| In the process of protecting genetic resources of local pig breeds,the way of in situ conservation in vivo is widely used.Due to the continuous decrease of genetic resources of local pigs,it is difficult to supplement new blood relationship.At the same time,in order to reduce the gene pollution of foreign varieties,the closed breeding mode of conservation population will inevitably aggravate the change of population genetic structure in the process of generation alternation.In this study,Qingyu pig and Liangshan pig,two typical southwest mountain type local pig breeds,were used as models to study the changes of population genetic structure in the process of Intergeneration.By using 50 K SNP gene chip,the SNP of the whole genome of 141 healthy and mature individuals in Qingyu and Liangshan pig populations were measured respeectively.The pedigree of the two populations and each generation of the population were corrected by various analysis,and then the genetic diversity,genetic distance and genetic structure change of the population were analyzed.The results are as follows:1.According to the pedigree data,Qingyu pig conservation population is a multi generation mixed closed breeding population composed of three generations.Among them,the number of individuals in the third generation is at least 10;the Liangshan pig population contains 6 overlapping generations,and the number of individuals in the sixth generation is at least 2.Both of the two breeds were established in 2011.They were also closed bred for 8 years.There were 3 generations in Qingyu pig and 6generations in Liangshan pig,indicating that the generation interval of Qingyu pig was longer than that of Liangshan pig.2.The genetic diversity analysis showed that the genetic relationship between the two populations was far.The effective content of Qingyu group was 12,and Liangshan group was 15.The polymorphism marker ratio of Liangshan group was higher than Qingyu group(0.8393),and the expected heterozygosity of the two populations is lower than the observed heterozygosity,which indicates that there may be a mixture of other species’ consanguinity in the two species conservation populations,or the sampling error caused by the small scale of the two closed populations,the same source and the consanguinity between individuals.3.The results of genetic analysis showed that most of the individuals in the two populations had a moderate degree of kinship,but some of them were close to each other,which indicated that a certain degree of inbreeding had taken place in the local subpopulation.However,the genetic distance between the boars in the two populations is relatively long,which shows that the selection and retention strategy is effective in general.4.In view of the importance of boars to the conservation population,further cluster analysis was carried out for all boars in the two populations,and the results showed that 26 Qingyu boar samples were divided into 6 families,and 14 Liangshan boars included 5 families;In addition to the boar family,there is a matrilineal family with only 5 sows in Qingyu pig population,and there is a matrilineal family with only 49 sows in Liangshan pig population.The results of inbreeding coefficient showed that the inbreeding coefficient of Qingyu pig increased from 0.039 of the first generation to0.075 of the third generation,while that of Liangshan pig increased first and then decreased,and the inbreeding coefficient of the whole population remained at 0.026.5.The analysis of population inbreeding coefficient shows that with the continuation of subculture,there is a serious generation overlap in the closed population,and in the process of cross generation,the population inbreeding coefficient shows an upward trend.Among them,the inbreeding coefficient of Qingyu pig population increased from 0.039 in the first generation to 0.075 in the third generation,while that of Liangshan pig population increased first and then decreased,and the inbreeding coefficient of the whole population remained at 0.026.6.The results of pedigree accuracy analysis combined with production records show that the error rate of paternal information is higher than 0.71% and that of maternal information is higher than 11.35% in Qingyu pig pedigree;the error rate of paternal information is higher than 11.35% and that of maternal information is higher than2.13% in Liangshan pig pedigree.7.Based on the information of 15 known reference groups of Chinese and foreign pig breeds,the origin of Liangshan pig and Qingyu pig breeds were compared and analyzed.It was found that most of the two breeds contained Tibetan pig breeds more or less,and some of them contained commercial and other local pig breeds at the same time.However,due to the limited number of reference groups and information accuracy and other constraints,this part of the results need more in-depth research to confirm.In conclusion,based on the study of population genetic structure at genome level of Qingyu and Liangshan pig conservation populations,it is indicated that the loss of population genetic diversity and the loss of boar consanguinity exist in the process of cross generation continuous closed breeding of the two conservation populations.It is necessary to strengthen the selection and retention,or introduce new individuals with pure consanguinity to ensure the long-term preservation of genetic resources of the two breeds.In addition,most of the local pig populations in China belong to the intergenerational mixed closed population.In order to improve the accuracy of population genetic structure analysis,it is necessary to change the traditional method of using a protected population as a fixed closed population analysis.A more detailed population analysis of mixed generation can reveal a series of genetic changes in the process of population intergeneration more accurately. |
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