Screening On LncRNAs From Cashmere Goat Skin And Correlation Analysis Between Its Target Gene And Cashmere Fineness

Cashmere fineness,whose phenotypic characteristics is determined by gene expression,is the key to measure the quality and price of cashmere.In recent years,candidate genes for cashmere fineness-related traits have been screened through high-throughput data analysis and genome-wide association analysis.However,the key regulatory genes,expression levels and molecular regulatory mechanisms of cashmere fineness are still unclear.At present,high throughput sequencing and bioinformatics analysis showed that non-coding RNA differentially expressed and regulated cashmere fineness-related target genes in the skin,secondary hair follicles and secondary hair follicles of different individuals among and within cashmere goats.Long-chain non-coding RNA(lnc RNA)is a kind of RNA whose transcript length is more than 200 nt and lacks coding ability.It participates in almost all biological processes.In this study,3,084 differentially expressed m RNAs and 93 lnc RNAs were obtained from the skin of Liaoning cashmere goats and Inner Mongolia cashmere goats by RNA-seq.Nine candidate lnc RNAs for cashmere fineness were screened for q RT-PCR.The NFKBIA gene regulated by lnc RNA and differentially expressed in cashmere goat skin was analyzed by ce RNA network regulation.From which,we get target gene mi RNA to be used for q PCR.Finally,the key candidate gene for cashmere fineness,NFKBIA,was obtained.The key cashmere fineness genotype G1547A(GG10)was obtained by SNP sequencing in CDS area of NFKBIA of 1,104 Liaoning cashmere goats.The results obtained are as follows: 1.Sequencing results of cashmere fineness-related lnc RNAs:The reads obtained by RNA-seq from skin tissue of Liaoning cashmere goats and Inner Mongolia cashmere goats was 128,989,956 and 146,038,848,respectively.A total of 27,947 m RNAs were obtained,of which 3,084 were differentially expressed(P < 0.05),including 2,076 up-regulated and 1,008 down-regulated m RNAs;437 lnc RNAs showed expression,93 of which were differentially expressed,including 43 up-regulated and 50 down-regulated lnc RNAs.149 target genes of lnc RNAs were identical to the differentially expressed m RNAs.GO enrichment analysis was mainly involved in the cytoskeleton synthesis of intermediate filaments and intermediate filaments in cell composition(CC).2.QRT-PC results for cashmere fineness-related lnc RNAs:In this study,9 lnc RNAs from Liaoning cashmere goats' coarse and fine skin tissues were tested by q RT-PCR,the results show that lnc RNAs XLOC?008679 and XLOC?011060 may play a positive role in regulating cashmere fineness.Lnc RNAs XLOC?016109 and XLOC?010430 may play a negative role in regulating cashmere fineness.The NFKBIA was analyzed by ce RNA to get related mi RNAs,detected them by q RT-PCR,the results showed that these mi RNAs were highly expressed in the fine type of LCG,which may play a positive role in regulating cashmere fineness.After that,NFKBIA was identified as a candidate gene for cashmere fineness.3.Detection of SNP on NFKBIA and its correlation with cashmere fineness:The CDS region of 1,104 Liaoning cashmere goats' NFKBIA was detected.15 SNP loci were found to investigate the correlation between different SNP loci and cashmere production.The correlation between NFKBIA and cashmere fineness was studied and analyzed from polymorphism effect,gene replacement effect and fetal effect.It was found that the good cashmere performance genotype of Liaoning cashmere goats was G1547A(GG10),which might be used as a marker-assisted selection index for cashmere performance of LCG.