不同来源大白猪总产仔数近交衰退评估

doi:10.11843/j.issn.0366-6964.2021.010.008

摘要/Abstract

摘要： 旨在评估两个不同来源大白猪群体经过近8个世代的选育后总产仔数（total number of piglets born，TNB）近交衰退的程度。本研究对1 937头大白猪使用GeneSeek GGP Porcine HD芯片进行分型，其中1 039头来自加系大白猪和898头来自法系大白猪，且两品系均有表型记录和系谱记录，系谱共由3 086头大白猪组成。分别使用系谱、SNP和ROH进行个体近交系数估计，并将近交系数作为协变量利用动物模型对总产仔数进行近交衰退评估。为了精准定位导致总产仔数衰退的基因组片段，又进一步对每条染色体以及显著染色体分段计算近交系数并估计其效应，检测是否能引起总产仔数发生近交衰退现象。对于加系群体，F_ROH、F_GRM和F_PED估计的近交系数均值分别为0.124、0.042和0.013，其中F_ROH和F_PED相关最高，相关系数为0.358；对于法系群体，F_ROH、F_GRM和F_PED均值分别为0.123、0.052和0.007，其中F_ROH和F_GRM相关最高，相关系数为0.371。利用3种不同计算方法所得近交系数用于估计近交衰退时，加系群体的总产仔数均检测到显著的近交衰退，而且当F_ROH、F_GRM和F_PED每增加10%时，总产仔数分别减少0.571、0.341和0.823头；但法系群体仅有F_ROH估计的总产仔数检测到显著近交衰退，F_ROH每增加10%时，总产仔数减少0.690头。为了锁定相关的染色体和基因组区段，首先利用ROH估计每条染色体近交系数并进行近交衰退分析发现，加系群体中检测到第6、7、8和13号染色体产生了显著近的总产仔数交衰退，而法系群体未检测到与近交衰退相关的染色体。然后，又将与加系总产仔数近交衰退显著相关的4条染色体平均分为2、4、6、8个片段进行近交衰退检测，其中平均分成8段后的染色片段的长度范围为15.1~25.8 Mb。在第6、7和8号染色体分别检测到1、2和3个与总产仔数相关的近交衰退染色体片段。这些区域注释到了CUL7、MAPK14和PPARD基因与胎盘发育相关，AREG和EREG基因与卵母细胞成熟有关。本研究利用3种近交系数计算方法对两个不同来源的大白猪总产仔数进行近交衰退评估，在加系大白猪中3种估计方法都能检测到近交衰退的现象，而法系群体中只有F_ROH才能检测到。而且通过ROH方法进一步确定了能引起加系大白猪总产仔数衰退的4条染色体和6个特定的染色体区段，还注释到了与繁殖相关的候选基因。这为揭示近交衰退的遗传机制提供了新的研究手段，也为基因组选种选配提供了参考依据。

关键词: 大白猪, 总产仔数, 连续纯合片段, 近交系数, 近交衰退

Abstract: The purpose of this study was to evaluate the inbreeding depression for TNB in Large White pigs with different genetic background after about 8 generations of selection. A total of 1 937 sows with phenotypic and pedigree records were genotyped with GeneSeek GGP Porcine HD chip. Out of them, 1 039 Large White pigs were from the Canadian line and 898 were from the French line. The pedigree of the two lines consisted of 3 086 Large White pigs. Inbreeding coefficients were estimated using 3 different measures based on pedigree data, SNPs and runs of homozygosity (ROH), respectively. Inbreeding depression of TNB was evaluated using an animal model in which the inbreeding coefficient was treated as a covariate. To fine mapping the genomic regions that lead to inbreeding depression of TNB, the inbreeding coefficients of each autosome and significant autosome segments were calculated and their effects were estimated. And then all the significant autosomes were divided into several segments with equal size and these genomic regions were further tested whether they were associated to inbreeding depression of TNB. In Canadian line, the average inbreeding coefficients of F_ROH, F_GRM and F_PED estimated were 0.124, 0.042 and 0.013, respectively. Among pairwise correlations between the different inbreeding coefficients across individuals, the highest correlation was between F_ROH and F_PED and the correlation coefficient was 0.358. In French line, the average inbreeding coefficients of F_ROH, F_GRMand F_PED estimated were 0.123, 0.052 and 0.007, respectively. The highest pairwise correlation was between F_ROH and F_GRM, and the correlation coefficient was 0.371. On the whole genome level, significant inbreeding depression was found for TNB in Canadian line using all 3 measures of inbreeding. Estimates of inbreeding depression were -0.571, -0.341 and -0.823 for TNB per 10% increase in F_ROH, F_GRMand F_PED, respectively. While in French line, only using F_ROH could detect significant inbreeding depression and a 10% increase in F_ROH resulted in a decrease of 0.690 for TNB. On the chromosome level, ROH-based inbreeding coefficient for each chromosome was used to perform inbreeding depression analysis. The results showed that chromosome 6, 7, 8 and 13 in the Canadian line were identified to be significant related to inbreeding depression for TNB, but in French line, no chromosome was associated to inbreeding depression. To narrow down the genomic regions causing inbreeding depression, the 4 significant chromosomes in Canadian lines were further divided into 2, 4, 6, 8 segments with equal size. When these 4 autosomes were divided into 8 segment, the segment lengths ranged from 15.1 to 25.8 Mb. Finally, one, two and three genomic segments on chromosome 6, 7 and 8 were found to be significantly associated with inbreeding depression, respectively. These regions harbored CUL7, MAPK14 and PPARD genes that were associated with placental development, and AREG and EREG genes involved in oocyte maturation. Three calculation measures of inbreeding coefficients were used to evaluate inbreeding depression for TNB in Large White pigs with different genetic background. At the genome level, significant inbreeding depression in Canadian line was detected for TNB using all 3 measures of inbreeding, but only the effect of F_ROH was significant in French lines. At the chromosome level, 4 autosomes showed significant effects. Use of ROH further identified the 4 chromosomes and 6 specific genomic segments that could lead to significant reduction in TNB of Canadian line. These specific genomic segments were annotated candidate genes related to reproduction. The study results not only provided a new sight into revealing the genetic mechanism of inbreeding depression, but also provided a reference for carrying out genomic selection and mating schemes in pigs.

Key words: Large White pigs, total number of piglets born, runs of homozygosity, inbreeding coefficient, inbreeding depression

中图分类号:

S828.2

史良玉, 王立刚, 张鹏飞, 莫家远, 李洋, 王立贤, 赵福平. 不同来源大白猪总产仔数近交衰退评估[J]. 畜牧兽医学报, 2021, 52(10): 2772-2782.

SHI Liangyu, WANG Ligang, ZHANG Pengfei, MO Jiayuan, LI Yang, WANG Lixian, ZHAO Fuping. Evaluation of Inbreeding Depression on the Total Numbers of Piglets Born in Different Groups of Large White Pigs[J]. Acta Veterinaria et Zootechnica Sinica, 2021, 52(10): 2772-2782.

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