全基因组扫描检测伯克夏猪和韩国本土猪品种间的选择信号。
A whole genomic scan to detect selection signatures between Berkshire and Korean native pig breeds.
机构信息
Department of Animal Science, Chungbuk National University, Cheongju, 361-763 Korea.
出版信息
J Anim Sci Technol. 2014 Nov 6;56:23. doi: 10.1186/2055-0391-56-23. eCollection 2014.
BACKGROUND
Scanning of the genome for selection signatures between breeds may play important role in understanding the underlie causes for observable phenotypic variations. The discovery of high density single nucleotide polymorphisms (SNPs) provide a useful starting point to perform genome-wide scan in pig populations in order to identify loci/candidate genes underlie phenotypic variation in pig breeds and facilitate genetic improvement programs. However, prior to this study genomic region under selection in commercially selected Berkshire and Korean native pig breeds has never been detected using high density SNP markers. To this end, we have genotyped 45 animals using Porcine SNP60 chip to detect selection signatures in the genome of the two breeds by using the F ST approach.
RESULTS
In the comparison of Berkshire and KNP breeds using the FDIST approach, a total of 1108 outlier loci (3.48%) were significantly different from zero at 99% confidence level with 870 of the outlier SNPs displaying high level of genetic differentiation (F ST ≥0.490). The identified candidate genes were involved in a wide array of biological processes and molecular functions. Results revealed that 19 candidate genes were enriched in phosphate metabolism (GO: 0006796; ADCK1, ACYP1, CAMK2D, CDK13, CDK13, ERN1, GALK2, INPP1; MAK, MAP2K5, MAP3K1, MAPK14, P14KB, PIK3C3, PRKC1, PTPRK, RNASEL, THBS1, BRAF, VRK1). We have identified a set of candidate genes under selection and have known to be involved in growth, size and pork quality (CART, AGL, CF7L2, MAP2K5, DLK1, GLI3, CA3 and MC3R), ear morphology and size (HMGA2 and SOX5) stress response (ATF2, MSRB3, TMTC3 and SCAF8) and immune response ( HCST and RYR1).
CONCLUSIONS
Some of the genes may be used to facilitate genetic improvement programs. Our results also provide insights for better understanding of the process and influence of breed development on the pattern of genetic variations.
背景
在品种间扫描选择信号对于理解可观察表型变异的潜在原因可能具有重要作用。高密度单核苷酸多态性 (SNP) 的发现为在猪群体中进行全基因组扫描提供了一个有用的起点，以鉴定导致猪品种表型变异的基因座/候选基因，并促进遗传改良计划。然而，在此之前，使用高密度 SNP 标记从未检测到商业选择的伯克希尔猪和韩国本地猪品种中的基因组选择区域。为此，我们使用 Porcine SNP60 芯片对 45 个动物进行了基因分型，通过 F ST 方法检测两个品种基因组中的选择信号。
结果
在使用 FDIST 方法比较伯克希尔猪和 KNP 品种时，在 99%置信水平下，共有 1108 个外显子（3.48%）显著不同于零，其中 870 个外显子 SNP 显示出高水平的遗传分化（F ST ≥0.490）。鉴定的候选基因参与了广泛的生物学过程和分子功能。结果表明，19 个候选基因在磷酸盐代谢中富集（GO：0006796；ADCK1、ACYP1、CAMK2D、CDK13、CDK13、ERN1、GALK2、INPP1；MAK、MAP2K5、MAP3K1、MAPK14、P14KB、PIK3C3、PRKC1、PTPRK、RNASEL、THBS1、BRAF、VRK1）。我们已经确定了一组候选基因受到选择，并已知其参与生长、大小和猪肉质量（CART、AGL、CF7L2、MAP2K5、DLK1、GLI3、CA3 和 MC3R）、耳朵形态和大小（HMGA2 和 SOX5）应激反应（ATF2、MSRB3、TMTC3 和 SCAF8）和免疫反应（HCST 和 RYR1）。
结论
其中一些基因可能被用于促进遗传改良计划。我们的结果还为更好地理解品种发展对遗传变异模式的影响和影响提供了线索。
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