基于表型和基因组信息评价北京油鸡保种群保种情况

doi:10.11843/j.issn.0366-6964.2021.09.004

摘要/Abstract

摘要： 旨在利用表型和基因组信息对北京油鸡随机交配保种群体近交系数、有效群体大小进行研究，评价北京油鸡保种群体保种情况。本研究以国家级北京油鸡保种场北京油鸡2019年随机交配保种群体40只鸡为研究对象，对表型记录进行整理，同时利用基因组SNP信息，使用PLINK软件分别计算基于ROH的近交系数（F_ROH）、基于纯合基因型的近交系数（F_HOM）、基于联合配子之间相关性的近交系数（F_UNI）；使用GCTA和R软件计算基于基因组关系G矩阵的近交系数（F_GRM）；使用SNeP软件估计北京油鸡历史世代的有效群体大小；使用NeEstimator软件估计基于连锁不平衡方法的当前世代的有效群体大小；使用R软件的PerformanceAnalytics包对F_ROH、F_HOM、F_GRM和F_UNI等不同算法所得近交系数进行相关性分析，评价北京油鸡的保种情况。结果显示，1979—2019年以来，北京油鸡保种群体凤冠、胫羽、五趾等典型的外貌特征明显且百分比稳定；保种群有效群体大小从98世代前的595逐渐降至13世代前的176；2019年北京油鸡随机交配保种群体F_ROH为0.079 8，与F_GRM显著相关（P<0.01），且相关系数为0.45；除此之外，F_HOM与F_GRM，F_HOM与F_UNI以及F_GRM与F_UNI之间也存在较高的线性相关。北京油鸡1979—2019年以来近交系数增长缓慢，国家级北京油鸡保种场随机交配保种群体的保种工作是十分有效的。基于目前情况，本研究建议每年随机选取一定数量的北京油鸡随机交配保种群体的个体，进行全基因组二代重测序检测，有利于对保种状况进行动态监控，以便随时调整保种工作方案。

关键词: 北京油鸡, 资源保护, 近交系数, 全基因组重测序技术, 连续性纯合片段

Abstract: Phenotype and genomic information were used to calculate inbreeding coefficient and the effective population size in Beijing You chicken conserved population, which could evaluate its conservation status. In this study, 40 individuals from Beijing You chicken breeding population in the national Beijing You chicken breeding farm, were used to collect phenotypic information in 2019. The genomic SNP information was used to evaluate the conservation status of Beijing You chicken. The inbreeding coefficients based on ROH (F_ROH), homozygous genotype (F_HOM) and the correlation between joint gametes (F_UNI) were calculated by PLINK. The G matrix constructed by genomic relationship was used to calculate the inbreeding coefficient (F_GRM) through GCTA and R softwares. The SNeP software was used to estimate the effective population size of the historical generation of Beijing You chicken; The NeEstimator software was used to estimate the effective population size of the current generation based on the linkage disequilibrium method. Correlation analysis of inbreeding coefficients among F_ROH, F_HOM, F_GRM and F_UNI was conducted by R-statistics software with the "PerformanceAnalytics" packages. The results showed that over the 40 years from 1979 to 2019, the typical external features including phoenix crest, shin feathers and five toes, were obvious and the percentage of phenotypes in the Beijing You chicken conservation population was stable. And the effective population size of the conserved population gradually decreased from 595 before 98 generations to 176 before 13 generations. And we found that the F_ROH of 0.079 8 for the Beijing You chicken random mating conserved population in 2019 was significantly correlated with F_GRM (P<0.01) with a correlation coefficient of 0.45. Besides, there were also high linear correlations between F_HOM and F_GRM, F_HOM and F_UNI, F_GRM and F_UNI. The inbreeding coefficient of Beijing You chicken has increased slowly in the 40 years from 1979 to 2019, and the conservation work of random mating conserved population in the national Beijing You chicken breeding farm is very effective. Based on the present results, it is suggested that a certain number of individuals from the random mating conserved population of Beijing You chicken should be randomly selected each year for whole genome sequencing, which is conducive to dynamic monitoring the conserved status so that the conserved work program can be adjusted at any time.

Key words: Beijing You chicken, resource protection, inbreeding coefficient, genome resequencing technology, ROH

中图分类号:

S831.2

王海龙, 王巧, 邢思远, 王杰, 李庆贺, 郑麦青, 崔焕先, 刘冉冉, 赵桂苹, 文杰. 基于表型和基因组信息评价北京油鸡保种群保种情况[J]. 畜牧兽医学报, 2021, 52(9): 2406-2415.

WANG Hailong, WANG Qiao, XING Siyuan, WANG Jie, LI Qinghe, ZHENG Maiqing, CUI Huanxian, LIU Ranran, ZHAO Guiping, WEN Jie. Evaluating Beijing You Chickens Conservation Status by Phenotype and Genome Information[J]. Acta Veterinaria et Zootechnica Sinica, 2021, 52(9): 2406-2415.

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