Design Of Goat SNP Chip With Applications In Genome-wide Association Study And Genomic Selection Of Important Economic Traits In Inner Mongolia Cashmere Goat

Inner Mongolia Cashmere goat is a well-known local cashmere goat breed in China.It is famous for excellent fleece quality and a significant advantage in cashmere yield compared to other cashmere goat breeds.Based on the genome sequencing data of different goat breeds completed in the early stage of the research group,the first chip suitable for local goat varieties in China was developed.Combined with the genealogy and production performance measurement record,a high quality reference group was constructed.The whole genome association analysis and big data genome selection research were carried out in Inner Mongolia cashmere.The genetic machine for the quality of villi was studied the best method of genome selection was selected by the preliminary analysis of the theory.To makes full use of the advantages of China cashmere goat germplasm resources,this work studies and excavates a number of molecular markers and gene resources related to cashmere production traits from the perspective of genome.Therefore,the results provide scientific basis for the protection and utilization of genetic resources of cashmere goats in the future,new gene resources and theoretical guidance for the cultivation of new cashmere goat high quality wool lines in Inner Mongolia.The main results of this paper are as follows:1.Based on the 616 113 production performance records of Inner Mongolia cashmere goats' collected in the past 30 years,the fixed effect of each character was determined by a generalized linear model,and then the genetic parameters of the important economic characters of Inner Mongolia cashmere goats were estimated by asreml software.The results showed that group,year of measurement and individual age had significant influence on all traits.Significant factors were included as fixed effects in the model.The heritabilities of cashmere production(CP),cashmere diameter(CD)and cashmere length(CL)were 0.24,0.27 and 0.32 respectively,which belonged to medium heritability(0.20-0.40),while weight and fiber length(FL)were low(0.12 and 0.14).The results showed that the genetic correlation among cashmere yield,body weight,cashmere length,cashmere fineness and wool length was-0.32 to 0.40,and the phenotypic correlation was-0.02 to 0.20;the additive variance of each character was smaller than that of previous studies,which indicated that BLUP breeding had good effect and the phenotype was more uniform.2.The genome and transcriptional data of 36 typical Chinese local varieties(372individuals)and 49 foreign breeds(226 individuals)were used.Meanwhile,the 52 K SNP chip sites of Illumina goats were maximized and the important functional sites accumulated by the research group over the years were added,and the total data was about 4 Five million SNPs with MAF greater than 0.2 were selected by conditional multi-objective localization optimization algorithm.After strict screening of SNPs,67088 SNPs sites were reserved,and a new goat 70 K SNP chip(GGP)was integrated?Goat?Based on the chip of 70 K SNP,the genotyping of Inner Mongolia cashmere goat population was carried out.All individuals were successfully genotyped,with an average call rate of 98.8%.It is suggested that the chip can be used to genotype goat,and the genotyping data of 920 individuals are obtained,which can be used in the subsequent GWAS and genome selection research.3.Based on the genotype data of 1920 individuals,the whole genome association analysis of cashmere length,cashmere diameter and cashmere production of Inner Mongolia cashmere goat was carried out.Firstly,the data of cashmere length,cashmere fineness and cashmere yield were sorted to detect whether the phenotypic data conformed to the normal distribution;at the same time,the principal component analysis of Inner Mongolia cashmere goat population was carried out to determine whether there was population stratification phenomenon;then the mixed linear model was used for GWAS analysis,and the quantile quantile(Q-Q)chart was used to determine the fitting degree of expected value and observed value.In this study,a genome-wide association study(GWAS)was used to investigate cashmere length(CL),cashmere diameter(CD)and cashmere production(CP)of 1920 Inner Mongolia cashmere goats using 70 K SNP panel.We discovered that four single nucleotide polymorphisms(SNPs)reached the genome-wide significance levels.These SNPs were located in some genes GALNTL5 ?CMASFGF12?POLN?TACC3?PRLR ?EVPL ?COL3A1and SOX5 were important candidate genes for cashmere traits of Inner Mongolia cashmere goat,which could be used for further research.4.Based on 70 K SNP chip was used to carry out genomic selection of cashmere goat in China.The heritability and genomic breeding value of cashmere length,cashmere diameter,cashmere production,body weight and fiber length of Inner Mongolia cashmere goat were estimated by GBLUP and SSGBLUP methods.The data were compared with the data obtained by ABLUP method,and the accuracy of breeding value prediction was evaluated by 5-fold cross validation with 5 replicates.The results showed that(1)the heritability of cashmereproduction estimated by gblup and ssgblup was 0.26 and 0.28;the heritability of body weight was 0.17 and 0.14;the heritability of cashmere length was 0.09;the heritability of cashmere diameter was 0.30;the heritability of fiber length was 0.31 and0.32.(2)The results showed that the accuracy of ssgblup was 45% to 82%,which was 19%to 25% higher than that of ablup;(3)ssgblup had higher prediction accuracy and unbiasedness than gblup and ablup,and ssgblup was the best method for genomic selection of Inner Mongolia cashmere goats;(4)generation interval of Inner Mongolia cashmere goats could be shortened from 4.5 years to 2 years by implementing genomic selection.