基于芯片数据估计不同方法对槐猪近交系数的影响

doi:10.11843/j.issn.0366-6964.2023.03.009

Abstract

Abstract: The study aimed to select applicable methods to assess the inbreeding degree of Huai pigs. In this study, Fhom1, Fhom2, Fvan1, Fvan2 and Fyang were calculated with “No.1 Zhongxin” porcine breeding chip data to estimate the inbreeding coefficient of 247 Huai pigs (300-days-old), and to explore the influence of SNP number on the inbreeding estimation and the correlation between different estimation methods. The results showed that the extreme variance of inbreeding coefficient Fhom1, Fhom2, Fvan1 and Fyang gradually decreased as the number of SNPs increased. When the number of SNPs reached 10 000, the inbreeding coefficients tended to be stable, which was close to the inbreeding coefficient calculated from 31 545 SNPs after quality control. The values of Fhom1, Fhom2, Fvan1, Fvan2 and Fyang were -0.216 5-0.344 0, -0.354 8-0.321 7, -0.322 8-0.892 1, -0.243 6-0.790 9, and -0.189 4-0.543 3, respectively. The values of Froh1 and Froh2 were 0.008 7-0.406 9 and 0.002 2-0.402 4, respectively. Person correlation and Spearman rank correlation of genomic inbreeding coefficients showed strong positive correlations between Fhom1 and Fhom2, Froh1, Froh5; The strong positive correlations were found between Fvan2 and Fvan1, Fyang; The strong positive correlation was observed between Froh1 and Froh5; Whereas Fhom2 was negatively correlated with Fvan1 and Fvan2. Since Froh took values from 0 to 1 that were identical to the inbreeding coefficient of a pedigree, it conformed to the evaluation habit of inbreeding coefficient; Moreover, Froh was positively correlated with the way in which genomic inbreeding coefficients were assessed, such as Fhom, Fvan and Fyang, with high applicability. The density of SNPs influenced the assessment of inbreeding coefficient, it was more appropriate to use Froh for genomic inbreeding coefficient estimation when the number and density were sufficient. The results may provide an advantageous technical means for assessing the inbreeding level of local pigs, preventing inbreeding depression and optimizing seed selection.

Key words: Huai pig, gene chip, inbreeding coefficient, correlation

CLC Number:

S828.2

HAN Yunzhen, YANG Wenpan, HONG Yuan, LONG Yi, LIU Xiangjie, FAN Xiaoping, LI Wenjing, DENG Zheng, LIU Minghui, ZHENG Sumei, RUAN Guorong, DING Nengshui. Estimating the Inbreeding Coefficient of Huai Pigs by Different Methods Based on Chip Data[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(3): 947-955.

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Estimating the Inbreeding Coefficient of Huai Pigs by Different Methods Based on Chip Data

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