2019, respectively. Based on fasted live-weight gain between the two weights, the experimental ewe goats were divided into two groups: 0-5.0 kg group (n = 30) and 5.0-10.0 kg group (n = 20). Skin samples and cashmere samples were collected. Results of a Pearson correlation analysis showed that fasted live-weight gain during the cashmere non-growing period had a moderate and strong positive correlation with cashmere yield (p = 0.021) and cashmere staple length (p = 0.002), respectively, but did not correlate with cashmere diameter (p = 0.254). Compared with cashmere goats with a fasted live-weight gain of 0-5.0 kg, cashmere goats with a fasted live-weight gain of 5.0-10.0 kg had a 17.10% increase in cashmere yield (p = 0.037) and an 8.09% increase in cashmere staple length (p = 0.045), but had no significant difference in cashmere diameter (p = 0.324). Results of a Pearson correlation analysis showed that there was a strong positive correlation between fasted live-weight gain and the population of active secondary hair follicles in the skin of cashmere goats (p < 0.01). Compared with cashmere goats with a fasted live-weight gain of 0-5.0 kg, cashmere goats with a fasted live-weight gain of 5.0-10.0 kg had an increase in the population of active secondary hair follicles (p < 0.05). In conclusion, the fasted live-weight gain during the cashmere non-growing period had a significant effect on secondary hair follicle activity and cashmere production performance in cashmere goats. Since fasted live-weight gain reflects nutritional level to a certain extent, this study suggests that nutritional manipulations such as supplementary feeding during cashmere non-growing periods can increase cashmere production performance. However, specific nutritional manipulations during the cashmere non-growing period need further research to increase cashmere production performance.

LncRNAs regulate the cyclic growth and development of hair follicles in Dorper sheep

Introduction

Hair follicles in Dorper sheep are characterized by seasonal cyclic growth and development, consequently resulting in hair shedding during spring. The cyclic growth and development of hair follicles are regulated by several influencing factors such as photoperiods, hormones, age of the animal, genes, long non-coding RNAs (lncRNAs), and signaling pathways.

Methods

In the present study, skin samples of five shedding sheep (S), used as experimental animals, and three non-shedding sheep (N), used as controls, were collected at three time points (September 27, 2019; January 3, 2020; and March 17, 2020) for RNA sequencing (RNA-seq) technology. Nine different groups (S1-vs-S2, S1-vs-S3, S2-vs-S3, N1- vs-N2, N1-vs-N3, N2-vs-N3, S1-vs-N1, S2-vs-N2, and S3-vs-N3) were compared using FDR < 0.05 and log 21 FC >as thresholds to assess the differences in the expression of lncRNAs.

Results and discussion

In total, 395 differentially expressed (DE) lncRNAs were screened. Cluster heatmap analysis identified two types of expression patterns, namely, high expression during the anagen phase (A pattern) and high expression during the telogen phase (T pattern). Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that the target genes were largely enriched in the Estrogen signaling pathway, PI3K-Akt signaling pathway, Fc gamma R-mediated phagocytosis, and cell adhesion molecules (CAMs), which are associated with hair follicle cyclic growth and development-related pathways. In addition, 17 pairs of lncRNAs-target genes related to hair follicle cyclic growth and development were screened, and a regulatory network was constructed. Altogether, candidate lncRNAs and their regulated target genes were screened that contributed to sheep hair follicle cyclic growth and development. We believe these findings will provide useful insights into the underlying regulatory mechanisms.

Convergent Genomic Signatures of Cashmere Traits: Evidence for Natural and Artificial Selection

Convergent evolution provides powerful opportunities to investigate the genetic basis of complex traits. The Tibetan antelope (Pantholops hodgsonii) and Siberian ibex (Capra sibirica) belong to different subfamilies in Bovidae, but both have evolved similar superfine cashmere characteristics to meet the cold temperature in plateau environments. The cashmere traits of cashmere goats underwent strong artificial selection, and some traces of domestication also remained in the genome. Hence, we investigated the convergent genomic signatures of cashmere traits between natural and artificial selection. We compared the patterns of convergent molecular evolution between Tibetan antelope and Siberian ibex by testing positively selected genes, rapidly evolving genes and convergent amino acid substitutions. In addition, we analyzed the selected genomic features of cashmere goats under artificial selection using whole-genome resequencing data, and skin transcriptome data of cashmere goats were also used to focus on the genes involved in regulating cashmere traits. We found that molecular convergent events were very rare, but natural and artificial selection genes were convergent enriched in similar functional pathways (e.g., ECM-receptor interaction, focal adhesion, PI3K-Akt signaling pathway) in a variety of gene sets. Type IV collagen family genes (COL4A2, COL4A4, COL4A5, COL6A5, COL6A6) and integrin family genes (ITGA2, ITGA4, ITGA9, ITGB8) may be important candidate genes for cashmere formation and development. Our results provide a comprehensive approach and perspective for exploring cashmere traits and offer a valuable reference for subsequent in-depth research on the molecular mechanisms regulating cashmere development and fineness.

Regulation of secondary hair follicle cycle in cashmere goats by miR-877-3p targeting IGFBP5 gene

Cashmere, a highly valuable animal product derived from cashmere goats, holds significant economic importance. MiRNAs serve as crucial regulators in the developmental processes of mammalian hair follicles. Understanding the regulation of miRNAs during the hair follicle cycle is essential for enhancing cashmere quality. In this investigation, we employed high-throughput sequencing technology to analyze the expression profiles of miRNAs in the secondary hair follicles of Jiangnan cashmere goats at different stages. Through bioinformatics analysis, we identified differentially expressed miRNAs (DE miRNAs). The regulatory relationships between miRNAs and their target genes were verified using multiple techniques, including RT-qPCR, western blot, Dual-Luciferase Reporter, and CKK-8 assays. Our findings revealed the presence of 193 DE miRNAs during various stages of the hair follicle cycle in Jiangnan cashmere goats. Based on the previously obtained mRNA data, the target genes of DE miRNA were predicted, and 1,472 negative regulatory relationships between DE miRNAs and target genes were obtained. Notably, the expression of chi-miR-877-3p was down-regulated during the telogen (Tn) phase compared to the anagen (An) and catagen (Cn) phases, while the IGFBP5 gene exhibited up-regulation. Further validation experiments confirmed that overexpression of chi-miR-877-3p in dermal papilla cells suppressed IGFBP5 gene expression and facilitated cell proliferation. The results of this study provide novel insights for analyzing the hair follicle cycle.