Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
Hainan Institute, Zhejiang University, Building 11, Yongyou Industrial Park, Yazhou Bay Science and Technology City, Yazhou District, Sanya 572025, China.
Genes (Basel). 2022 Oct 28;13(11):1969. doi: 10.3390/genes13111969.
In Chinese pig populations in which crossbreeding is used, these animals show a level of weakness compared with their original purebred ancestors. For instance, in the Lulai pig, a newly developed Chinese breed that is raised on the basis of the Laiwu pig (a Chinese indigenous breed with exceptionally high intramuscular fat content) and the Yorkshire pig using a method of systematic crossbreeding, both their market acceptance and performance are inferior. To reveal the practical role of these admixed breeds and traditional systematic crossbreeding methods at the genomic level, we explored population structure, genetic signatures, and introgression. We conducted this study based on the SNP chip data of 381 Lulai pigs, 182 Laiwu pigs, and 127 Yorkshires, which showed deficient genome coverage during our study. Therefore, we further selected the Genotyping by Genome Reducing and Sequencing (GGRS) method, which has a high density and suitable genome coverage as a supplement. We applied the GGRS data of 38 Lulai pigs, 75 Laiwu pigs, and 75 Yorkshires. In terms of the SNP chip data, by analysis, we detected 782 significantly different genes between Lulai pigs and Yorkshires, including 3 major genes associated with growth (LEPR) and meat quality (SCD and TBC1D1), and we detected 426 significantly different genes between Lulai pigs and Laiwu pigs. With rIBD, we detected 12 genomic regions that included 182 genes that Yorkshires introgressed to Lulai pigs, and we detected 27 genomic regions that included 229 genes with a major gene (SCD) that Laiwu pigs introgressed to Lulai pigs. Regarding the GGRS data, we detected 601 significantly different genes between Lulai pigs and Yorkshires by analysis, including 3 major genes associated with growth and fat deposits (IGF2 and FTO) and with hair color (KIT), and we detected 634 significantly different genes between Lulai pigs and Laiwu pigs, including 3 major genes related to their body composition (MYPN), hair color (KIT), and ear size (PPARD). By rIBD, we detected 94 deep sections that included 363 genes that Yorkshires introgressed to Lulai pigs, and we detected 149 deep sections that included 727 genes with a major gene (ESR1) that Laiwu pigs introgressed to Lulai pigs. Altogether, this study provides both insight into the molecular background of synthesized breeds of Lulai pigs and a reference for the evaluation of systematic crossbreeding in China.
在中国使用杂交的猪种群中，这些动物与它们的原始纯种祖先相比表现出一定程度的劣势。例如，在中国新开发的鲁莱猪品种中，是基于莱芜猪（一种肌肉内脂肪含量特别高的中国本土品种）和约克夏猪进行系统杂交的基础上培育的，其市场接受度和表现都较差。为了在基因组水平上揭示这些混合品种和传统系统杂交方法的实际作用，我们探讨了种群结构、遗传特征和渐渗。我们根据 381 头鲁莱猪、182 头莱芜猪和 127 头约克夏猪的 SNP 芯片数据进行了这项研究，在研究过程中，这些数据显示基因组覆盖度不足。因此，我们进一步选择了基因组降低测序和基因分型（GGRS）方法作为补充，该方法具有高密度和合适的基因组覆盖度。我们应用了 38 头鲁莱猪、75 头莱芜猪和 75 头约克夏猪的 GGRS 数据。在 SNP 芯片数据方面，通过 分析，我们在鲁莱猪和约克夏猪之间检测到了 782 个显著差异的基因，包括 3 个与生长（LEPR）和肉质（SCD 和 TBC1D1）相关的主要基因，在鲁莱猪和莱芜猪之间检测到了 426 个显著差异的基因。通过 rIBD，我们在包括 182 个基因的 12 个基因组区域中检测到了约克夏猪渐渗到鲁莱猪的基因，在包括 229 个基因的 27 个基因组区域中检测到了莱芜猪渐渗到鲁莱猪的主要基因（SCD）。关于 GGRS 数据，通过 分析，我们在鲁莱猪和约克夏猪之间检测到了 601 个显著差异的基因，包括 3 个与生长和脂肪沉积（IGF2 和 FTO）和毛色（KIT）相关的主要基因，在鲁莱猪和莱芜猪之间检测到了 634 个显著差异的基因，包括 3 个与体成分（MYPN）、毛色（KIT）和耳大小（PPARD）相关的主要基因。通过 rIBD，我们在包括 363 个基因的 94 个深部分区中检测到了约克夏猪渐渗到鲁莱猪的基因，在包括 727 个基因的 149 个深部分区中检测到了莱芜猪渐渗到鲁莱猪的主要基因（ESR1）。总之，本研究不仅为鲁莱猪杂种的分子背景提供了深入的了解，也为中国系统杂交的评估提供了参考。
