恩施黑猪基因组群体遗传学参数的估计与选择信号研究

doi:10.11843/j.issn.0366-6964.2019.03.003

摘要/Abstract

摘要：

旨在调查恩施黑猪基因组群体遗传学参数与选择信号。本研究利用Porcine 80K SNP芯片，通过计算亲缘系数、近交系数、连锁不平衡程度与有效群体大小等群体遗传学层面的参数评估恩施黑猪种群结构关系，运用CLR和iHS方法检测恩施黑猪基因组选择信号，并通过生物信息学分析揭示其潜在受选择基因。亲缘系数计算发现，咸丰县恩施黑猪个体间平均亲缘系数为0.12；近交系数计算表明，16%的样本近交系数大于0.125，存在明显近交累积。此外，本研究构建了恩施黑猪全基因组连锁不平衡图谱；利用连锁不平衡信息，恩施黑猪估计历史有效群体大小呈现逐代下降趋势，其中5世代前有效群体大小约为25头。基于CLR方法共检测到126个显著选择信号候选区域，总长约为51.6 Mb，占基因组总长的2.1%。利用iHS方法，共发现248个显著选择信号候选区域，长度约为78.78 Mb，约占基因组总长的3.2%。富集分析表明，与选择信号区域重叠的LPAR2、NDUFA13、MEF2B、AHR基因分别与胴体长度（滴水损失）、精子形成、骨骼肌分化和总产仔数相关。研究表明，现存恩施黑猪群体血统较窄，近交累积严重，有效群体大小较小，并呈现继续缩小的趋势。选择信号分析揭示的一系列潜在受选择基因能够为未来恩施黑猪的遗传改良提供一定的参考依据。

Abstract:

This study was designed to investigate the population genetics parameters and selection signatures of Enshi Black pig. Using the Porcine 80K SNP chip, a series of population genetics parameters, including the relationship coefficient, the inbreeding coefficient, the linkage disequilibrium and the effective population size, were calculated to evaluate the population structure relationship of Enshi Black pig. In addition, the CLR and iHS methods were used to identify the potential selection signatures and then the corresponding selected genes were revealed by bioinformatics analysis. The results indicated that the mean value of relationship coefficient was 0.12 for all individual-pairs in Xianfeng county, the inbreeding coefficient of 16% of all individuals was higher than 0.125. In addition, this study presented a linkage disequilibrium map for the whole genome of Enshi Black pig. Analysis of the past effective population size based on the information of linkage disequilibrium suggested a decline in effective population size, and up to Ne=25 before 5th generation. Based on CLR method, a total of 126 significant potential selection signature regions were detected, which were approximately 51.6 Mb in length, accounting for approximately 2.1% of the total length of the genome. Similarly, a total of 248 significant potential selection signature regions were detected using iHS method, which spanned approximately 78.78 Mb and accounted for approximately 3.2% of the total genome length. Enrichment analysis showed that genes such as LPAR2, NDUFA13, MEF2B and AHR overlapping with the selection signatures region were associated with carcass length (drip loss), sperm formation, skeletal muscle differentiation and total litter size. This study suggests that the genetic basis of Enshi black pig is narrow and inbreeding is obvious, and the effective population size is limited, and it continues to shrink. The candidate genes revealed by sweep analysis can provide some references for the future genetic improvement of Enshi Black pig.

中图分类号:

S828.2

吴林慧, 孙琦, 王荔茹, 张凯丽, 谢胜松, 李新云, 赵书红, 马云龙. 恩施黑猪基因组群体遗传学参数的估计与选择信号研究[J]. 畜牧兽医学报, 2019, 50(3): 485-494.

WU Linhui, SUN Qi, WANG Liru, ZHANG Kaili, XIE Shengsong, LI Xinyun, ZHAO Shuhong, MA Yunlong. A Study of the Population Genetics Parameters and Selection Signatures in Enshi Black Pig[J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2019, 50(3): 485-494.

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