PDF(Pubmed)
Abstract：
BACKGROUND: Jianli pig, a renowned indigenous breed in China, has the characteristics of a two-end black (TEB) coat color, excellent meat quality, strong adaptability and increased prolificacy. However, there is limited information available regarding the genetic diversity, population structure and genomic regions under selection of Jianli pig. On the other hand, the genetic mechanism of TEB coat color has remained largely unknown.
RESULTS: In this study, the whole genome resequencing of 30 Jianli pigs within a context of 153 individuals representing 13 diverse breeds was performed. The population structure analysis revealed that Jianli pigs have close genetic relationships with the Tongcheng pig breed, their geographical neighbors. Three methods (observed heterozygosity, expected heterozygosity, and runs of homozygosity) implied a relatively high level of genetic diversity and, a low inbreeding coefficient in Jianli compared with other pigs. We used Fst and XP-EHH to detect the selection signatures in Jianli pigs compared with Asian wild boar. A total of 451 candidate genes influencing meat quality (CREBBP, ADCY9, EEPD1 and HDAC9), reproduction (ESR1 and FANCA), and coat color (EDNRB, MITF and MC1R), were detected by gene annotation analysis. Finally, to fine-map the genomic region for the two-end black (TEB) coat color phenotype in Jianli pigs, we performed three signature selection methods between the TEB coat color and no-TEB coat color pig breeds. The current study, further confirmed that the EDNRB gene is a candidate gene for TEB color phenotype found in Chinese pigs, including Jinhua pigs, and the haplotype harboring 25 SNPs in the EDNRB gene may promote the formation of TEB coat color. Further ATAC-seq and luciferase reporter assays of these regions suggest that the 25-SNPs region was a strong candidate causative mutation that regulates the TEB coat color phenotype by altering enhancer function.
CONCLUSIONS: Our results advanced the understanding of the genetic mechanism behind artificial selection, and provided further resources for the protection and breeding improvement of Jianli pigs.
RESULTS: In this study, the whole genome resequencing of 30 Jianli pigs within a context of 153 individuals representing 13 diverse breeds was performed. The population structure analysis revealed that Jianli pigs have close genetic relationships with the Tongcheng pig breed, their geographical neighbors. Three methods (observed heterozygosity, expected heterozygosity, and runs of homozygosity) implied a relatively high level of genetic diversity and, a low inbreeding coefficient in Jianli compared with other pigs. We used Fst and XP-EHH to detect the selection signatures in Jianli pigs compared with Asian wild boar. A total of 451 candidate genes influencing meat quality (CREBBP, ADCY9, EEPD1 and HDAC9), reproduction (ESR1 and FANCA), and coat color (EDNRB, MITF and MC1R), were detected by gene annotation analysis. Finally, to fine-map the genomic region for the two-end black (TEB) coat color phenotype in Jianli pigs, we performed three signature selection methods between the TEB coat color and no-TEB coat color pig breeds. The current study, further confirmed that the EDNRB gene is a candidate gene for TEB color phenotype found in Chinese pigs, including Jinhua pigs, and the haplotype harboring 25 SNPs in the EDNRB gene may promote the formation of TEB coat color. Further ATAC-seq and luciferase reporter assays of these regions suggest that the 25-SNPs region was a strong candidate causative mutation that regulates the TEB coat color phenotype by altering enhancer function.
CONCLUSIONS: Our results advanced the understanding of the genetic mechanism behind artificial selection, and provided further resources for the protection and breeding improvement of Jianli pigs.
摘要：
背景：健力猪，中国著名的土著品种，具有两端黑色（TEB）涂层颜色的特征，优良的肉质，适应性强，多生增加。然而,关于遗传多样性的信息有限，健力猪的种群结构和基因组区域选择。另一方面,TEB毛色的遗传机制在很大程度上仍然未知。
结果：在这项研究中，在代表13个不同品种的153个个体的背景下，对30只健力猪进行了全基因组重测序。种群结构分析表明，健力猪与桐城猪品种具有密切的亲缘关系，地理上的邻居。三种方法(观察杂合性，预期杂合性，和纯合性运行)意味着相对较高的遗传多样性水平，与其他猪相比，监利的近交系数较低。我们使用Fst和XP-EHH检测了健力猪与亚洲野猪的选择特征。共有451个影响肉质的候选基因(CREBBP，ADCY9、EEPD1和HDAC9），复制（ESR1和FANCA），和外套颜色(EDNRB，MITF和MC1R)，通过基因注释分析进行检测。最后,为了精细映射健力猪的两端黑色（TEB）皮毛颜色表型的基因组区域，我们在TEB皮毛颜色和非TEB皮毛颜色猪品种之间进行了三种特征选择方法。目前的研究,进一步证实EDNRB基因是在中国猪中发现的TEB颜色表型的候选基因，包括金华猪,EDNRB基因中包含25个SNP的单倍型可能促进TEB外壳颜色的形成。这些区域的进一步ATAC-seq和荧光素酶报告基因测定表明25-SNP区域是通过改变增强子功能来调节TEB涂层颜色表型的强候选致病突变。
结论：我们的研究结果促进了对人工选择背后的遗传机制的理解，为健力猪的保护和育种改良提供了进一步的资源。
结果：在这项研究中，在代表13个不同品种的153个个体的背景下，对30只健力猪进行了全基因组重测序。种群结构分析表明，健力猪与桐城猪品种具有密切的亲缘关系，地理上的邻居。三种方法(观察杂合性，预期杂合性，和纯合性运行)意味着相对较高的遗传多样性水平，与其他猪相比，监利的近交系数较低。我们使用Fst和XP-EHH检测了健力猪与亚洲野猪的选择特征。共有451个影响肉质的候选基因(CREBBP，ADCY9、EEPD1和HDAC9），复制（ESR1和FANCA），和外套颜色(EDNRB，MITF和MC1R)，通过基因注释分析进行检测。最后,为了精细映射健力猪的两端黑色（TEB）皮毛颜色表型的基因组区域，我们在TEB皮毛颜色和非TEB皮毛颜色猪品种之间进行了三种特征选择方法。目前的研究,进一步证实EDNRB基因是在中国猪中发现的TEB颜色表型的候选基因，包括金华猪,EDNRB基因中包含25个SNP的单倍型可能促进TEB外壳颜色的形成。这些区域的进一步ATAC-seq和荧光素酶报告基因测定表明25-SNP区域是通过改变增强子功能来调节TEB涂层颜色表型的强候选致病突变。
结论：我们的研究结果促进了对人工选择背后的遗传机制的理解，为健力猪的保护和育种改良提供了进一步的资源。
