Study On Character Variation And Molecular Genetic Mechanism Of Different Hair Coat Types In Inner Mongolia Cashmere Goat

Inner Mongolia Cashmere Goat is a well-known local Cashmere goat breeds.It is not only famous for its excellent cashmere quality,but also has a significant advantage in cashmere production compared to other Cashmere goat breeds after more than 30 years of systematic selection program.With the change of breeding goals and market demand,the production of high-quality cashmere fibers is the main goal of Cashmere goat breeding plan.How to reduce the fineness of cashmere fibers while maintaining the amount of cashmere production is the main direction of molecular biology and quantitative genetic breeding research.In the practical production and previous study of our group,we found that there is genetic diversity on the hair coat type of Cashmere goat population.The statistics and genetic parameter analysis of the different hair coat type showed that there was some genetic and phenotypic correlation between guard hair fiber traits and cashmere quality traits and the long-hair type has advantages in economic aspects of each economic.However,the genetic mechanism and character variation in different hair coat type is still unclear,which greatly hinders the progress of genetic improvement of cashmere goats to a certain extent.The development of high-throughput sequencing technology and the rapid reduction in sequencing costs also provide the possibility to analyze the genetic mechanism of complex traits from a multi-omics perspective.This study is based on sample collection of fleece from April to May in the Inner Mongolia Cashmere Goat Albas Breeding Farm from 2018 to 2019.Through the detailed phenotypic observation description of the hair coat type,the pedigree record information,the laboratory measurement of the coarse and cashmere fiber,whole-genome DNA resequencing and cycle transcriptome sequencing of skin hair follicle were used for mining analysis to underpin differences in phenotypic characteristics,genetic pattern,genetic basis and expression regulation of different hair type,providing a basis for future molecular breeding and indirect selection of Cashmere goats.The main findings are as follows:1.Through observation and descriptive statistical analysis of different hair coat types of Inner Mongolian Cashmere goat Albas type,it was found that the main feature of the long-hair coat type is that the whole body coat is covered with long and bright coarse guard fiber,which has advantage among different group of ages,range from 57.90%to 78.70%;and the main feature of the short-hair coat type is that the whole body guard fiber is short and sparse without partional of the limbs and the back is long and dull,accounting for 21.30-42.12%in all age’s groups.According to the genetic deduction of hair coat type with pedigree and hair coat type data,it is found that the hair coat type may be autosomal inheritance,of which the long-hair type is the dominant trait.Long-hair type cashmere goats have advantages in weight,cashmere diameter and cashmere yield,and imply that can be used as candidates or subgroups for breed improvement in the future.2.Whole genome re-sequencing genetic variation detection found a total of 13,259,614 SNPs and 2,646,292 InDels respectively.Annotations in the genomic region found that 0.60%of SNPs and 0.16%of InDels were exon mutations respectively.The genes contained missense mutations and frameshift mutations were 10,479 and 1,343,respectively.Screening based on the genome-wide SNP locus of population genetic differentiation index FST>0.15,80,625 SNPs and 4,953 genes were found.GO functional analysis notes found that genes enriched in cell part,nuclear part,mitochondrial envelope,mitochondrial membrane,lyase activity,hydrolase activity,stimulation reaction,cell communication and other biological functions.KEGG pathway analysis found a total of 262 signal pathways,including Calcium signaling pathway,lysine degradation,Notch signaling pathway,MAPK signaling pathway,WNT signaling pathway,etc.are significantly enriched in the signaling pathways related to the growth and development of skin follicles.3.A total of 1,227 genes were screened using genome sliding selection signal FST and θπ combined methods,including 558 candidate genes for long-hair coat type and 686 candidate genes for short-hair coat type,of which ADA,ARID1B,UNC5C and ZEB1 are the 17 selected genes shared by the long-and short-hair coat types are related to the growth and development of skin follicles,and mutations can cause abnormal hair.PKIG,CDX1,GCC2,PPP1CB,LIMS1,HDAC9,GFRA1,PDGFRB,Myo10,LATS2,PROM1 and other 13 genes in long-hair coat type individuals and LRPAP1,TRPV4,NELFA,CPLX1,DGKQ,NFKB1,EDA,CXCR3,FGF10,FGF13,FGFBP1,LTBP1 in short-hair coat type individuals,MBTPS2,PPP1CB,SHOC2,SOS2,KRT10,SLC6A14,SLC45A1,CACNG1,CCL19,COL4A5,FABP5,CTBP1 and other 24 genes are potential candidate genes related to the different hair coat type.The method based on genome selection signal provides an effective method for genetic locating the genetic basis of different hair coat types.4.Through GWAS analysis of case-control and hair length(mixed linear model),12 and 603 candidate genes were detected respectively.Among which C6H4orf48,DGKQ,LOC108636241,LRPAP1,NAT8L,NELFA,POLN,RGS12,SLBP,TACC3,TMEM129 and other genes are related to the recombination rate,speculating that there is a potential relationship between recombination hotspots and hair coat types.In addition,functional analysis of hair length found LRPAP1,TRPV4,NELFA,CPLX1,DGKQ,ABCC4,ARHGAP10,AEBP1,IL-6,DUSP6,ERRFI1,ENPP2,FARP2,ZNF407,CDH7,KIF7,TSPEAR,WNT16 and CDH19 may be related to hair length or hair coat type.5.Combining the nominally significant candidate genes from GWAS of different hair coat type and the cyclic transcriptome data with the skin of different hair coat types in the previous research,we conducting mining and analysis of by WGCNA method.It is found that the Yellow module has a strong correlation with the different hair coat type.Among them,CPLX1,LRPAP1,DGKQ,NELFA,CDK5RAP2,COL18A1,FARP2,KIF7,RECQL5,RHBDF2,RIPK1,SEMA4B,TRPV4,UVSSA,ZFAT and other candidate genes may be potentially related to different coat types.6.The genotype of(G→A)locus 115544377 of LRPAP1 gene was significantly correlated with the hair coat type.That is genotype(GG)was associated with short-hair coat type,while AA or AG was associated with long-hair coat type.This study proves that LRPAP1,TRPV4,NELFA,CPLX1,DGKQ and other 24 genes potentially related to hair coat types at the genomic level through genome scan,genome-wide association analysis,and WGCNA.And it provides the molecular regulatory mechanism for the research of hair coat types.A large number of functional mutation sites obtained through genetic variation detection also provide a large number of potential molecular genetic markers for the molecular genetic improvement of Cashmere goat breeds in the future.