【作者】 刘彬；

【导师】 朱砺； 李强；

【作者基本信息】 四川农业大学 ， 农业硕士（专业学位）， 2020， 硕士

【摘要】 在地方猪品种遗传资源保护过程中,普遍实行在原产地建保种场的活体原位保种方式。受地方猪遗传资源持续减少,难以补充新的血缘的客观条件限制。同时,为了减少外来品种的基因污染,保种群体的闭锁繁育模式必然加剧世代交替过程中的群体遗传结构改变。本研究以青峪猪和凉山猪这两个典型的西南山地型地方猪保种群体为模型,研究闭锁繁育群体在跨世代过程中所发生的群体遗传结构变化规律。利用50K SNP基因芯片,分别对青峪猪保种群内全部141头健康成熟个体和凉山猪保种群内全部141头健康成熟个体进行了全基因组范围的SNP测定,通过多种分析对两个群体以及群体中各个世代进行系谱校正,进而实施群体遗传多样性、遗传距离以及遗传结构变化等分析。结果如下:1.通过系谱资料整理,青峪猪保种群是由3个重叠世代构成的一个多世代混合闭锁繁育群体。其中,第3世代个体数量最少仅为10头;凉山猪保种群则包含6个重叠世代,其中第6世代个体数最少仅为2头。且两品种都是2011年组建基础群,同样闭锁繁育了8年,青峪猪包含3个世代,凉山猪包含6个世代,说明青峪猪的世代间隔长于凉山猪。2.群体间遗传多样性分析发现,两个品种群体间的亲缘关系较远。青峪猪保种群体的有效含量为12头,凉山猪保种群体为15头;凉山猪保种群的多态性标记比例(0.8393)大于青峪猪保种群(0.6424);两个群体的期望杂合度都低于观察杂合度,表明两个品种的保种群体中均可能出现了其他品种血缘的混入,或者是由于两个封闭群体规模较小,且来源一致,个体间存在亲缘关系而出现的抽样误差所致。3.亲缘关系分析结果表明两个保种群体中大部分个体之间存在中等程度的亲缘关系,也都存在部分个体间亲缘关系较近的情况,说明在局部的亚群体中已经发生了一定程度的近交。而两个群体中的公猪个体之间都保持着较远的遗传距离,说明其选留策略总体是有效的。4.鉴于公猪对于保种群体的重要性,进一步对两个群体中的所有公猪进行了聚类分析,结果显示26头青峪猪公猪样本分为了6个家系,14头凉山猪公猪包含了5个家系;将保种群体内各母猪与不同公猪家系间进行亲缘关系和聚类分析发现,除公猪家系外,青峪猪保种群还存在一个只含有5头母猪的独立母系家系,凉山猪保种群还存在一个只含有49头母猪的独立母系家系,表明在跨世代的继代繁育过程中都出现了一定程度的公猪血缘丢失。5.群体近交系数分析表明,随着继代繁育的延续,闭锁的保种群体内出现了较严重的世代重叠,在跨世代的过程中,群体的近交系数出现了上升的趋势。其中,青峪猪保种群从第一世代的0.039上升到第3世代的0.075,而凉山猪保种群的近交系数出现了先增加后降低的趋势,整个群体的近交系数保持在0.026。6.结合生产记录的系谱准确度分析结果显示,青峪猪保种群系谱的父本信息错误率高于0.71%,母本信息错误率高于11.35%;凉山猪保种群系谱的父本信息错误率高于11.35%,母本信息错误率高于2.13%。7.利用已知的15个中外猪品种参考群体信息,对凉山猪及青峪猪保种群的血统来源进行比对分析,发现这两个品种保种群中的大部分个体或多或少的含有藏猪血统,部分个体同时含有商业化品系及其它地方猪品种的血缘。但是,受到有限参考群体数量和信息准确度等限制因素的影响,这部分结果还需要更深入的研究才能确认。综上所述,通过对青峪猪和凉山猪保种群基因组水平的群体遗传结构研究表明,两个保种群体在跨世代的持续闭锁繁育过程中存在群体遗传多样性的损失和公猪血缘的流失,需要加强选配和选留,或引入血缘纯正的新个体以确保两品种遗传资源的长期保存。目前,中国的地方猪保种群大多属于跨世代的混合闭锁群体,为了提高对群体遗传结构分析的准确度,必须改变之前将一个保种群体作为一个固定闭锁群体分析的传统方法;实施更为精细的混合世代群体分析,才能更准确地揭示群体跨世代过程中出现的一系列遗传变化。更多还原

【Abstract】 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.更多还原