| China has the world’s largest scale of cashmere goat farming,with the most abundant breed resources.Inner Mongolia cashmere goats are one of China’s important cashmere goat breeds,and their produced cashmere is soft,fine,lustrous,and smooth,known as the "fiber gemstone".During the production and breeding process of Inner Mongolia cashmere goats,it was discovered that the cashmere goat population has significant differences in hair morphology.The research team classified them into long hair type(LHG),short hair type(SHG),and mediate hair type(MHG)based on the length of coarse hair,and conducted years of research and exploration on different hair types of cashmere goats.Early research found that hair length has a certain reference value for the indirect selection of other economic traits,and can improve and enhance the quality of cashmere through hair length selection.Indirect selection based on the correlation between hair length and other cashmere traits will help improve breeding accuracy and accelerate the genetic improvement progress of cashmere goats.Currently,the molecular mechanism of different hair types is not clear.Building on previous research,this study explored the key factors affecting the genetic variation of different hair types of Inner Mongolia cashmere goats by using whole transcriptome sequencing and lipidome techniques,starting from the phenotype differences of different hair types,and investigated their roles in the growth and development of skin hair follicles.This study provides a theoretical basis and scientific evidence for further exploring the genetic variation mechanism of cashmere goat different hair types.The following are the main results of the study:1.There were significant differences in the hair length traits between LHG and SHG at various stages.The growth rate of coat length for SHG remains relatively consistent across months.However,from December to March,the growth rate of hair length for LHG is significantly faster than that of SHG.Additionally,the fiber fineness of LHG is significantly higher than that of SHG,indicating that the fibers of LHG are finer than those of SHG.2.In the whole transcriptome sequencing,a total of 26,78,758,726 clean reads were obtained from the strand-specific library,and 383,495,280 clean reads were obtained from the small RNA library,with a Q30 score greater than 91.8%.Differential analysis of different hair types yielded 299 differentially expressed m RNAs,497 differentially expressed lnc RNAs,217 differentially expressed circ RNAs,and 29 differentially expressed micro RNAs.3.GO enrichment analysis revealed that different hair types exhibited significant enrichment of RNA and target genes in various cellular components,especially in the categories of keratin filament,intermediate filament,and intermediate filament cytoskeleton.KEGG pathway analysis showed significant enrichment in several pathways,including the PI3K-Akt signaling pathway,MAPK signaling pathway,ribosome,and Wnt signaling pathway.GSEA analysis identified 15 gene sets that were significantly enriched in different hair types,mainly including keratin filament,intermediate filament,protein localization,PI3K-Akt signaling pathway,Wnt signaling pathway,and TGF-β signaling pathway.WGCNA analysis of various RNA molecules identified the sienna3 module in m RNA,midnightblue and blue modules in lnc RNA,lightgreen module in circ RNA,and blue module in micro RNA,and the molecules in these modules were significantly correlated with different hair types.Based on the results of the transcriptome analysis of different hair types,57 candidate differentially expressed genes related to different hair types were preliminarily screened,including FCGBP,FGF21,KRT7,KRT79,NES,XLOC＿003734,XLOC＿068673,XLOC＿079663,cric＿0465,cric＿5535,and chi-mi R-221-5p.4.In the lipidome,differential analysis was performed on lipid compounds of different hair types at various time points,and a total of 359 differentially expressed lipid compounds were identified.KEGG pathway analysis showed that these lipids were mainly enriched in the biosynthesis of unsaturated fatty acids and phospholipid metabolism.WGCNA analysis was conducted on all lipidome data,identifying 11 modules,and the pink module was found to be strongly associated with hair types,with a large number of triglyceride lipid compounds distributed in this module.By mining the lipidome data,31 candidate differential lipid compounds were identified,including arecoline,Linoleyl carnitine,Spermine,arachidonic acid,and TAG,among others,which were related to different hair types.5.Based on the WGCNA analysis was performed on the whole transcriptome sequencing and lipidome datasets,and a total of 43 modules were identified.A co-expression network related to different hair types was excavated,and the blue module was found to be strongly associated with hair types.This module contained 116 differentially expressed m RNAs,193 lnc RNAs,66 circ RNAs,3 micro RNAs,and 62 lipid compounds related to different hair types.6.In the candidate RNA regulatory network of different hair types,circ RNAs are located at the central position and regulate multiple micro RNAs,wh ich target multiple m RNAs and lnc RNAs.Correlation analysis between candidate RNAs and candidate lipid compounds revealed significant direct correlations between several RNA molecules and lipid compounds.Key RNA molecules were verified through q RT-PCR experiments,and a regulatory network associated with different hair types was predicted based on the validation results.circ＿0284 and circ＿5535 competitively bind to chi-mi R-423-5p,and circ＿3928 competitively binds to chi-mi R-221-5p.Three key micro RNAs target some key m RNAs,including DTNBP1,FCGBP,FGF21,FGF5,KRT4,KRT36,KRT72,KRT84,LOC102175427,LOC102177561,LOC106503217,LOC108636548,NES,RPS15 A,and TNC.Additionally,KRT79 is correlated with various lipid compounds such as TAG,SM,Juniperic acid,and L-Pyroglutamic acid;Spermine is associated with multiple key m RNAs;TNC is associated with PC and FAHFA;and FGF21 is associated with oleic acid and palmitic acid. |
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