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

Abstract

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

CLC Number:

S831.2

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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Evaluating Beijing You Chickens Conservation Status by Phenotype and Genome Information

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