Addo Sowah, Jung Lisa
Animal Breeding Section, University of Kassel, Witzenhausen, Germany.
Front Genet. 2022 Oct 18;13:909986. doi: 10.3389/fgene.2022.909986. eCollection 2022.
Mangalitsa pigs exhibit three distinct coat color patterns based on which they are described as Red, Blond, and Swallow-bellied. The current study investigated genome-wide diversity and selection signatures in the three breeds using fixation index, runs of homozygosity and population structure analyses. The analyses were originally based on quality-controlled data on 77 Mangalitsa animals from Germany, including 23 Blond, 30 Swallow-bellied and 24 Red Mangalitsa genotyped with a customized version of the ProcineSNP60 v2 Genotyping Bead Chip. Also, 20 Hungarian Mangalitsa genotypes were included as outgroup data for comparison. Estimates of observed heterozygosity were 0.27, 0.28, and 0.29, and inbreeding coefficients estimated based on runs of homozygosity were 24.11%, 20.82%, and 16.34% for Blond, Swallow-bellied and Red Mangalitsa, respectively. ROH islands were detected in all breeds, however, none of these were shared amongst them. The KIF16B gene previously reported to play a role in synaptic signaling was found in a ROH island (SSC17: 16-26) in Swallow-bellied Mangalitsa. The same gene was found to harbor a significantly differentiated SNP (MARC0032380) while contrasting either Blond or Red to Swallow-belied Mangalitsa. In the Red Mangalitsa, some ROH islands were associated with genes that play a role in meat quality traits, i.e., ABCA12, VIL1, PLSCR5, and USP37. Our population structure analysis highlighted a separation of the three breeds, but also showed the closest relatedness between Red and Blond Mangalitsa pigs. Findings of this study improve our understanding of the diversity in the three breeds of Mangalitsa pigs.
曼加利察猪呈现出三种不同的毛色模式，据此它们被描述为红色、金色和白腹色。本研究使用固定指数、纯合子片段以及群体结构分析，调查了这三个品种全基因组的多样性和选择印记。分析最初基于来自德国的77头曼加利察猪的质量控制数据，包括23头金色、30头白腹色和24头红色曼加利察猪，这些猪使用定制版的猪60K SNP芯片v2进行基因分型。此外，还纳入了20头匈牙利曼加利察猪的基因型作为外群数据用于比较。观察到的杂合度估计值分别为0.27、0.28和0.29，基于纯合子片段估计的金色、白腹色和红色曼加利察猪的近亲繁殖系数分别为24.11%、20.82%和16.34%。在所有品种中均检测到了纯合子片段岛，但它们之间没有共享的片段岛。先前报道在突触信号传导中起作用的KIF16B基因，在白腹色曼加利察猪的一个纯合子片段岛（SSC17: 16 - 26）中被发现。在将金色或红色曼加利察猪与白腹色曼加利察猪进行对比时，发现该基因存在一个显著分化的单核苷酸多态性（MARC0032380）。在红色曼加利察猪中，一些纯合子片段岛与肉质性状相关的基因有关，即ABCA12、VIL1、PLSCR5和USP37。我们的群体结构分析突出了这三个品种的分离，但也显示红色和金色曼加利察猪之间的亲缘关系最为密切。本研究的结果增进了我们对曼加利察猪这三个品种多样性的理解。
