| Ningxiang pig has the characteristics of good meat flavor,high nutritional value,resistance to rough feeding and strong adaptability.Because of its low lean meat rate and slaughter rate,it is not favored by the market.In addition,it is impacted by foreign lean pig breeds and is being used in breeding.During the process,the inbreeding rate was relatively high,which led to the limited development of Ningxiang pig population and the continuous reduction of the effective population.In order to solve the above problems and ensure the healthy and sustainable development of the Ningxiang pig population,we use the genomic breed composition(GBC)identification technology and the population gene flow analysis technology to carry out research on the existing Ningxiang pig population to analyze the purity of individual breeds,Blood composition and group evolution history,etc.,provide a reference for protecting the diversity of Ningxiang pig population’s germplasm resources and formulating breed improvement plans.In this study,the common SNP markers(15K reference SNP panel)of three commercial SNP chips(Illumina 60 K,GGP 50 K,Zhongxin 1)were used to obtain four SNP panels with different densities(500,1K,5K and 8K,a total of 12 SNP panels)by three screening methods(uniform distribution method,maximum genetic distance method and Wright’s FST method);A reference group including 6 pig breeds(Rongchang pig,Bama Xiang pig,Duroc pig,Landrace pig,Yorkshire pig,Ningxiang pig)was formed.Using the above-mentioned SNP panel and reference population,the GBC of 100 individual Ningxiang pigs was estimated based on three statistical models(linear regression model,ADMIXTURE model,path analysis model).Finally,the influence of SNP panel screening method and GBC statistical model on the accuracy of individual GBC estimation of Ningxiang pigs is analyzed,and the most suitable combination of statistical model and SNP screening method is found under the premise of ensuring the accuracy of estimation.In addition,using the southern Balkan wild boar as an out group,ABBA-BABA analysis was performed on the Ningxiang pig population to understand the genetic exchange relationship between the Ningxiang pig population and other breeds.The main results of this study are as follows:1.This study finally constructed a reference group containing 2912 individual animals and 6 pig breeds(Ningxiang pig,Bama pig,Rongchang pig,Duroc pig,Landrace pig,Yorkshire pig).Through the statistical analysis of the reference population A allele frequency(Freq-A),it is found that there is a big difference between lean pig breeds and Chinese local pig breeds.The distribution of allele frequencies among the three lean pig breeds was similar,and approximately evenly distributed;while the distribution of Freq-A in different intervals was quite different among Chinese native pig breeds.2.Analyze the gene exchange relationship between Ningxiang pigs and each pig breed in the reference group.The results show that there is significant gene exchange between Ningxiang pigs and Bama fragrant pigs.And the direction of gene exchange is from Ningxiang pigs to Bama fragrant pigs.Bama xiang pig ancestors may be mixed or mated with Ningxiang pigs.3.The results showed that the distribution of SNP markers screened by the maximum genetic distance method and Wright’s FST method was similar on chromosomes;The SNP panel constructed by uniform distribution method was more evenly distributed on chromosomes and had higher genome coverage.4.Using the screened SNP panel to estimate the individual GBC,the accuracy rate is higher than that of the 15 k reference panel;among the three screening methods.Using the uniform distribution method to screen the different density SNP panels to estimate the GBC,the result is more accurate Stable(52%-84%).The GBC estimation accuracy of the SNP panel constructed by Wright’s Fst method is the highest(98%).5.Based on the 12 SNP panels constructed in this study,three statistical models were used to estimate the individual GBC of Ningxiang pigs.The results showed that the mixed model had the highest and most stable estimation accuracy,with an average accuracy of 87%.Path analysis model is better than linear regression model in estimating GBC,but there is little difference.In conclusion,the information content of SNP markers screened by different methods is inconsistent with their distribution on chromosomes,which leads to the difference in the accuracy of GBC estimation;When selecting ultra-low density SNP panel(such as 500 or 1k)to estimate individual GBC of Ningxiang pig,the statistical model should choose ADMIXTURE model,and the SNP panel construction method should use Wright’s FST method.This combination of Ningxiang pig GBC estimation accuracy is high,and can provide reference for the development of low density SNP chip. |
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