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

Abstract

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.

CLC Number:

S828.2

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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A Study of the Population Genetics Parameters and Selection Signatures in Enshi Black Pig

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