基于SNP芯片的浦东鸡保种分析

Analysis of Conservation Effect in Pudong Chicken Based on SNP Chip

为了解上海市优质地方品种浦东鸡的保种效果,采用“京芯一号”SNP芯片对现有60个家系的浦东鸡群体进行了群体结构分析。结果显示:浦东鸡群体的基因型检出率平均为0.9914,说明该SNP芯片适用于浦东鸡遗传多样性的评价与分析;浦东鸡群体期望杂合度为0.3786、观察杂合度为0.3805,说明该群体的遗传多样性较低,选育程度较高;G矩阵基因组亲缘关系表明,该群体存在近交趋势;ROH分析结果显示,群体中含有23~28个ROH的个体数最多,个体ROH总长度在70~80 Mb内的个体数最多,该群体平均近交系数为0.089;根据聚类分析,将120只公鸡划分为38个家系,并将180个母鸡划分入不同家系,其中F52_3号母鸡与所有公鸡亲缘系数均小于0.1,将其归入“其他”分类中。综上,建议在今后的浦东鸡配种选留工作中:①同一家系的公母鸡避免配种;②F52_3号母鸡可与任一只公鸡配种;③注意3、11、26、27、38家系的选留,避免造成优良家系丢失。

In order to profile the conservation effect of Pudong chicken,the population structure of Pudong chicken in 60 families was analyzed by using"Jingxin No.1"SNP chip.The results showed that the average genotype detection rate of 300 Pudong chicken individuals was 0.9914,which indicated that the SNP chip was suitable for the evaluation and analysis of Pudong chicken genetic diversity.The expected heterozygosity of Pudong chicken population was0.3786,and the observed heterozygosity was 0.3805,indicating that the genetic diversity of Pudong chicken population was low,the breeding degree of the population was high.According to the genetic heat map of G-matrix,there was a trend of inbreeding among these individuals.ROH results showed that the majority was 23 to 28 ROHs in each individual;the total length of ROH in most of individuals was 70 to 80 Mb,and the average inbreeding coefficient of this population was 0.089.According to the cluster analysis,120 roosters were roughly divided into 38 families,and180 hens were divided into different families.Among them,the coefficient of inbreeding between F523 hens and all roosters was less than 0.1,which was classified into"other"classification.According to these results,the following suggestions were given:①Males and females of the same family were not recommended to be bred;②F523 hens could be bred with any rooster;③The attention should be more paid to family 3,11,26,27 and 38 in of selection and breeding to avoid the loss of excellent families.