Study On SNP Chip Design And Genome Association Analysis Of Important Economic Traits In Cashmere Goats

With the development of high-throughput sequencing technology,the cost of large-scale genotyping technology has been greatly reduced,making it possible for the application of gene chips in animal breeding.The continuous development of gene chip technology provides an effective tool for the application of genome-wide association analysis in breeding.Relying on the high-throughput molecular genetic markers discovered by the gene chips and genome-wide association analysis,a reference group can be established,which can estimate the breeding value of the genome accurately.This research will lay a solid foundation for the application and promotion of precise genome selection in the future.Inner Mongolian Cashmere goat is excellent local breed of cashmere and meat dual-purpose that have been cultivated through long-term natural selection and artificial selection.They are famouse for their high-yield and high-quality cashmere,as well as stable genetic performance.Cashmere quality traits are quantitative traits controlled by micro-effects and multiple genes,with low heritability and complicated for measurement.It is difficult to carry out rapid breeding improvement through traditional breeding value estimation and breeding methods.Through genome-wide association analysis,the combination of SNPs obtained by SNP chip genotyping and fiber dimeter records is designed to explore the genetic mechanism of cashmere fiber dimeter variation.Moreover,we try to develop SNPs and genes closely related to ultra fine cashmere traits to fully explore the advantages of cashmere germplasm resources.A group of information on genomic genetic resources with independent intellectual property rights related to cashmere traits were abtained from the whole genome level,providing a strong support for the protection and utilization of cashmere goats in China,meanwhile sharing a new theoretical basis for the improvement and cultivation of super cashmere goat and genomic genetic resources.Based on the next-generation high-throughput sequencing technology,whole-genome resequencing was performed on famous local breeds in China(Inner Mongolia Cashmere goat and Liaoning Cashmere goat).And combined the genomic data of 38 individuals of other goat breeds from home and abroad.For the first time,the enrichment strategy was uscd to design animal SNP chips,and the goat 66K capture chip was successfully obtaincd.In order to test the effectiveness of the SNP chip in the study of important economic traits of cashmere goats,a genome-wide association analysis of important economic traits was carried out on Inner Mongolian Cashmere goats(Erlangshan type),and analysis of gene function annotation and biological function explored on the obtained candidate SNP loci.The main conclusions are as follows:1.Based on next-generation high-throughput sequencing technology,73 individuals of China's famous cashmere goat breeds were re-sequenced.A total of 5.52 M single nucleotide variants(SNPs)and 710,600 Indels were detected in all samples.About 87.25%SNP genetic variation is newly discovered.Through the analysis and screening of these high-quality SNP genetic markers,it can be used for the subsequent development of genetic markers for cashmere goat SNP chip.2.Using the re-sequencing data of cashmere goats and the genomic data of 38 individuals of other goat breeds from home and abroad,the cashmere goat 66K SNP chip was designed,based on the whole genome capture sequencing strategy.And a set of technical processes based on solution hybrid selection technology was established,which be used as a reference for SNP chip design of other species.3.Established a universal analysis process of SNP capture chip.Low-cost whole genome capture sequencing was achieved successfully using cashmere goat 66K SNP chip and obtained 161,125 high-quality SNP data sets from 423 individuals,which can be used for subsequent GWAS research.4.A genome-wide association analysis was conducted on the fineness traits of Inner Mongolian Cashmere goats(Erlangshan-type cashmere).KEGG analysis was performed on the top 26 SNP screened sites,and the genes AKT1,ALX4,HK1,NT-3,where 4 SNP sites were located,were selected can be used as a candidate gene for cashmere fineness traits for further research.MALDI-TOF-MS detection of 48 SNP sites in the GWAS results showed that 1 SNP sites were related to fineness traits,indicating that the GWAS results are reliable,and the chip can be applied to relevant studies on important economic traits of cashmere goats.