| Goat milk has attracted much more attention in animal husbandry because of its unique nutritional value.However,the low yield of goat milk due to the lack of good dairy goat germplasm resources and accurate breeding technology has become a"bottleneck"problem that restricts the high-quality development of Dairy goat industry in China.Genome-wide association study（GWAS）can combine multiple factors that influence traits and screen for single nucleotide polymorphism（SNP）associated with traits.Besides,using loci information as markers to select individual traits can improve breeding accuracy and shorten breeding process.This study is based on the genotype-imputation.The 10 x and 1 x genome data of dairy goats were integrated and single nucleotide polymorphisms（SNPs）loci which are significantly associated with the lactation of milk goats were screened with GWAS technology..From the sites of significance(P<10-6),10 loci were randomly selected to perform correlation analysis to test and verify the reliability of GWAS results.Using SNP loci that has significant influence on milk yield,we developed liquid chip for molecular breeding of dairy goats to overcome the"bottleneck"problem of dairy goat breeding technology,which is of great significance for the select of high-yield dairy goat germplasm as well as the high-quality development of dairy goat industry.The main results were as follows:1.Screening of significant SNPs loci for lactating traits in dairy goats.A total of 28,956,670 SNPs were obtained by 10×high depth resequencing of the samples comparing the data with goat genome after quality control（Capra hircus＿ARS1）.Using 10×high depth resequencing data of 50 dairy goats as reference,genotype-imputation was carried out on the data of 1×low depth resequencing of 300 dairy goats.After quality control comparison,1,561,775,909 SNPs were obtained.Based on the 1,590,732,579 SNPs loci achieved by sequencing,GWAS was conducted with the milk yield of dairy goats as phenotypic traits and finally 311 SNPs loci and their candidate genes were screened according to significance threshold(P<10-6)using mixed linear model.2.Validation of significant SNP sites affecting milk yield in dairy goats.Ten loci were randomly selected from the selected SNPs:SNP-1（located in CDC14A）,SNP-2（located between LOC108636124 and PHLDA1）,SNP-3（located in 3’UTR of ZNF609）,SNP-4（located in 3’UTR of RBPJL）,SNP-5（located in 3’UTR of LOC102191110）,SNP-6（located in exon 5 of LOC102177517）,SNP-7（located in LOC102183585）,SNP-8（located in exon ZSCAN9）,SNP-9（located in upstream of 2 kb of ZFAND2A）and SNP-10（located in exon 10 of F11）.The effects of these 10 loci on milk yield of dairy goats were analyzed.The results showed that the GG genotype of SNP-1,the TT genotype of SNP-4,the TT genotype of SNP-6,the AA genotype of SNP-7,the AA genotype of SNP-8,the AA genotype of and the SNP-9 and CC genotype of SNP-10 could significantly improve milk yield of dairy goats（P<0.05）.There was no significant difference in the effects of SNP-2,3 and 5 loci（P>0.05）.Using the significant SNP sequences obtained by screening as the template,the custom-made probe was designed and with the hybridization buffer,and ultimately liquid chip was developed for dairy goat genotyping detection.With our liquid chip the genotypes of each locus could be quickly detected after the sample DNA was concentrated.In conclusion,in this study,dairy goat samples were re-sequenced and analyzed with GWAS.SNPs loci significantly related to milk yield of dairy goat were screened out.After verification,the obtained loci could used to develop liquid chip for rapid detection of the genotype of dairy goat samples. |
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